From bd4038ac85fd46223be8011fdb5716e763ed3738 Mon Sep 17 00:00:00 2001
From: Ben Haller <github@sticksoftware.com>
Date: Thu, 12 Sep 2024 12:58:40 -0400
Subject: [PATCH] add terminology autofixes, revise recipes and cal...()
 functions

---
 QtSLiM/QtSLiMWindow.cpp                       | 190 +++++++++++++++---
 QtSLiM/recipes.qrc                            |   2 +-
 ...ion of genomic background, Epistasis I.txt |   4 +-
 ...on of genomic background, Epistasis II.txt |   4 +-
 ...n selection and the green-beard effect.txt |   2 +-
 .../Recipe 11.1 - Assortative mating.txt      |   4 +-
 ....3 - Gametophytic self-incompatibility.txt |   6 +-
 .../Recipe 12.2 - Lethal epistasis I.txt      |   8 +-
 .../Recipe 12.2 - Lethal epistasis II.txt     |   8 +-
 .../Recipe 12.3 - Simulating gene drive.txt   |  10 +-
 .../Recipe 13.1 - Polygenic selection.txt     |   2 +-
 ...L effects with a structured chromosome.txt |   2 +-
 ...ative phenotypic traits and pleiotropy.txt |   2 +-
 ...edness, inbreeding, and heterozygosity.txt |   2 +-
 ...ecipe 14.11 - Modeling microsatellites.txt |  16 +-
 ...14.12 - Modeling transposable elements.txt |  26 +--
 ...elic loci with a mutation() callback I.txt |   4 +-
 ...lic loci with a mutation() callback II.txt |  18 +-
 ...lation state from an MS output file II.txt |  10 +-
 ...rsions with a recombination() callback.txt |  10 +-
 ...s with a Pseudo-Autosomal Region (PAR).txt |  10 +-
 ...ng local ancestry along the chromosome.txt |   6 +-
 ...cipe 14.9 - Modeling haploid organisms.txt |   8 +-
 ...in a nonWF model with addRecombinant().txt |   2 +-
 ...bacteria with horizontal gene transfer.txt |   8 +-
 ...ipe 15.14 - Alternation of generations.txt |  18 +-
 .../recipes/Recipe 15.15 - Meiotic drive.txt  |  14 +-
 ...ng haplodiploidy with addRecombinant().txt |  16 +-
 ...eficial mutations and absolute fitness.txt |   2 +-
 ...n after simulation with recapitation I.txt |   2 +-
 ...tion of a sweep, preserving ancestry I.txt |   2 +-
 ...ion of a sweep, preserving ancestry II.txt |   2 +-
 ...xture (analyzing ancestry in Python) I.txt |   4 +-
 ... WF model with a coalescent history II.txt |   2 +-
 ...eling GC-biased gene conversion (gBGC).txt |   2 +-
 ... files to create nucleotide-based SNPs.txt |   2 +-
 ...back-mutations to the ancestral state).txt |   6 +-
 ...ce output from nucleotide-based models.txt |   6 +-
 ...nt mutational lineages, and VCF output.txt |   2 +-
 ...and equilibrium nucleotide frequencies.txt |   2 +-
 ...roduced non-nucleotide-based mutations.txt |   2 +-
 ...itness effects at the nucleotide level.txt |   4 +-
 ...itness effects at the amino acid level.txt |   6 +-
 ...ry host-parasite matching-allele model.txt |   4 +-
 ...ng individuals rather than haplosomes.txt} |   2 +-
 ...output, Automatic logging with LogFile.txt |   2 +-
 ...Basic output, Custom output with Eidos.txt |  12 +-
 ... random, sparse spatial metapopulation.txt |   2 +-
 ... IV (Custom display colors in SLiMgui).txt |   2 +-
 ...e 9.1 - Introducing adaptive mutations.txt |   2 +-
 ...cking the fate of background mutations.txt |   2 +-
 ...ion size versus census population size.txt |   4 +-
 ... Making sweeps conditional on fixation.txt |   4 +-
 ...ng sweeps conditional on establishment.txt |   4 +-
 .../recipes/Recipe 9.4 - Partial sweeps.txt   |   2 +-
 ...e novo mutations in a large population.txt |   4 +-
 ...with a fixed de novo mutation schedule.txt |   4 +-
 ...ith a random de novo mutation schedule.txt |   2 +-
 ...ing variation at a predetermined locus.txt |   4 +-
 .../Recipe 9.7 - Adaptive introgression.txt   |   2 +-
 ...eeping a reference to a sweep mutation.txt |   2 +-
 ...ion of genomic background, Epistasis I.txt |   4 +-
 ...on of genomic background, Epistasis II.txt |   4 +-
 ...n selection and the green-beard effect.txt |   2 +-
 .../Recipe 11.1 - Assortative mating.txt      |   4 +-
 ....3 - Gametophytic self-incompatibility.txt |   6 +-
 .../Recipe 12.2 - Lethal epistasis I.txt      |   8 +-
 .../Recipe 12.2 - Lethal epistasis II.txt     |   8 +-
 .../Recipe 12.3 - Simulating gene drive.txt   |  10 +-
 .../Recipe 13.1 - Polygenic selection.txt     |   2 +-
 ...L effects with a structured chromosome.txt |   2 +-
 ...ative phenotypic traits and pleiotropy.txt |   2 +-
 ...edness, inbreeding, and heterozygosity.txt |   2 +-
 ...ecipe 14.11 - Modeling microsatellites.txt |  16 +-
 ...14.12 - Modeling transposable elements.txt |  26 +--
 ...elic loci with a mutation() callback I.txt |   4 +-
 ...lic loci with a mutation() callback II.txt |  18 +-
 ...lation state from an MS output file II.txt |  10 +-
 ...rsions with a recombination() callback.txt |  10 +-
 ...s with a Pseudo-Autosomal Region (PAR).txt |  10 +-
 ...ng local ancestry along the chromosome.txt |   6 +-
 ...cipe 14.9 - Modeling haploid organisms.txt |   8 +-
 ...in a nonWF model with addRecombinant().txt |   2 +-
 ...bacteria with horizontal gene transfer.txt |   8 +-
 ...ipe 15.14 - Alternation of generations.txt |  18 +-
 .../Recipes/Recipe 15.15 - Meiotic drive.txt  |  14 +-
 ...ng haplodiploidy with addRecombinant().txt |  16 +-
 ...eficial mutations and absolute fitness.txt |   2 +-
 ...n after simulation with recapitation I.txt |   2 +-
 ...tion of a sweep, preserving ancestry I.txt |   2 +-
 ...ion of a sweep, preserving ancestry II.txt |   2 +-
 ...xture (analyzing ancestry in Python) I.txt |   4 +-
 ... WF model with a coalescent history II.txt |   2 +-
 ...eling GC-biased gene conversion (gBGC).txt |   2 +-
 ... files to create nucleotide-based SNPs.txt |   2 +-
 ...back-mutations to the ancestral state).txt |   6 +-
 ...ce output from nucleotide-based models.txt |   6 +-
 ...nt mutational lineages, and VCF output.txt |   2 +-
 ...and equilibrium nucleotide frequencies.txt |   2 +-
 ...roduced non-nucleotide-based mutations.txt |   2 +-
 ...itness effects at the nucleotide level.txt |   4 +-
 ...itness effects at the amino acid level.txt |   6 +-
 ...ry host-parasite matching-allele model.txt |   4 +-
 ...ng individuals rather than haplosomes.txt} |   2 +-
 ...output, Automatic logging with LogFile.txt |   2 +-
 ...Basic output, Custom output with Eidos.txt |  12 +-
 ... random, sparse spatial metapopulation.txt |   2 +-
 ... IV (Custom display colors in SLiMgui).txt |   2 +-
 ...e 9.1 - Introducing adaptive mutations.txt |   2 +-
 ...cking the fate of background mutations.txt |   2 +-
 ...ion size versus census population size.txt |   4 +-
 ... Making sweeps conditional on fixation.txt |   4 +-
 ...ng sweeps conditional on establishment.txt |   4 +-
 .../Recipes/Recipe 9.4 - Partial sweeps.txt   |   2 +-
 ...e novo mutations in a large population.txt |   4 +-
 ...with a fixed de novo mutation schedule.txt |   4 +-
 ...ith a random de novo mutation schedule.txt |   2 +-
 ...ing variation at a predetermined locus.txt |   4 +-
 .../Recipe 9.7 - Adaptive introgression.txt   |   2 +-
 ...eeping a reference to a sweep mutation.txt |   2 +-
 VERSIONS                                      |   7 +-
 core/slim_functions.cpp                       |  10 +-
 122 files changed, 494 insertions(+), 367 deletions(-)
 rename QtSLiM/recipes/{Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt => Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt} (93%)
 rename SLiMgui/Recipes/{Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt => Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt} (93%)

diff --git a/QtSLiM/QtSLiMWindow.cpp b/QtSLiM/QtSLiMWindow.cpp
index 9008e2489..7dabdd804 100644
--- a/QtSLiM/QtSLiMWindow.cpp
+++ b/QtSLiM/QtSLiMWindow.cpp
@@ -1703,6 +1703,8 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
     QTextCursor selection = ui->scriptTextEdit->textCursor();
     QString selectionString = selection.selectedText();
     
+    // Note that is important to test the selection string to make sure it makes sense, because the error position might not be correct!
+    
     // get the four characters prior to the selected error range, to recognize if the error is preceded by "sim."; note this is a heuristic, not precise
     QTextCursor beforeSelection4 = selection;
     beforeSelection4.setPosition(beforeSelection4.selectionStart(), QTextCursor::MoveAnchor);
@@ -1710,6 +1712,10 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
     beforeSelection4.movePosition(QTextCursor::Right, QTextCursor::KeepAnchor, 4);
     QString beforeSelection4String = beforeSelection4.selectedText();
     
+    //
+    //  Changes for SLiM 4.0: multispecies SLiM, mostly, plus fitness() -> mutationEffect() and fitness(NULL) -> fitnessEffect()
+    //
+    
     // early() events are no longer default
     if (terminationMessage.contains("unexpected token {") &&
             terminationMessage.contains("expected an event declaration") &&
@@ -1718,91 +1724,124 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
         return offerAndExecuteAutofix(selection, "early() {", "Script blocks no longer default to `early()`; `early()` must be explicitly specified.", terminationMessage);
     
     // sim to community changes
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method createLogFile() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "createLogFile") &&
+            terminationMessage.contains("method createLogFile() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `createLogFile()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method deregisterScriptBlock() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "deregisterScriptBlock") &&
+            terminationMessage.contains("method deregisterScriptBlock() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `deregisterScriptBlock()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method registerFirstEvent() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "registerFirstEvent") &&
+            terminationMessage.contains("method registerFirstEvent() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `registerFirstEvent()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method registerEarlyEvent() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "registerEarlyEvent") &&
+            terminationMessage.contains("method registerEarlyEvent() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `registerEarlyEvent()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method registerLateEvent() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "registerLateEvent") &&
+            terminationMessage.contains("method registerLateEvent() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `registerLateEvent()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method rescheduleScriptBlock() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "rescheduleScriptBlock") &&
+            terminationMessage.contains("method rescheduleScriptBlock() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `rescheduleScriptBlock()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method simulationFinished() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "simulationFinished") &&
+            terminationMessage.contains("method simulationFinished() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `simulationFinished()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("method outputUsage() is not defined on object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "outputUsage") &&
+            terminationMessage.contains("method outputUsage() is not defined on object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `outputUsage()` method has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("property logFiles is not defined for object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "logFiles") &&
+            terminationMessage.contains("property logFiles is not defined for object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `logFiles` property has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("property generationStage is not defined for object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "generationStage") &&
+            terminationMessage.contains("property generationStage is not defined for object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `generationStage` property has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("property modelType is not defined for object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "modelType") &&
+            terminationMessage.contains("property modelType is not defined for object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `modelType` property has been moved to the Community class.", terminationMessage);
     
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("property verbosity is not defined for object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "verbosity") &&
+            terminationMessage.contains("property verbosity is not defined for object element type Species"))
         return offerAndExecuteAutofix(beforeSelection4, "community.", "The `verbosity` property has been moved to the Community class.", terminationMessage);
     
     // generation to tick changes
-    if (terminationMessage.contains("property originGeneration is not defined for object element type Mutation"))
+    if (terminationMessage.contains("property originGeneration is not defined for object element type Mutation") &&
+            (selectionString == "originGeneration"))
         return offerAndExecuteAutofix(selection, "originTick", "The `originGeneration` property has been removed from Mutation; in its place is `originTick` (which measures in ticks, not generations).", terminationMessage);
 
-    if (terminationMessage.contains("property originGeneration is not defined for object element type Substitution"))
+    if (terminationMessage.contains("property originGeneration is not defined for object element type Substitution") &&
+            (selectionString == "originGeneration"))
         return offerAndExecuteAutofix(selection, "originTick", "The `originGeneration` property has been removed from Substitution; in its place is `originTick` (which measures in ticks, not generations).", terminationMessage);
 
-    if (terminationMessage.contains("property fixationGeneration is not defined for object element type Substitution"))
+    if (terminationMessage.contains("property fixationGeneration is not defined for object element type Substitution") &&
+            (selectionString == "fixationGeneration"))
         return offerAndExecuteAutofix(selection, "fixationTick", "The `fixationGeneration` property has been removed from Substitution; in its place is `fixationTick` (which measures in ticks, not generations).", terminationMessage);
     
     // generation to cycle changes
-    if (terminationMessage.contains("property generation is not defined for object element type Species"))
+    if (terminationMessage.contains("property generation is not defined for object element type Species") &&
+            (selectionString == "generation"))
         return offerAndExecuteAutofix(selection, "cycle", "The `generation` property of Species has been renamed to `cycle`.", terminationMessage);
     
-    if (terminationMessage.contains("property generationStage is not defined for object element type Community"))
+    if (terminationMessage.contains("property generationStage is not defined for object element type Community") &&
+            (selectionString == "generationStage"))
         return offerAndExecuteAutofix(selection, "cycleStage", "The `generationStage` property of Community has been renamed to `cycleStage`.", terminationMessage);
     
-    if (terminationMessage.contains("method addGeneration() is not defined on object element type LogFile"))
+    if (terminationMessage.contains("method addGeneration() is not defined on object element type LogFile") &&
+            (selectionString == "addGeneration"))
         return offerAndExecuteAutofix(selection, "addCycle", "The `addGeneration()` method of Community has been renamed to `addCycle()`.", terminationMessage);
     
-    if (terminationMessage.contains("method addGenerationStage() is not defined on object element type LogFile"))
+    if (terminationMessage.contains("method addGenerationStage() is not defined on object element type LogFile") &&
+            (selectionString == "addGenerationStage"))
         return offerAndExecuteAutofix(selection, "addCycleStage", "The `addGenerationStage()` method of Community has been renamed to `addCycleStage()`.", terminationMessage);
     
     // removal of various callback pseudo-parameters
-    if (terminationMessage.contains("undefined identifier genome1"))
-        return offerAndExecuteAutofix(selection, "individual.genome1", "The `genome1` pseudo-parameter has been removed; it is now accessed as `individual.genome1`.", terminationMessage);
-
-    if (terminationMessage.contains("undefined identifier genome2"))
-        return offerAndExecuteAutofix(selection, "individual.genome2", "The `genome2` pseudo-parameter has been removed; it is now accessed as `individual.genome2`.", terminationMessage);
-
-    if (terminationMessage.contains("undefined identifier childGenome1"))
+    // genome1 and genome2 are now handled below, since there are two possible fixes now
+    if (terminationMessage.contains("undefined identifier childGenome1") &&
+            (selectionString == "childGenome1"))
         return offerAndExecuteAutofix(selection, "child.genome1", "The `childGenome1` pseudo-parameter has been removed; it is now accessed as `child.genome1`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier childGenome2"))
+    if (terminationMessage.contains("undefined identifier childGenome2") &&
+            (selectionString == "childGenome2"))
         return offerAndExecuteAutofix(selection, "child.genome2", "The `childGenome2` pseudo-parameter has been removed; it is now accessed as `child.genome2`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier parent1Genome1"))
+    if (terminationMessage.contains("undefined identifier parent1Genome1") &&
+            (selectionString == "parent1Genome1"))
         return offerAndExecuteAutofix(selection, "parent1.genome1", "The `parent1Genome1` pseudo-parameter has been removed; it is now accessed as `parent1.genome1`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier parent1Genome2"))
+    if (terminationMessage.contains("undefined identifier parent1Genome2") &&
+            (selectionString == "parent1Genome2"))
         return offerAndExecuteAutofix(selection, "parent1.genome2", "The `parent1Genome2` pseudo-parameter has been removed; it is now accessed as `parent1.genome2`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier parent2Genome1"))
+    if (terminationMessage.contains("undefined identifier parent2Genome1") &&
+            (selectionString == "parent2Genome1"))
         return offerAndExecuteAutofix(selection, "parent2.genome1", "The `parent2Genome1` pseudo-parameter has been removed; it is now accessed as `parent2.genome1`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier parent2Genome2"))
+    if (terminationMessage.contains("undefined identifier parent2Genome2") &&
+            (selectionString == "parent2Genome2"))
         return offerAndExecuteAutofix(selection, "parent2.genome2", "The `parent2Genome2` pseudo-parameter has been removed; it is now accessed as `parent2.genome2`.", terminationMessage);
 
-    if (terminationMessage.contains("undefined identifier childIsFemale"))
+    if (terminationMessage.contains("undefined identifier childIsFemale") &&
+            (selectionString == "childIsFemale"))
         return offerAndExecuteAutofix(selection, "(child.sex == \"F\")", "The `childIsFemale` pseudo-parameter has been removed; it is now accessed as `child.sex == \"F\"`.", terminationMessage);
     
     // changes to InteractionType -evaluate()
@@ -1915,7 +1954,9 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
         return offerAndExecuteAutofix(selection, "effect", "The `relFitness` pseudo-parameter has been renamed to `effect`.", terminationMessage);
     
     // other deprecated APIs, unrelated to multispecies and multi-phenotype
-    if ((beforeSelection4String == "sim.") && terminationMessage.contains("property inSLiMgui is not defined for object element type Species"))
+    if ((beforeSelection4String == "sim.") &&
+            (selectionString == "inSLiMgui") &&
+            terminationMessage.contains("property inSLiMgui is not defined for object element type Species"))
     {
         QTextCursor simAndSelection = beforeSelection4;
         simAndSelection.setPosition(selection.selectionEnd(), QTextCursor::KeepAnchor);
@@ -1923,6 +1964,89 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
         return offerAndExecuteAutofix(simAndSelection, "exists(\"slimgui\")", "The `inSLiMgui` property has been removed; now use `exists(\"slimgui\")`.", terminationMessage);
     }
     
+    //
+    //  Shift from genome to haplosome, probably for SLiM 5.0
+    //
+    
+    if (terminationMessage.contains("could not find an Eidos class named 'Genome'") &&
+            (selectionString == "Genome"))
+        return offerAndExecuteAutofix(selection, "Haplosome", "The `Genome` class has been renamed to `Haplosome`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genomeType is not defined for object element type Haplosome") &&
+            (selectionString == "genomeType"))
+        return offerAndExecuteAutofix(selection, "chromosome.type", "The `genomeType` property of Haplosome has been removed; it is now accessed as `chromosome.type`.", terminationMessage);
+    
+    if (terminationMessage.contains("property isNullGenome is not defined for object element type Haplosome") &&
+            (selectionString == "isNullGenome"))
+        return offerAndExecuteAutofix(selection, "isNullHaplosome", "The `isNullGenome` property of Haplosome has been renamed to `isNullHaplosome`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genomePedigreeID is not defined for object element type Haplosome") &&
+            (selectionString == "genomePedigreeID"))
+        return offerAndExecuteAutofix(selection, "haplosomePedigreeID", "The `genomePedigreeID` property of Haplosome has been renamed to `haplosomePedigreeID`.", terminationMessage);
+    
+    if (terminationMessage.contains("method mutationCountsInGenomes() is not defined on object element type Haplosome") &&
+            (selectionString == "mutationCountsInGenomes"))
+        return offerAndExecuteAutofix(selection, "mutationCountsInHaplosomes", "The `mutationCountsInGenomes` method of Haplosome has been renamed to `mutationCountsInHaplosomes`.", terminationMessage);
+    
+    if (terminationMessage.contains("method mutationFrequenciesInGenomes() is not defined on object element type Haplosome") &&
+            (selectionString == "mutationFrequenciesInGenomes"))
+        return offerAndExecuteAutofix(selection, "mutationFrequenciesInHaplosomes", "The `mutationFrequenciesInGenomes` property of Haplosome has been renamed to `mutationFrequenciesInHaplosomes`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genomes is not defined for object element type Individual") &&
+            (selectionString == "genomes"))
+        return offerAndExecuteAutofix(selection, "haplosomes", "The `genomes` property of Individual has been renamed to `haplosomes`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genomesNonNull is not defined for object element type Individual") &&
+            (selectionString == "genomesNonNull"))
+        return offerAndExecuteAutofix(selection, "haplosomesNonNull", "The `genomesNonNull` property of Individual has been renamed to `haplosomesNonNull`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genome1 is not defined for object element type Individual") &&
+            (selectionString == "genome1"))
+        return offerAndExecuteAutofix(selection, "haplosomesFromParent1", "The `genome1` property of Individual has been renamed to `haplosomesFromParent1`.", terminationMessage);
+
+    if (terminationMessage.contains("property genome2 is not defined for object element type Individual") &&
+            (selectionString == "genome2"))
+        return offerAndExecuteAutofix(selection, "haplosomesFromParent2", "The `genome2` property of Individual has been renamed to `haplosomesFromParent2`.", terminationMessage);
+    
+    if (terminationMessage.contains("property genomes is not defined for object element type Subpopulation") &&
+            (selectionString == "genomes"))
+        return offerAndExecuteAutofix(selection, "haplosomes", "The `genomes` property of Subpopulation has been renamed to `haplosomes`.", terminationMessage);
+
+    if (terminationMessage.contains("property genomesNonNull is not defined for object element type Subpopulation") &&
+            (selectionString == "genomesNonNull"))
+        return offerAndExecuteAutofix(selection, "haplosomesNonNull", "The `genomesNonNull` property of Subpopulation has been renamed to `haplosomesNonNull`.", terminationMessage);
+
+    if (terminationMessage.contains("property chromosome is not defined for object element type Species") &&
+            (selectionString == "chromosome"))
+        return offerAndExecuteAutofix(selection, "chromosomes", "The `chromosome` property of Species has been renamed to `chromosomes`.", terminationMessage);
+
+    if (terminationMessage.contains("property chromosomeType is not defined for object element type Species") &&
+            (selectionString == "chromosomeType"))
+        return offerAndExecuteAutofix(selection, "chromosomes.type", "The `chromosomeType` property of Species has been removed; it is now accessed as `chromosomes.type`.", terminationMessage);
+
+    if (terminationMessage.contains("undefined identifier genome") &&
+            (selectionString == "genome"))
+        return offerAndExecuteAutofix(selection, "haplosome", "The `genome` pseudo-parameter has been renamed to `haplosome`.", terminationMessage);
+
+    // genome1 and genome2 for some callback types were removed in favor of individual.genome1 and individual.genome2 for SLiM 4.0,
+    // and used to be autofixed above; however, in recombination() callbacks genome1 has become haplosome1 and genome2 has
+    // become haplosome2, which conflicted with the previous autofix.  This sequence of fixes works for all cases.
+    if (terminationMessage.contains("undefined identifier genome1") &&
+            (selectionString == "genome1"))
+        return offerAndExecuteAutofix(selection, "haplosome1", "The `genome1` pseudo-parameter has been renamed to `haplosome1`.", terminationMessage);
+
+    if (terminationMessage.contains("undefined identifier haplosome1") &&
+            (selectionString == "haplosome1"))
+        return offerAndExecuteAutofix(selection, "individual.haplosomesFromParent1", "The `haplosome1` pseudo-parameter has been removed; it is now accessed as `individual.haplosomesFromParent1`.", terminationMessage);
+
+    if (terminationMessage.contains("undefined identifier genome2") &&
+            (selectionString == "genome2"))
+        return offerAndExecuteAutofix(selection, "haplosome2", "The `genome2` pseudo-parameter has been renamed to `haplosome2`.", terminationMessage);
+
+    if (terminationMessage.contains("undefined identifier haplosome2") &&
+            (selectionString == "haplosome2"))
+        return offerAndExecuteAutofix(selection, "individual.haplosomesFromParent2", "The `haplosome2` pseudo-parameter has been removed; it is now accessed as `individual.haplosomesFromParent2`.", terminationMessage);
+    
     return false;
 }
 
diff --git a/QtSLiM/recipes.qrc b/QtSLiM/recipes.qrc
index 89a25f75a..b65222849 100644
--- a/QtSLiM/recipes.qrc
+++ b/QtSLiM/recipes.qrc
@@ -4,7 +4,7 @@
         <file>recipes/Recipe 4.1 - A basic neutral simulation.txt</file>
         <file>recipes/Recipe 4.2.1 - Basic output, Entire population.txt</file>
         <file>recipes/Recipe 4.2.2 - Basic output, Random population sample.txt</file>
-        <file>recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt</file>
+        <file>recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt</file>
         <file>recipes/Recipe 4.2.4 - Basic output, Substitutions.txt</file>
         <file>recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt</file>
         <file>recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt</file>
diff --git a/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt b/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt
index a550fb5ad..b1891e502 100644
--- a/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt	
+++ b/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt	
@@ -18,9 +18,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;
diff --git a/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt b/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt
index 02b7cb2c6..80aa8c287 100644
--- a/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt	
+++ b/QtSLiM/recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt	
@@ -20,9 +20,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;
diff --git a/QtSLiM/recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt b/QtSLiM/recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt
index 95288da4e..408bef7b7 100644
--- a/QtSLiM/recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt	
+++ b/QtSLiM/recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt	
@@ -12,7 +12,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1 late() {
-	target = sample(p1.genomes, 100);
+	target = sample(p1.haplosomes, 100);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1: late() {
diff --git a/QtSLiM/recipes/Recipe 11.1 - Assortative mating.txt b/QtSLiM/recipes/Recipe 11.1 - Assortative mating.txt
index 261c148ef..92e6667c0 100644
--- a/QtSLiM/recipes/Recipe 11.1 - Assortative mating.txt	
+++ b/QtSLiM/recipes/Recipe 11.1 - Assortative mating.txt	
@@ -16,7 +16,7 @@ initialize() {
 	p2.setMigrationRates(p1, 0.1);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 mutationEffect(m2, p2) { return 0.2; }
@@ -40,7 +40,7 @@ mutationEffect(m2, p2) { return 0.2; }
 		return weights * sourceSubpop.getValue("weights2");
 }
 10000: late() {
-	FST = calcFST(p1.genomes, p2.genomes);
+	FST = calcFST(p1.haplosomes, p2.haplosomes);
 	sim.setValue("FST", sim.getValue("FST") + FST);
 }
 19999 late() {
diff --git a/QtSLiM/recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt b/QtSLiM/recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt
index 2124b011c..aa3959d95 100644
--- a/QtSLiM/recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt	
+++ b/QtSLiM/recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt	
@@ -17,9 +17,9 @@ initialize() {
 	cat("m2 mutation count: " + sim.countOfMutationsOfType(m2) + "\n");
 }
 modifyChild(p1) {
-	pollenSMuts = child.genome2.mutationsOfType(m2);
-	styleSMuts1 = parent1.genome1.mutationsOfType(m2);
-	styleSMuts2 = parent1.genome2.mutationsOfType(m2);
+	pollenSMuts = child.haplosomesFromParent2.mutationsOfType(m2);
+	styleSMuts1 = parent1.haplosomesFromParent1.mutationsOfType(m2);
+	styleSMuts2 = parent1.haplosomesFromParent2.mutationsOfType(m2);
 	if (identical(pollenSMuts, styleSMuts1))
 		if (runif(1) < 0.99)
 			return F;
diff --git a/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis I.txt b/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis I.txt
index 976f34aa3..87d209e30 100644
--- a/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis I.txt	
+++ b/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis I.txt	
@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	hasMutA = any(child.genomes.countOfMutationsOfType(m2) > 0);
-	hasMutB = any(child.genomes.countOfMutationsOfType(m3) > 0);
+	hasMutA = any(child.haplosomes.countOfMutationsOfType(m2) > 0);
+	hasMutB = any(child.haplosomes.countOfMutationsOfType(m3) > 0);
 	if (hasMutA & hasMutB)
 		return F;
 	return T;
diff --git a/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis II.txt b/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis II.txt
index d1e62e19f..5be4323f3 100644
--- a/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis II.txt	
+++ b/QtSLiM/recipes/Recipe 12.2 - Lethal epistasis II.txt	
@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	mutACount = sum(child.genomes.countOfMutationsOfType(m2));
-	mutBCount = sum(child.genomes.countOfMutationsOfType(m3));
+	mutACount = sum(child.haplosomes.countOfMutationsOfType(m2));
+	mutBCount = sum(child.haplosomes.countOfMutationsOfType(m3));
 	if ((mutACount == 2) & (mutBCount == 2))
 		return F;
 	return T;
diff --git a/QtSLiM/recipes/Recipe 12.3 - Simulating gene drive.txt b/QtSLiM/recipes/Recipe 12.3 - Simulating gene drive.txt
index 3a28ccc88..9ae33724d 100644
--- a/QtSLiM/recipes/Recipe 12.3 - Simulating gene drive.txt	
+++ b/QtSLiM/recipes/Recipe 12.3 - Simulating gene drive.txt	
@@ -17,7 +17,7 @@ initialize() {
 		sim.subpopulations[i].setMigrationRates(i+1, 0.1);
 }
 100 late() {
-	p0.genomes[0:49].addNewDrawnMutation(m2, 10000);
+	p0.haplosomes[0:49].addNewDrawnMutation(m2, 10000);
 }
 100:10000 late() {
 	if (sim.countOfMutationsOfType(m2) == 0)
@@ -34,12 +34,12 @@ mutationEffect(m2) {
 	mut = sim.mutationsOfType(m2);
 	if (size(mut) == 1)
 	{
-		hasMutOnChromosome1 = child.genome1.containsMutations(mut);
-		hasMutOnChromosome2 = child.genome2.containsMutations(mut);
+		hasMutOnChromosome1 = child.haplosomesFromParent1.containsMutations(mut);
+		hasMutOnChromosome2 = child.haplosomesFromParent2.containsMutations(mut);
 		if (hasMutOnChromosome1 & !hasMutOnChromosome2)
-			child.genome2.addMutations(mut);
+			child.haplosomesFromParent2.addMutations(mut);
 		else if (hasMutOnChromosome2 & !hasMutOnChromosome1)
-			child.genome1.addMutations(mut);
+			child.haplosomesFromParent1.addMutations(mut);
 	}
 	return T;
 }
diff --git a/QtSLiM/recipes/Recipe 13.1 - Polygenic selection.txt b/QtSLiM/recipes/Recipe 13.1 - Polygenic selection.txt
index e1b55e7a3..0af39c7fd 100644
--- a/QtSLiM/recipes/Recipe 13.1 - Polygenic selection.txt	
+++ b/QtSLiM/recipes/Recipe 13.1 - Polygenic selection.txt	
@@ -15,7 +15,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 fitnessEffect() {
-	phenotype = sum(individual.genomes.countOfMutationsOfType(m2));
+	phenotype = sum(individual.haplosomes.countOfMutationsOfType(m2));
 	return 1.5 - (phenotype - 10.0)^2 * 0.005;
 }
 5000 late() {
diff --git a/QtSLiM/recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt b/QtSLiM/recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt
index 396bbc8f8..5360e7d4d 100644
--- a/QtSLiM/recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt	
+++ b/QtSLiM/recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt	
@@ -52,7 +52,7 @@ initialize() {
 	community.registerEarlyEvent("s2", s1.source, 2, 2);
 	
 	// optional: give m2 mutations to everyone, as standing variation
-	g = sim.subpopulations.genomes;
+	g = sim.subpopulations.haplosomes;
 	
 	for (q in Q)
 	{
diff --git a/QtSLiM/recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt b/QtSLiM/recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt
index 091d92edd..a34cce59b 100644
--- a/QtSLiM/recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt	
+++ b/QtSLiM/recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt	
@@ -71,7 +71,7 @@ late() {
 	for (ind in sim.subpopulations.individuals)
 	{
 		// construct phenotypes from additive effects of QTL mutations
-		muts = ind.genomes.mutationsOfType(m2);
+		muts = ind.haplosomes.mutationsOfType(m2);
 		phenotype0 = size(muts) ? sum(muts.getValue("e0")) else 0.0;
 		phenotype1 = size(muts) ? sum(muts.getValue("e1")) else 0.0;
 		ind.setValue("phenotype0", phenotype0);
diff --git a/QtSLiM/recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt b/QtSLiM/recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt
index 1db7945df..ac3d744e7 100644
--- a/QtSLiM/recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt	
+++ b/QtSLiM/recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt	
@@ -17,6 +17,6 @@ mateChoice() {
 }
 1000 late() {
 	// Print mean heterozygosity across the population
-	heterozygosity = calcHeterozygosity(p1.genomes);
+	heterozygosity = calcHeterozygosity(p1.haplosomes);
 	cat("Mean heterozygosity = " + heterozygosity + "\n");
 }
diff --git a/QtSLiM/recipes/Recipe 14.11 - Modeling microsatellites.txt b/QtSLiM/recipes/Recipe 14.11 - Modeling microsatellites.txt
index 540782324..099dc3dab 100644
--- a/QtSLiM/recipes/Recipe 14.11 - Modeling microsatellites.txt	
+++ b/QtSLiM/recipes/Recipe 14.11 - Modeling microsatellites.txt	
@@ -21,14 +21,14 @@ initialize() {
 	sim.addSubpop("p1", 500);
 	
 	// create some microsatellites at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(msatCount, 0, L-1);
 	repeats = rpois(msatCount, 20) + 5;
 	
 	for (msatIndex in 0:(msatCount-1))
 	{
 		pos = positions[msatIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = repeats[msatIndex];
 	}
 	
@@ -37,14 +37,14 @@ initialize() {
 }
 modifyChild() {
 	// mutate microsatellites with rate msatMu
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
 		mutCount = rpois(1, msatMu * msatCount);
 		
 		if (mutCount)
 		{
 			mutSites = sample(msatPositions, mutCount);
-			msats = genome.mutationsOfType(m2);
+			msats = haplosome.mutationsOfType(m2);
 			
 			for (mutSite in mutSites)
 			{
@@ -66,15 +66,15 @@ modifyChild() {
 					
 					if (matchingMut.size() == 1)
 					{
-						genome.removeMutations(msat);
-						genome.addMutations(matchingMut);
+						haplosome.removeMutations(msat);
+						haplosome.addMutations(matchingMut);
 						next;
 					}
 				}
 				
 				// make a new mutation with the new repeat count
-				genome.removeMutations(msat);
-				msat = genome.addNewDrawnMutation(m2, mutSite);
+				haplosome.removeMutations(msat);
+				msat = haplosome.addNewDrawnMutation(m2, mutSite);
 				msat.tag = repeats;
 			}
 		}
diff --git a/QtSLiM/recipes/Recipe 14.12 - Modeling transposable elements.txt b/QtSLiM/recipes/Recipe 14.12 - Modeling transposable elements.txt
index f74d7c32f..1f7ceb770 100644
--- a/QtSLiM/recipes/Recipe 14.12 - Modeling transposable elements.txt	
+++ b/QtSLiM/recipes/Recipe 14.12 - Modeling transposable elements.txt	
@@ -28,22 +28,22 @@ initialize() {
 	sim.tag = 0;	// the next unique tag value to use for TEs
 	
 	// create some transposons at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(teInitialCount, 0, L-1);
 	
 	for (teIndex in 0:(teInitialCount-1))
 	{
 		pos = positions[teIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = sim.tag;
 		sim.tag = sim.tag + 1;
 	}
 }
 modifyChild() {
 	// disable transposons with rate teDisableP
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
-		tes = genome.mutationsOfType(m2);
+		tes = haplosome.mutationsOfType(m2);
 		teCount = tes.size();
 		mutatedCount = teCount ? rpois(1, teCount * teDisableP) else 0;
 		
@@ -59,14 +59,14 @@ modifyChild() {
 				if (size(disabledTE))
 				{
 					// use the existing disabled TE mutation
-					genome.removeMutations(te);
-					genome.addMutations(disabledTE);
+					haplosome.removeMutations(te);
+					haplosome.addMutations(disabledTE);
 					next;
 				}
 				
 				// make a new disabled TE mutation with the right tag
-				genome.removeMutations(te);
-				disabledTE = genome.addNewDrawnMutation(m3, te.position);
+				haplosome.removeMutations(te);
+				disabledTE = haplosome.addNewDrawnMutation(m3, te.position);
 				disabledTE.tag = te.tag;
 			}
 		}
@@ -78,9 +78,9 @@ late() {
 	// make active transposons copy themselves with rate teJumpP
 	for (individual in sim.subpopulations.individuals)
 	{
-		for (genome in individual.genomes)
+		for (haplosome in individual.haplosomes)
 		{
-			tes = genome.mutationsOfType(m2);
+			tes = haplosome.mutationsOfType(m2);
 			teCount = tes.size();
 			jumpCount = teCount ? rpois(1, teCount * teJumpP) else 0;
 			
@@ -92,7 +92,7 @@ late() {
 				{
 					// make a new TE mutation
 					pos = rdunif(1, 0, L-1);
-					jumpTE = genome.addNewDrawnMutation(m2, pos);
+					jumpTE = haplosome.addNewDrawnMutation(m2, pos);
 					jumpTE.tag = sim.tag;
 					sim.tag = sim.tag + 1;
 				}
@@ -104,7 +104,7 @@ late() {
 	// print information on each TE, including the fraction of it disabled
 	all_tes = sortBy(sim.mutationsOfType(m2), "position");
 	all_disabledTEs = sortBy(sim.mutationsOfType(m3), "position");
-	genomeCount = size(sim.subpopulations.genomes);
+	haplosomeCount = size(sim.subpopulations.haplosomes);
 	
 	catn("Active TEs:");
 	for (te in all_tes)
@@ -126,7 +126,7 @@ late() {
 		
 		total = active + disabled;
 		
-		cat("frequency " + format("%0.3f", total / genomeCount) + ", ");
+		cat("frequency " + format("%0.3f", total / haplosomeCount) + ", ");
 		catn(round(active / total * 100) + "% active");
 	}
 	
diff --git a/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt b/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt
index f4e2981d2..5815360a9 100644
--- a/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt	
+++ b/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt	
@@ -24,7 +24,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 	
 	// create the canonical mutation objects
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT2", target.mutations);
 	target.removeMutations();
@@ -33,7 +33,7 @@ initialize() {
 	target.removeMutations();
 	
 	// start homozygous "aa" at every position
-	p1.genomes.addMutations(MUT3);
+	p1.haplosomes.addMutations(MUT3);
 	
 	// log results
 	log = community.createLogFile("freq.csv", logInterval=10);
diff --git a/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt b/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt
index 0eaff07e7..51e63457e 100644
--- a/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt	
+++ b/QtSLiM/recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt	
@@ -22,7 +22,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 	
 	// create the permanent m2 mutation objects we will use
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT", target.mutations);
 	
@@ -37,7 +37,7 @@ initialize() {
 mutation(m3) {
 	// if we already have an m2 mutation at the site, allow
 	// the new m3 mutation; we will remove the stack below
-	if (genome.containsMarkerMutation(m2, mut.position))
+	if (haplosome.containsMarkerMutation(m2, mut.position))
 		return T;
 	
 	// no m2 mutation is present, so unique down
@@ -51,18 +51,18 @@ late() {
 	// if so, we have m2/m3 stacked mutations to remove
 	if (m3muts.length() > 0)
 	{
-		genomes = sim.subpopulations.genomes;
-		counts = genomes.countOfMutationsOfType(m3);
-		hasStacked = genomes[counts > 0];
+		haplosomes = sim.subpopulations.haplosomes;
+		counts = haplosomes.countOfMutationsOfType(m3);
+		hasStacked = haplosomes[counts > 0];
 		
-		for (genome in hasStacked)
+		for (haplosome in hasStacked)
 		{
-			stacked_m3 = genome.mutationsOfType(m3);
+			stacked_m3 = haplosome.mutationsOfType(m3);
 			stackPositions = stacked_m3.position;
-			all_m2 = genome.mutationsOfType(m2);
+			all_m2 = haplosome.mutationsOfType(m2);
 			s = (match(all_m2.position, stackPositions) >= 0);
 			stacked_m2 = all_m2[s];
-			genome.removeMutations(c(stacked_m3, stacked_m2));
+			haplosome.removeMutations(c(stacked_m3, stacked_m2));
 		}
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt b/QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt
index ce7b702fe..d1852a5d5 100644
--- a/QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt	
+++ b/QtSLiM/recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt	
@@ -38,15 +38,15 @@ initialize() {
 	if (parts[0] != "positions:") stop("Missing positions.");
 	positions = asFloat(parts[1:(size(parts)-1)]);
 	
-	// create all mutations in a genome in a dummy subpopulation
+	// create all mutations in a haplosome in a dummy subpopulation
 	sim.addSubpop("p2", 1);
-	g = p2.genomes[0];
-	L = sim.chromosome.lastPosition;
+	g = p2.haplosomes[0];
+	L = sim.chromosomes.lastPosition;
 	intPositions = asInteger(round(positions * L));
 	muts = g.addNewMutation(m1, 0.0, intPositions);
 	
-	// add the appropriate mutations to each genome
-	for (g in p1.genomes)
+	// add the appropriate mutations to each haplosome
+	for (g in p1.haplosomes)
 	{
 		f = asLogical(asInteger(strsplit(lines[index], "")));
 		index = index + 1;
diff --git a/QtSLiM/recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt b/QtSLiM/recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt
index 91ec540e2..a63474a02 100644
--- a/QtSLiM/recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt	
+++ b/QtSLiM/recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt	
@@ -21,8 +21,8 @@ initialize() {
 1 late() {
 	sim.addSubpop("p1", N);
 
-	// give some genomes an inversion
-	inverted = sample(p1.genomes, 100);
+	// give some haplosomes an inversion
+	inverted = sample(p1.haplosomes, 100);
 	inverted.addNewDrawnMutation(m2, INV_START);
 	inverted.addNewDrawnMutation(m3, INV_END);
 }
@@ -41,8 +41,8 @@ mutationEffect(m2) {
 }
 
 recombination() {
-	gm1 = genome1.containsMarkerMutation(m2, INV_START);
-	gm2 = genome2.containsMarkerMutation(m2, INV_START);
+	gm1 = haplosome1.containsMarkerMutation(m2, INV_START);
+	gm2 = haplosome2.containsMarkerMutation(m2, INV_START);
 	if (!(gm1 | gm2)) {
 		// homozygote non-inverted
 		return F;
@@ -61,7 +61,7 @@ recombination() {
 	} else {
 		// heterozygote inverted: resample to get an even number of breakpoints
 		// this is *recursive*: it calls this recombination callback again!
-		breakpoints = sim.chromosome.drawBreakpoints(individual);
+		breakpoints = sim.chromosomes.drawBreakpoints(individual);
 	}
 	return T;
 }
diff --git a/QtSLiM/recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt b/QtSLiM/recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt
index f115ac350..f7cd2ade8 100644
--- a/QtSLiM/recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt	
+++ b/QtSLiM/recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt	
@@ -25,15 +25,15 @@ initialize()
 	// initialize the pop, with a Y marker for each male
 	sim.addSubpop("p1", 1000);
 	i = p1.individuals;
-	i[i.sex == "M"].genome2.addNewMutation(m3, 0.0, 5999999);
+	i[i.sex == "M"].haplosomesFromParent2.addNewMutation(m3, 0.0, 5999999);
 }
 
 modifyChild() {
 	// females should not have a Y, males should have a Y
 	if (child.sex == "F")
-		return !child.genome2.containsMarkerMutation(m3, 5999999);
+		return !child.haplosomesFromParent2.containsMarkerMutation(m3, 5999999);
 	else
-		return child.genome2.containsMarkerMutation(m3, 5999999);
+		return child.haplosomesFromParent2.containsMarkerMutation(m3, 5999999);
 }
 
 1:10000 late() {
@@ -46,7 +46,7 @@ modifyChild() {
 		// look at the mutations in a single Y chromosome
 		// to find mutations that are fixed in all Y's
 		firstMale = p1.individuals[p1.individuals.sex == "M"][0];
-		fMG = firstMale.genomes;
+		fMG = firstMale.haplosomes;
 		
 		if (fMG[0].containsMarkerMutation(m3, 5999999)) {
 			firstY = fMG[0];
@@ -70,7 +70,7 @@ modifyChild() {
 		cat(removeX.size() + "/" + removeY.size() + " on X/Y\n");
 		
 		removes = c(removeY, removeX);
-		sim.subpopulations.genomes.removeMutations(removes, T);
+		sim.subpopulations.haplosomes.removeMutations(removes, T);
 	}
 }
 
diff --git a/QtSLiM/recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt b/QtSLiM/recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt
index f7117ae64..169595234 100644
--- a/QtSLiM/recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt	
+++ b/QtSLiM/recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt	
@@ -30,11 +30,11 @@ initialize() {
 	     muttype in c(m1,m2,m3),
 	     symbol in c("M1","M2","M3"))
 	{
-		genomes = subpop.genomes;
-		muts = genomes.addNewDrawnMutation(muttype, positions);
+		haplosomes = subpop.haplosomes;
+		muts = haplosomes.addNewDrawnMutation(muttype, positions);
 		defineConstant(symbol, muts);
 		
-		mut = genomes.addNewDrawnMutation(m4, integerDiv(Z, 2));
+		mut = haplosomes.addNewDrawnMutation(m4, integerDiv(Z, 2));
 		catn("Beneficial mutation: s == " + mut.selectionCoeff);
 	}
 	
diff --git a/QtSLiM/recipes/Recipe 14.9 - Modeling haploid organisms.txt b/QtSLiM/recipes/Recipe 14.9 - Modeling haploid organisms.txt
index a29f44e5c..faff72216 100644
--- a/QtSLiM/recipes/Recipe 14.9 - Modeling haploid organisms.txt	
+++ b/QtSLiM/recipes/Recipe 14.9 - Modeling haploid organisms.txt	
@@ -12,14 +12,14 @@ initialize() {
 	p1.setCloningRate(1.0);
 }
 late() {
-	// remove any new mutations added to the disabled diploid genomes
-	sim.subpopulations.individuals.genome2.removeMutations();
+	// remove any new mutations added to the disabled diploid haplosomes
+	sim.subpopulations.individuals.haplosomesFromParent2.removeMutations();
 	
-	// remove mutations in the haploid genomes that have fixed
+	// remove mutations in the haploid haplosomes that have fixed
 	muts = sim.mutationsOfType(m1);
 	freqs = sim.mutationFrequencies(NULL, muts);
 	if (any(freqs == 0.5))
-		sim.subpopulations.genomes.removeMutations(muts[freqs == 0.5], T);
+		sim.subpopulations.haplosomes.removeMutations(muts[freqs == 0.5], T);
 }
 200000 late() {
 	sim.outputFixedMutations();
diff --git a/QtSLiM/recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt b/QtSLiM/recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt
index 488f598b4..3568a6cb2 100644
--- a/QtSLiM/recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt	
+++ b/QtSLiM/recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt	
@@ -11,7 +11,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 reproduction() {
-	subpop.addRecombinant(individual.genome1, NULL, NULL, NULL, NULL, NULL);
+	subpop.addRecombinant(individual.haplosomesFromParent1, NULL, NULL, NULL, NULL, NULL);
 }
 1 early() {
 	sim.addSubpop("p1", 500, haploid=T);
diff --git a/QtSLiM/recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt b/QtSLiM/recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt
index 00df94d7d..9f2c6c859 100644
--- a/QtSLiM/recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt	
+++ b/QtSLiM/recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt	
@@ -16,7 +16,7 @@ reproduction() {
 	if (runif(1) < H)
 	{
 		// horizontal gene transfer from a randomly chosen individual
-		HGTsource = p1.sampleIndividuals(1, exclude=individual).genome1;
+		HGTsource = p1.sampleIndividuals(1, exclude=individual).haplosomesFromParent1;
 		
 		// draw two distinct locations; redraw if we get a duplicate
 		do breaks = rdunif(2, max=L-1);
@@ -26,12 +26,12 @@ reproduction() {
 		if (breaks[0] > breaks[1])
 			breaks = c(0, breaks[1], breaks[0]);
 		
-		subpop.addRecombinant(individual.genome1, HGTsource, breaks, NULL, NULL, NULL);
+		subpop.addRecombinant(individual.haplosomesFromParent1, HGTsource, breaks, NULL, NULL, NULL);
 	}
 	else
 	{
 		// no horizontal gene transfer; clonal replication
-		subpop.addRecombinant(individual.genome1, NULL, NULL, NULL, NULL, NULL);
+		subpop.addRecombinant(individual.haplosomesFromParent1, NULL, NULL, NULL, NULL, NULL);
 	}
 }
 1 early() {
@@ -39,7 +39,7 @@ reproduction() {
 	sim.addSubpop("p1", 2, haploid=T);
 	
 	// add beneficial mutations to each bacterium, but at different loci
-	g = p1.individuals.genome1;
+	g = p1.individuals.haplosomesFromParent1;
 	g[0].addNewDrawnMutation(m2, asInteger(L * 0.25));
 	g[1].addNewDrawnMutation(m2, asInteger(L * 0.75));
 }
diff --git a/QtSLiM/recipes/Recipe 15.14 - Alternation of generations.txt b/QtSLiM/recipes/Recipe 15.14 - Alternation of generations.txt
index 1b677fb11..9f28ad51b 100644
--- a/QtSLiM/recipes/Recipe 15.14 - Alternation of generations.txt	
+++ b/QtSLiM/recipes/Recipe 15.14 - Alternation of generations.txt	
@@ -23,24 +23,24 @@ initialize()
 }
 reproduction(p1)
 {
-	g_1 = individual.genome1;
-	g_2 = individual.genome2;
+	g_1 = individual.haplosomesFromParent1;
+	g_2 = individual.haplosomesFromParent2;
 	
 	for (meiosisCount in 1:5)
 	{
 		if (individual.sex == "M")
 		{
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			s_1 = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "M");
 			s_2 = p2.addRecombinant(g_2, g_1, breaks, NULL, NULL, NULL, "M");
 			
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			s_3 = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "M");
 			s_4 = p2.addRecombinant(g_2, g_1, breaks, NULL, NULL, NULL, "M");
 		}
 		else if (individual.sex == "F")
 		{
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			e = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "F",
 				randomizeStrands=T);
 		}
@@ -51,8 +51,8 @@ reproduction(p2, "F")
 	mate = p2.sampleIndividuals(1, sex="M", tagL0=F);
 	mate.tagL0 = T;
 	
-	child = p1.addRecombinant(individual.genome1, NULL, NULL,
-		mate.genome1, NULL, NULL);
+	child = p1.addRecombinant(individual.haplosomesFromParent1, NULL, NULL,
+		mate.haplosomesFromParent1, NULL, NULL);
 }
 early()
 {
@@ -60,13 +60,13 @@ early()
 	{
 		p1.fitnessScaling = 0.0;
 		p2.individuals.tagL0 = F;
-		sim.chromosome.setMutationRate(0.0);
+		sim.chromosomes.setMutationRate(0.0);
 	}
 	else
 	{
 		p2.fitnessScaling = 0.0;
 		p1.fitnessScaling = K / p1.individualCount;
-		sim.chromosome.setMutationRate(MU);
+		sim.chromosomes.setMutationRate(MU);
 	}
 }
 10000 late()
diff --git a/QtSLiM/recipes/Recipe 15.15 - Meiotic drive.txt b/QtSLiM/recipes/Recipe 15.15 - Meiotic drive.txt
index 0b133755c..90b28c351 100644
--- a/QtSLiM/recipes/Recipe 15.15 - Meiotic drive.txt	
+++ b/QtSLiM/recipes/Recipe 15.15 - Meiotic drive.txt	
@@ -1,11 +1,11 @@
 // Keywords: nonWF, non-Wright-Fisher, meiotic drive, segregation distortion, intragenomic conflict
 
-function (i)driveBreakpoints(o<Genome>$ gen1, o<Genome>$ gen2)
+function (i)driveBreakpoints(o<Haplosome>$ gen1, o<Haplosome>$ gen2)
 {
 	// start with default breakpoints generated by the chromosome
-	breaks = sim.chromosome.drawBreakpoints();
+	breaks = sim.chromosomes.drawBreakpoints();
 	
-	// if both genomes have the drive, or neither, then just return
+	// if both haplosomes have the drive, or neither, then just return
 	gen1has = gen1.containsMarkerMutation(m2, D_pos);
 	gen2has = gen2.containsMarkerMutation(m2, D_pos);
 	if (gen1has == gen2has)
@@ -42,9 +42,9 @@ initialize() {
 }
 reproduction() {
 	m = subpop.sampleIndividuals(1);
-	b1 = driveBreakpoints(individual.genome1, individual.genome2);
-	b2 = driveBreakpoints(m.genome1, m.genome2);
-	subpop.addRecombinant(individual.genome1, individual.genome2, b1, m.genome1, m.genome2, b2);
+	b1 = driveBreakpoints(individual.haplosomesFromParent1, individual.haplosomesFromParent2);
+	b2 = driveBreakpoints(m.haplosomesFromParent1, m.haplosomesFromParent2);
+	subpop.addRecombinant(individual.haplosomesFromParent1, individual.haplosomesFromParent2, b1, m.haplosomesFromParent1, m.haplosomesFromParent2, b2);
 }
 1 early() {
 	sim.addSubpop("p1", 10);
@@ -53,7 +53,7 @@ early() {
 	p1.fitnessScaling = K / p1.individualCount;
 }
 100 early() {
-	target = sample(p1.genomes, 10);
+	target = sample(p1.haplosomes, 10);
 	target.addNewDrawnMutation(m2, D_pos);
 }
 100:1000 late() {
diff --git a/QtSLiM/recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt b/QtSLiM/recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt
index 10a784b85..194a9c859 100644
--- a/QtSLiM/recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt	
+++ b/QtSLiM/recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt	
@@ -14,26 +14,26 @@ initialize() {
 	initializeSex("A");
 }
 reproduction(NULL, "F") {
-	gen1 = individual.genome1;
-	gen2 = individual.genome2;
-	breaks = sim.chromosome.drawBreakpoints(individual);
+	gen1 = individual.haplosomesFromParent1;
+	gen2 = individual.haplosomesFromParent2;
+	breaks = sim.chromosomes.drawBreakpoints(individual);
 	
 	// decide whether we're generating a haploid male or a diploid female
 	if (rbinom(1, 1, P_OFFSPRING_MALE))
 	{
 		// didn't find a mate; make a haploid male from an unfertilized egg:
-		//		- one genome comes from recombination of the female's genomes
-		//		- the other genome is a null genome (a placeholder)
+		//		- one haplosome comes from recombination of the female's haplosomes
+		//		- the other haplosome is a null haplosome (a placeholder)
 		subpop.addRecombinant(gen1, gen2, breaks, NULL, NULL, NULL, "M",
 			randomizeStrands=T);
 	}
 	else
 	{
 		// found a mate; make a diploid female from a fertilized egg:
-		//		- one genome comes from recombination of the female's genomes
-		//		- the other genome comes from the mate (a haploid male)
+		//		- one haplosome comes from recombination of the female's haplosomes
+		//		- the other haplosome comes from the mate (a haploid male)
 		mate = subpop.sampleIndividuals(1, sex="M");
-		subpop.addRecombinant(gen1, gen2, breaks, mate.genome1, NULL, NULL, "F",
+		subpop.addRecombinant(gen1, gen2, breaks, mate.haplosomesFromParent1, NULL, NULL, "F",
 			randomizeStrands=T);
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt b/QtSLiM/recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt
index 35bf5f83e..c9ba9f74d 100644
--- a/QtSLiM/recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt	
+++ b/QtSLiM/recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt	
@@ -21,7 +21,7 @@ reproduction() {
 	sim.addSubpop("p1", 10);
 }
 100 early() {
-	mutant = sample(p1.individuals.genomes, 10);
+	mutant = sample(p1.individuals.haplosomes, 10);
 	mutant.addNewDrawnMutation(m2, 10000);
 }
 early() {
diff --git a/QtSLiM/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt b/QtSLiM/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt
index 2a3208754..8b55068a1 100644
--- a/QtSLiM/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt	
+++ b/QtSLiM/recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 1e5);
 }
 100 late() {
-	sample(p1.genomes, 1).addNewDrawnMutation(m2, 5e5);
+	sample(p1.haplosomes, 1).addNewDrawnMutation(m2, 5e5);
 }
 100:10000 late() {
 	mut = sim.mutationsOfType(m2);
diff --git a/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt b/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
index d274adcaa..dd06e056d 100644
--- a/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt	
+++ b/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt	
@@ -14,7 +14,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
 	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
 	sim.outputFull(PATH);
diff --git a/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt b/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
index a5107673f..2813e6f93 100644
--- a/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt	
+++ b/QtSLiM/recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt	
@@ -23,7 +23,7 @@ initialize() {
 	// record tag values and pedigree IDs in metadata
 	metadataDict = Dictionary("tags", tags, "ids", inds.pedigreeID);
 	
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
 	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
 	sim.treeSeqOutput(PATH, metadata=metadataDict);
diff --git a/QtSLiM/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt b/QtSLiM/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt
index b78423641..94ba44755 100644
--- a/QtSLiM/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt	
+++ b/QtSLiM/recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt	
@@ -14,8 +14,8 @@ initialize() {
 	sim.addSubpop("p2", 500);
 	sim.treeSeqRememberIndividuals(sim.subpopulations.individuals);
 	
-	p1.genomes.addNewDrawnMutation(m1, asInteger(L * 0.2));
-	p2.genomes.addNewDrawnMutation(m1, asInteger(L * 0.8));
+	p1.haplosomes.addNewDrawnMutation(m1, asInteger(L * 0.2));
+	p2.haplosomes.addNewDrawnMutation(m1, asInteger(L * 0.8));
 	
 	sim.addSubpop("p3", 1000);
 	p3.setMigrationRates(c(p1, p2), c(0.5, 0.5));
diff --git a/QtSLiM/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt b/QtSLiM/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt
index d35988776..9e3533fde 100644
--- a/QtSLiM/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt	
+++ b/QtSLiM/recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt	
@@ -14,7 +14,7 @@ initialize() {
 }
 1 late() {
 	sim.readFromPopulationFile("coalasex.trees");
-	target = sample(sim.subpopulations.genomes, 1);
+	target = sample(sim.subpopulations.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1: late() {
diff --git a/QtSLiM/recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt b/QtSLiM/recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt
index 4c60bf89e..97d34d8c5 100644
--- a/QtSLiM/recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt	
+++ b/QtSLiM/recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt	
@@ -18,6 +18,6 @@ initialize() {
 1:500001 early() {
 	if (sim.cycle % 1000 == 1) {
 		cat(sim.cycle + ": ");
-		print(nucleotideFrequencies(sim.chromosome.ancestralNucleotides()));
+		print(nucleotideFrequencies(sim.chromosomes.ancestralNucleotides()));
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt b/QtSLiM/recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt
index 7b9547f9c..4ae6ee7d6 100644
--- a/QtSLiM/recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt	
+++ b/QtSLiM/recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt	
@@ -14,7 +14,7 @@ initialize() {
 }
 1 late() {
 	sim.addSubpop("p1", 99);
-	p1.genomes.readFromVCF("chr22_filtered.recode.vcf", m1);
+	p1.haplosomes.readFromVCF("chr22_filtered.recode.vcf", m1);
 	p1.setSubpopulationSize(1000);
 }
 5 late() {
diff --git a/QtSLiM/recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt b/QtSLiM/recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt
index 5591e40f6..ea2f7c1b0 100644
--- a/QtSLiM/recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt	
+++ b/QtSLiM/recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt	
@@ -25,18 +25,18 @@ late() {
 	for (mut in new_muts)
 	{
 		pos = mut.position;
-		if (mut.nucleotide == sim.chromosome.ancestralNucleotides(pos, pos))
+		if (mut.nucleotide == sim.chromosomes.ancestralNucleotides(pos, pos))
 			back_muts = c(back_muts, mut);
 	}
 	if (size(back_muts))
-		sim.subpopulations.genomes.removeMutations(back_muts);
+		sim.subpopulations.haplosomes.removeMutations(back_muts);
 }
 1000 late() {
 	for (pos in 0:99)
 	{
 		muts = sim.subsetMutations(position=pos);
 		nucs = muts.nucleotide;
-		ancestral = sim.chromosome.ancestralNucleotides(pos, pos);
+		ancestral = sim.chromosomes.ancestralNucleotides(pos, pos);
 		cat(pos + " : " + paste(nucs));
 		if (size(nucs) != size(unique(nucs)))
 			cat("     DUPLICATES!");
diff --git a/QtSLiM/recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt b/QtSLiM/recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt
index 2efc9654d..5a31b6ce6 100644
--- a/QtSLiM/recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt	
+++ b/QtSLiM/recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt	
@@ -10,7 +10,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	c = sim.chromosome;
+	c = sim.chromosomes;
 	catn("Ancestral: " + c.ancestralNucleotides());
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="char")));
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="integer")));
@@ -25,14 +25,14 @@ initialize() {
 	catn("positions: " + paste(sim.substitutions.position));
 	catn();
 	
-	c = sim.chromosome;
+	c = sim.chromosomes;
 	catn("Ancestral: " + c.ancestralNucleotides());
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="char")));
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="integer")));
 	catn("positions: " + paste(0:(L-1)));
 	catn();
 	
-	g = p1.genomes[0];
+	g = p1.haplosomes[0];
 	
 	catn("SNPs:      " + paste(g.mutations.nucleotide));
 	catn("SNPs:      " + paste(g.mutations.nucleotideValue));
diff --git a/QtSLiM/recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt b/QtSLiM/recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt
index 67b7aef5e..c10085da0 100644
--- a/QtSLiM/recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt	
+++ b/QtSLiM/recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 5000 late() {
-	g = p1.sampleIndividuals(5).genomes;
+	g = p1.sampleIndividuals(5).haplosomes;
 	g.outputVCF(simplifyNucleotides=F);
 	g.outputVCF(simplifyNucleotides=T);
 }
diff --git a/QtSLiM/recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt b/QtSLiM/recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt
index c9c84d0a1..ad59d357c 100644
--- a/QtSLiM/recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt	
+++ b/QtSLiM/recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt	
@@ -26,6 +26,6 @@ initialize() {
 1:10000000 early() {
 	if (sim.cycle % 10000 == 1) {
 		cat(sim.cycle + ": ");
-		print(nucleotideFrequencies(sim.chromosome.ancestralNucleotides()));
+		print(nucleotideFrequencies(sim.chromosomes.ancestralNucleotides()));
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt b/QtSLiM/recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt
index 5891977d6..79a80ef33 100644
--- a/QtSLiM/recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt	
+++ b/QtSLiM/recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt	
@@ -15,7 +15,7 @@ initialize() {
 }
 1 late() {
 	sim.addSubpop("p1", 500);
-	sample(p1.genomes, 10).addNewDrawnMutation(m2, 20000);
+	sample(p1.haplosomes, 10).addNewDrawnMutation(m2, 20000);
 }
 2000 late() {
 	print(sim.mutationsOfType(m2));
diff --git a/QtSLiM/recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt b/QtSLiM/recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt
index 8d0435bdf..63f5c3178 100644
--- a/QtSLiM/recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt	
+++ b/QtSLiM/recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt	
@@ -21,8 +21,8 @@ late() {
 		s1.active = 0;
 }
 s1 fitnessEffect() {
-	nuc1 = individual.genome1.nucleotides(100, 100, format="integer");
-	nuc2 = individual.genome2.nucleotides(100, 100, format="integer");
+	nuc1 = individual.haplosomesFromParent1.nucleotides(100, 100, format="integer");
+	nuc2 = individual.haplosomesFromParent2.nucleotides(100, 100, format="integer");
 	return EFF[nuc1] * EFF[nuc2];
 }
 10000 late() {
diff --git a/QtSLiM/recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt b/QtSLiM/recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt
index e158f8641..a2446caa5 100644
--- a/QtSLiM/recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt	
+++ b/QtSLiM/recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt	
@@ -28,7 +28,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 fitnessEffect() {
-	for (g in individual.genomes)
+	for (g in individual.haplosomes)
 	{
 		seq = g.nucleotides(253, 670) + g.nucleotides(871, 1034);
 		codons = nucleotidesToCodons(seq);
@@ -41,8 +41,8 @@ fitnessEffect() {
 100000 late() {
 	catn(sim.substitutions.size() + " fixed mutations.");
 	
-	as1 = sim.chromosome.ancestralNucleotides(253, 670, "integer");
-	as2 = sim.chromosome.ancestralNucleotides(871, 1034, "integer");
+	as1 = sim.chromosomes.ancestralNucleotides(253, 670, "integer");
+	as2 = sim.chromosomes.ancestralNucleotides(871, 1034, "integer");
 	as = c(as1, as2);
 	codons = nucleotidesToCodons(as);
 	catn("Final AA sequence: " + codonsToAminoAcids(codons));
diff --git a/QtSLiM/recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt b/QtSLiM/recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt
index 3f77b3f7c..45861183f 100644
--- a/QtSLiM/recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt	
+++ b/QtSLiM/recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt	
@@ -27,7 +27,7 @@ species parasite initialize() {
 }
 
 function (float$)nucleotideFreq(o<Species>$ species, s$ nuc) {
-	nucs = species.subpopulations.individuals.genomes.nucleotides();
+	nucs = species.subpopulations.individuals.haplosomes.nucleotides();
 	return mean(nucs == nuc);
 }
 
@@ -55,7 +55,7 @@ ticks all late() {
 	for (p in parasites, h in chosen_hosts)
 	{
 		// infection depends upon a match (diploid matching-allele model)
-		all_nucleotides = c(p.genomes.nucleotides(), h.genomes.nucleotides());
+		all_nucleotides = c(p.haplosomes.nucleotides(), h.haplosomes.nucleotides());
 		
 		if (size(unique(all_nucleotides, preserveOrder=F)) == 1)
 		{
diff --git a/QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt b/QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt
similarity index 93%
rename from QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt
rename to QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt
index 0a54862db..72f1edbb7 100644
--- a/QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt	
+++ b/QtSLiM/recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt	
@@ -18,5 +18,5 @@ initialize() {
 	allIndividuals = sim.subpopulations.individuals;
 	w = asFloat(allIndividuals.countOfMutationsOfType(m2) + 1);
 	sampledIndividuals = sample(allIndividuals, 10, weights=w);
-	sampledIndividuals.genomes.output();
+	sampledIndividuals.haplosomes.output();
 }
diff --git a/QtSLiM/recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt b/QtSLiM/recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt
index b68038630..9da5273c7 100644
--- a/QtSLiM/recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt	
+++ b/QtSLiM/recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt	
@@ -14,6 +14,6 @@ initialize() {
 	p2.setMigrationRates(p1, 0.001);
 	log = community.createLogFile("sim_log.txt", logInterval=10);
 	log.addCycle();
-	log.addCustomColumn("FST", "calcFST(p1.genomes, p2.genomes);");
+	log.addCustomColumn("FST", "calcFST(p1.haplosomes, p2.haplosomes);");
 }
 20000 late() { }
diff --git a/QtSLiM/recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt b/QtSLiM/recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt
index 2cb99a3fd..bb9e6afcf 100644
--- a/QtSLiM/recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt	
+++ b/QtSLiM/recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt	
@@ -14,8 +14,8 @@ initialize() {
 
 // custom MS-style output from a multi-subpop sample
 2000 late() {
-	// obtain a random sample of genomes from the whole population
-	g = sample(sim.subpopulations.genomes, 10, T);
+	// obtain a random sample of haplosomes from the whole population
+	h = sample(sim.subpopulations.haplosomes, 10, T);
 	
 	// get the unique mutations in the sample, sorted by position
 	m = sortBy(unique(g.mutations), "position");
@@ -24,13 +24,13 @@ initialize() {
 	cat("\n\nsegsites: " + size(m) + "\n");
 	
 	// print the positions
-	positions = format("%.6f", m.position / sim.chromosome.lastPosition);
+	positions = format("%.6f", m.position / sim.chromosomes.lastPosition);
 	cat("positions: " + paste(positions, sep=" ") + "\n");
 	
-	// print the sampled genomes
-	for (genome in g)
+	// print the sampled haplosomes
+	for (haplosome in h)
 	{
-		hasMuts = (match(m, genome.mutations) >= 0);
+		hasMuts = (match(m, haplosome.mutations) >= 0);
 		cat(paste(asInteger(hasMuts), sep="") + "\n");
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt b/QtSLiM/recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt
index 23913ec76..6c01133a2 100644
--- a/QtSLiM/recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt	
+++ b/QtSLiM/recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt	
@@ -39,6 +39,6 @@ initialize() {
 	
 	// introduce a beneficial mutation
 	target_subpop = sample(sim.subpopulations, 1);
-	sample(target_subpop.genomes, 10).addNewDrawnMutation(m2, 20000);
+	sample(target_subpop.haplosomes, 10).addNewDrawnMutation(m2, 20000);
 }
 10000 late() { sim.outputFixedMutations(); }
diff --git a/QtSLiM/recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt b/QtSLiM/recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt
index 44a2b547e..19f222911 100644
--- a/QtSLiM/recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt	
+++ b/QtSLiM/recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt	
@@ -59,7 +59,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	sim.chromosome.colorSubstitution = "";
+	sim.chromosomes.colorSubstitution = "";
 	sim.addSubpop("p1", 5000);
 }
 10000 early() { sim.simulationFinished(); }
diff --git a/QtSLiM/recipes/Recipe 9.1 - Introducing adaptive mutations.txt b/QtSLiM/recipes/Recipe 9.1 - Introducing adaptive mutations.txt
index 992eb4e61..f3a952b01 100644
--- a/QtSLiM/recipes/Recipe 9.1 - Introducing adaptive mutations.txt	
+++ b/QtSLiM/recipes/Recipe 9.1 - Introducing adaptive mutations.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:100000 late() {
diff --git a/QtSLiM/recipes/Recipe 9.10 - Tracking the fate of background mutations.txt b/QtSLiM/recipes/Recipe 9.10 - Tracking the fate of background mutations.txt
index 0ecfdadaa..32eda7b8a 100644
--- a/QtSLiM/recipes/Recipe 9.10 - Tracking the fate of background mutations.txt	
+++ b/QtSLiM/recipes/Recipe 9.10 - Tracking the fate of background mutations.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	defineConstant("BACKGROUND", target.mutations);
 	mut = target.addNewDrawnMutation(m2, asInteger(L/2));
 	defineConstant("SWEEP", mut);
diff --git a/QtSLiM/recipes/Recipe 9.11 - Effective population size versus census population size.txt b/QtSLiM/recipes/Recipe 9.11 - Effective population size versus census population size.txt
index 2308b719c..a29b0d99a 100644
--- a/QtSLiM/recipes/Recipe 9.11 - Effective population size versus census population size.txt	
+++ b/QtSLiM/recipes/Recipe 9.11 - Effective population size versus census population size.txt	
@@ -32,7 +32,7 @@ initialize() {
 	p1.setValue("previous_N", p1.individualCount);
 }
 10000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, integerDiv(L, 2));
 }
 20000 late() {
@@ -49,7 +49,7 @@ function (float)mutTypeFrequency(o<MutationType>$ mutType)
 
 function (float)estimateNe_Heterozygosity(o<Subpopulation>$ subpop)
 {
-	pi = calcHeterozygosity(p1.genomes);
+	pi = calcHeterozygosity(p1.haplosomes);
 	return pi / (4 * MU);
 }
 
diff --git a/QtSLiM/recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt b/QtSLiM/recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt
index bf7859af5..0dbb0f2f8 100644
--- a/QtSLiM/recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt	
+++ b/QtSLiM/recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:100000 late() {
@@ -43,7 +43,7 @@ initialize() {
 			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 			
 			// re-introduce the sweep mutation
-			target = sample(p1.genomes, 1);
+			target = sample(p1.haplosomes, 1);
 			target.addNewDrawnMutation(m2, 10000);
 		}
 	}
diff --git a/QtSLiM/recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt b/QtSLiM/recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt
index b149a22c6..df1086fe7 100644
--- a/QtSLiM/recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt	
+++ b/QtSLiM/recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000: late() {
@@ -44,7 +44,7 @@ initialize() {
 		setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 		
 		// re-introduce the sweep mutation
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		target.addNewDrawnMutation(m2, 10000);
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 9.4 - Partial sweeps.txt b/QtSLiM/recipes/Recipe 9.4 - Partial sweeps.txt
index f192d43e3..c625551e1 100644
--- a/QtSLiM/recipes/Recipe 9.4 - Partial sweeps.txt	
+++ b/QtSLiM/recipes/Recipe 9.4 - Partial sweeps.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:10000 late() {
diff --git a/QtSLiM/recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt b/QtSLiM/recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt
index d5ca891e3..f98614b2a 100644
--- a/QtSLiM/recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt	
+++ b/QtSLiM/recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 100000);
 }
 1:10000 early() {
-	counts = p1.genomes.countOfMutationsOfType(m1);
+	counts = p1.haplosomes.countOfMutationsOfType(m1);
 	freq = mean(counts > 0);
 	
 	if (freq == 1.0)
@@ -22,7 +22,7 @@ initialize() {
 		
 		for (mut in sortBy(sim.mutations, "originTick"))
 		{
-			mutFreq = mean(p1.genomes.containsMutations(mut));
+			mutFreq = mean(p1.haplosomes.containsMutations(mut));
 			cat("Origin " + mut.originTick + ": " + mutFreq + "\n");
 		}
 		
diff --git a/QtSLiM/recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt b/QtSLiM/recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt
index f7692ae87..791d93928 100644
--- a/QtSLiM/recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt	
+++ b/QtSLiM/recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt	
@@ -15,7 +15,7 @@ initialize() {
 1000:1100 late() {
 	if (sim.cycle % 10 == 0)
 	{
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		if (target.countOfMutationsOfType(m2) == 0)
 			target.addNewDrawnMutation(m2, 10000);
 	}
@@ -36,7 +36,7 @@ initialize() {
 			}
 		}
 	}
-	if (all(p1.genomes.countOfMutationsOfType(m2) > 0)) {
+	if (all(p1.haplosomes.countOfMutationsOfType(m2) > 0)) {
 		cat("Soft sweep ended in cycle " + sim.cycle + "\n");
 		cat("Frequencies:\n");
 		print(sim.mutationFrequencies(p1, sim.mutationsOfType(m2)));
diff --git a/QtSLiM/recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt b/QtSLiM/recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt
index e2e94b0b3..8ed98b152 100644
--- a/QtSLiM/recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt	
+++ b/QtSLiM/recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt	
@@ -21,7 +21,7 @@ initialize() {
 	community.deregisterScriptBlock(s1);
 }
 s1 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	mut = sim.mutationsOfType(m2);
 	if (mut.size() > 0)
 		target.addMutations(mut);
diff --git a/QtSLiM/recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt b/QtSLiM/recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt
index d966f98e7..b23841f9c 100644
--- a/QtSLiM/recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt	
+++ b/QtSLiM/recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000: late() {
@@ -45,7 +45,7 @@ initialize() {
 		setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 		
 		// re-introduce the sweep mutation
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		target.addNewDrawnMutation(m2, 10000);
 	}
 }
diff --git a/QtSLiM/recipes/Recipe 9.7 - Adaptive introgression.txt b/QtSLiM/recipes/Recipe 9.7 - Adaptive introgression.txt
index 76f6f3d95..bdb9ffa52 100644
--- a/QtSLiM/recipes/Recipe 9.7 - Adaptive introgression.txt	
+++ b/QtSLiM/recipes/Recipe 9.7 - Adaptive introgression.txt	
@@ -18,7 +18,7 @@ initialize() {
 		sim.subpopulations[i-1].setMigrationRates(i+1, 0.2);
 }
 100 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 100:100000 late() {
diff --git a/QtSLiM/recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt b/QtSLiM/recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt
index b6694b10c..2494f90d6 100644
--- a/QtSLiM/recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt	
+++ b/QtSLiM/recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	mut = target.addNewDrawnMutation(m2, 10000);
 	defineConstant("SWEEP", mut);
 }
diff --git a/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt b/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt
index a550fb5ad..b1891e502 100644
--- a/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt	
+++ b/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis I.txt	
@@ -18,9 +18,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;
diff --git a/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt b/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt
index 02b7cb2c6..80aa8c287 100644
--- a/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt	
+++ b/SLiMgui/Recipes/Recipe 10.3.1 - Fitness as a function of genomic background, Epistasis II.txt	
@@ -20,9 +20,9 @@ initialize() {
 1 early() { sim.addSubpop("p1", 500); }
 10000 early() { sim.simulationFinished(); }
 mutationEffect(m3) {
-	if (individual.genome1.countOfMutationsOfType(m2))
+	if (individual.haplosomesFromParent1.countOfMutationsOfType(m2))
 		return 0.5;
-	else if (individual.genome2.countOfMutationsOfType(m2))
+	else if (individual.haplosomesFromParent2.countOfMutationsOfType(m2))
 		return 0.5;
 	else
 		return effect;
diff --git a/SLiMgui/Recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt b/SLiMgui/Recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt
index 95288da4e..408bef7b7 100644
--- a/SLiMgui/Recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt	
+++ b/SLiMgui/Recipes/Recipe 10.4.3 - Fitness as a function of population composition, Kin selection and the green-beard effect.txt	
@@ -12,7 +12,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1 late() {
-	target = sample(p1.genomes, 100);
+	target = sample(p1.haplosomes, 100);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1: late() {
diff --git a/SLiMgui/Recipes/Recipe 11.1 - Assortative mating.txt b/SLiMgui/Recipes/Recipe 11.1 - Assortative mating.txt
index 261c148ef..92e6667c0 100644
--- a/SLiMgui/Recipes/Recipe 11.1 - Assortative mating.txt	
+++ b/SLiMgui/Recipes/Recipe 11.1 - Assortative mating.txt	
@@ -16,7 +16,7 @@ initialize() {
 	p2.setMigrationRates(p1, 0.1);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 mutationEffect(m2, p2) { return 0.2; }
@@ -40,7 +40,7 @@ mutationEffect(m2, p2) { return 0.2; }
 		return weights * sourceSubpop.getValue("weights2");
 }
 10000: late() {
-	FST = calcFST(p1.genomes, p2.genomes);
+	FST = calcFST(p1.haplosomes, p2.haplosomes);
 	sim.setValue("FST", sim.getValue("FST") + FST);
 }
 19999 late() {
diff --git a/SLiMgui/Recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt b/SLiMgui/Recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt
index 2124b011c..aa3959d95 100644
--- a/SLiMgui/Recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt	
+++ b/SLiMgui/Recipes/Recipe 11.3 - Gametophytic self-incompatibility.txt	
@@ -17,9 +17,9 @@ initialize() {
 	cat("m2 mutation count: " + sim.countOfMutationsOfType(m2) + "\n");
 }
 modifyChild(p1) {
-	pollenSMuts = child.genome2.mutationsOfType(m2);
-	styleSMuts1 = parent1.genome1.mutationsOfType(m2);
-	styleSMuts2 = parent1.genome2.mutationsOfType(m2);
+	pollenSMuts = child.haplosomesFromParent2.mutationsOfType(m2);
+	styleSMuts1 = parent1.haplosomesFromParent1.mutationsOfType(m2);
+	styleSMuts2 = parent1.haplosomesFromParent2.mutationsOfType(m2);
 	if (identical(pollenSMuts, styleSMuts1))
 		if (runif(1) < 0.99)
 			return F;
diff --git a/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis I.txt b/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis I.txt
index 976f34aa3..87d209e30 100644
--- a/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis I.txt	
+++ b/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis I.txt	
@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	hasMutA = any(child.genomes.countOfMutationsOfType(m2) > 0);
-	hasMutB = any(child.genomes.countOfMutationsOfType(m3) > 0);
+	hasMutA = any(child.haplosomes.countOfMutationsOfType(m2) > 0);
+	hasMutB = any(child.haplosomes.countOfMutationsOfType(m3) > 0);
 	if (hasMutA & hasMutB)
 		return F;
 	return T;
diff --git a/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis II.txt b/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis II.txt
index d1e62e19f..5be4323f3 100644
--- a/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis II.txt	
+++ b/SLiMgui/Recipes/Recipe 12.2 - Lethal epistasis II.txt	
@@ -15,12 +15,12 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1 late() {
-	sample(p1.genomes, 20).addNewDrawnMutation(m2, 10000);  // add A
-	sample(p1.genomes, 20).addNewDrawnMutation(m3, 20000);  // add B
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m2, 10000);  // add A
+	sample(p1.haplosomes, 20).addNewDrawnMutation(m3, 20000);  // add B
 }
 modifyChild() {
-	mutACount = sum(child.genomes.countOfMutationsOfType(m2));
-	mutBCount = sum(child.genomes.countOfMutationsOfType(m3));
+	mutACount = sum(child.haplosomes.countOfMutationsOfType(m2));
+	mutBCount = sum(child.haplosomes.countOfMutationsOfType(m3));
 	if ((mutACount == 2) & (mutBCount == 2))
 		return F;
 	return T;
diff --git a/SLiMgui/Recipes/Recipe 12.3 - Simulating gene drive.txt b/SLiMgui/Recipes/Recipe 12.3 - Simulating gene drive.txt
index 3a28ccc88..9ae33724d 100644
--- a/SLiMgui/Recipes/Recipe 12.3 - Simulating gene drive.txt	
+++ b/SLiMgui/Recipes/Recipe 12.3 - Simulating gene drive.txt	
@@ -17,7 +17,7 @@ initialize() {
 		sim.subpopulations[i].setMigrationRates(i+1, 0.1);
 }
 100 late() {
-	p0.genomes[0:49].addNewDrawnMutation(m2, 10000);
+	p0.haplosomes[0:49].addNewDrawnMutation(m2, 10000);
 }
 100:10000 late() {
 	if (sim.countOfMutationsOfType(m2) == 0)
@@ -34,12 +34,12 @@ mutationEffect(m2) {
 	mut = sim.mutationsOfType(m2);
 	if (size(mut) == 1)
 	{
-		hasMutOnChromosome1 = child.genome1.containsMutations(mut);
-		hasMutOnChromosome2 = child.genome2.containsMutations(mut);
+		hasMutOnChromosome1 = child.haplosomesFromParent1.containsMutations(mut);
+		hasMutOnChromosome2 = child.haplosomesFromParent2.containsMutations(mut);
 		if (hasMutOnChromosome1 & !hasMutOnChromosome2)
-			child.genome2.addMutations(mut);
+			child.haplosomesFromParent2.addMutations(mut);
 		else if (hasMutOnChromosome2 & !hasMutOnChromosome1)
-			child.genome1.addMutations(mut);
+			child.haplosomesFromParent1.addMutations(mut);
 	}
 	return T;
 }
diff --git a/SLiMgui/Recipes/Recipe 13.1 - Polygenic selection.txt b/SLiMgui/Recipes/Recipe 13.1 - Polygenic selection.txt
index e1b55e7a3..0af39c7fd 100644
--- a/SLiMgui/Recipes/Recipe 13.1 - Polygenic selection.txt	
+++ b/SLiMgui/Recipes/Recipe 13.1 - Polygenic selection.txt	
@@ -15,7 +15,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 fitnessEffect() {
-	phenotype = sum(individual.genomes.countOfMutationsOfType(m2));
+	phenotype = sum(individual.haplosomes.countOfMutationsOfType(m2));
 	return 1.5 - (phenotype - 10.0)^2 * 0.005;
 }
 5000 late() {
diff --git a/SLiMgui/Recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt b/SLiMgui/Recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt
index 396bbc8f8..5360e7d4d 100644
--- a/SLiMgui/Recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt	
+++ b/SLiMgui/Recipes/Recipe 13.3 - A model of discrete QTL effects with a structured chromosome.txt	
@@ -52,7 +52,7 @@ initialize() {
 	community.registerEarlyEvent("s2", s1.source, 2, 2);
 	
 	// optional: give m2 mutations to everyone, as standing variation
-	g = sim.subpopulations.genomes;
+	g = sim.subpopulations.haplosomes;
 	
 	for (q in Q)
 	{
diff --git a/SLiMgui/Recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt b/SLiMgui/Recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt
index 091d92edd..a34cce59b 100644
--- a/SLiMgui/Recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt	
+++ b/SLiMgui/Recipes/Recipe 13.5 - A QTL-based model with two quantitative phenotypic traits and pleiotropy.txt	
@@ -71,7 +71,7 @@ late() {
 	for (ind in sim.subpopulations.individuals)
 	{
 		// construct phenotypes from additive effects of QTL mutations
-		muts = ind.genomes.mutationsOfType(m2);
+		muts = ind.haplosomes.mutationsOfType(m2);
 		phenotype0 = size(muts) ? sum(muts.getValue("e0")) else 0.0;
 		phenotype1 = size(muts) ? sum(muts.getValue("e1")) else 0.0;
 		ind.setValue("phenotype0", phenotype0);
diff --git a/SLiMgui/Recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt b/SLiMgui/Recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt
index 1db7945df..ac3d744e7 100644
--- a/SLiMgui/Recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt	
+++ b/SLiMgui/Recipes/Recipe 14.1 - Relatedness, inbreeding, and heterozygosity.txt	
@@ -17,6 +17,6 @@ mateChoice() {
 }
 1000 late() {
 	// Print mean heterozygosity across the population
-	heterozygosity = calcHeterozygosity(p1.genomes);
+	heterozygosity = calcHeterozygosity(p1.haplosomes);
 	cat("Mean heterozygosity = " + heterozygosity + "\n");
 }
diff --git a/SLiMgui/Recipes/Recipe 14.11 - Modeling microsatellites.txt b/SLiMgui/Recipes/Recipe 14.11 - Modeling microsatellites.txt
index 540782324..099dc3dab 100644
--- a/SLiMgui/Recipes/Recipe 14.11 - Modeling microsatellites.txt	
+++ b/SLiMgui/Recipes/Recipe 14.11 - Modeling microsatellites.txt	
@@ -21,14 +21,14 @@ initialize() {
 	sim.addSubpop("p1", 500);
 	
 	// create some microsatellites at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(msatCount, 0, L-1);
 	repeats = rpois(msatCount, 20) + 5;
 	
 	for (msatIndex in 0:(msatCount-1))
 	{
 		pos = positions[msatIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = repeats[msatIndex];
 	}
 	
@@ -37,14 +37,14 @@ initialize() {
 }
 modifyChild() {
 	// mutate microsatellites with rate msatMu
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
 		mutCount = rpois(1, msatMu * msatCount);
 		
 		if (mutCount)
 		{
 			mutSites = sample(msatPositions, mutCount);
-			msats = genome.mutationsOfType(m2);
+			msats = haplosome.mutationsOfType(m2);
 			
 			for (mutSite in mutSites)
 			{
@@ -66,15 +66,15 @@ modifyChild() {
 					
 					if (matchingMut.size() == 1)
 					{
-						genome.removeMutations(msat);
-						genome.addMutations(matchingMut);
+						haplosome.removeMutations(msat);
+						haplosome.addMutations(matchingMut);
 						next;
 					}
 				}
 				
 				// make a new mutation with the new repeat count
-				genome.removeMutations(msat);
-				msat = genome.addNewDrawnMutation(m2, mutSite);
+				haplosome.removeMutations(msat);
+				msat = haplosome.addNewDrawnMutation(m2, mutSite);
 				msat.tag = repeats;
 			}
 		}
diff --git a/SLiMgui/Recipes/Recipe 14.12 - Modeling transposable elements.txt b/SLiMgui/Recipes/Recipe 14.12 - Modeling transposable elements.txt
index f74d7c32f..1f7ceb770 100644
--- a/SLiMgui/Recipes/Recipe 14.12 - Modeling transposable elements.txt	
+++ b/SLiMgui/Recipes/Recipe 14.12 - Modeling transposable elements.txt	
@@ -28,22 +28,22 @@ initialize() {
 	sim.tag = 0;	// the next unique tag value to use for TEs
 	
 	// create some transposons at random positions
-	genomes = sim.subpopulations.genomes;
+	haplosomes = sim.subpopulations.haplosomes;
 	positions = rdunif(teInitialCount, 0, L-1);
 	
 	for (teIndex in 0:(teInitialCount-1))
 	{
 		pos = positions[teIndex];
-		mut = genomes.addNewDrawnMutation(m2, pos);
+		mut = haplosomes.addNewDrawnMutation(m2, pos);
 		mut.tag = sim.tag;
 		sim.tag = sim.tag + 1;
 	}
 }
 modifyChild() {
 	// disable transposons with rate teDisableP
-	for (genome in child.genomes)
+	for (haplosome in child.haplosomes)
 	{
-		tes = genome.mutationsOfType(m2);
+		tes = haplosome.mutationsOfType(m2);
 		teCount = tes.size();
 		mutatedCount = teCount ? rpois(1, teCount * teDisableP) else 0;
 		
@@ -59,14 +59,14 @@ modifyChild() {
 				if (size(disabledTE))
 				{
 					// use the existing disabled TE mutation
-					genome.removeMutations(te);
-					genome.addMutations(disabledTE);
+					haplosome.removeMutations(te);
+					haplosome.addMutations(disabledTE);
 					next;
 				}
 				
 				// make a new disabled TE mutation with the right tag
-				genome.removeMutations(te);
-				disabledTE = genome.addNewDrawnMutation(m3, te.position);
+				haplosome.removeMutations(te);
+				disabledTE = haplosome.addNewDrawnMutation(m3, te.position);
 				disabledTE.tag = te.tag;
 			}
 		}
@@ -78,9 +78,9 @@ late() {
 	// make active transposons copy themselves with rate teJumpP
 	for (individual in sim.subpopulations.individuals)
 	{
-		for (genome in individual.genomes)
+		for (haplosome in individual.haplosomes)
 		{
-			tes = genome.mutationsOfType(m2);
+			tes = haplosome.mutationsOfType(m2);
 			teCount = tes.size();
 			jumpCount = teCount ? rpois(1, teCount * teJumpP) else 0;
 			
@@ -92,7 +92,7 @@ late() {
 				{
 					// make a new TE mutation
 					pos = rdunif(1, 0, L-1);
-					jumpTE = genome.addNewDrawnMutation(m2, pos);
+					jumpTE = haplosome.addNewDrawnMutation(m2, pos);
 					jumpTE.tag = sim.tag;
 					sim.tag = sim.tag + 1;
 				}
@@ -104,7 +104,7 @@ late() {
 	// print information on each TE, including the fraction of it disabled
 	all_tes = sortBy(sim.mutationsOfType(m2), "position");
 	all_disabledTEs = sortBy(sim.mutationsOfType(m3), "position");
-	genomeCount = size(sim.subpopulations.genomes);
+	haplosomeCount = size(sim.subpopulations.haplosomes);
 	
 	catn("Active TEs:");
 	for (te in all_tes)
@@ -126,7 +126,7 @@ late() {
 		
 		total = active + disabled;
 		
-		cat("frequency " + format("%0.3f", total / genomeCount) + ", ");
+		cat("frequency " + format("%0.3f", total / haplosomeCount) + ", ");
 		catn(round(active / total * 100) + "% active");
 	}
 	
diff --git a/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt b/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt
index f4e2981d2..5815360a9 100644
--- a/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt	
+++ b/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback I.txt	
@@ -24,7 +24,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 	
 	// create the canonical mutation objects
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT2", target.mutations);
 	target.removeMutations();
@@ -33,7 +33,7 @@ initialize() {
 	target.removeMutations();
 	
 	// start homozygous "aa" at every position
-	p1.genomes.addMutations(MUT3);
+	p1.haplosomes.addMutations(MUT3);
 	
 	// log results
 	log = community.createLogFile("freq.csv", logInterval=10);
diff --git a/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt b/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt
index 0eaff07e7..51e63457e 100644
--- a/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt	
+++ b/SLiMgui/Recipes/Recipe 14.15 - Modeling biallelic loci with a mutation() callback II.txt	
@@ -22,7 +22,7 @@ initialize() {
 	sim.addSubpop("p1", 100);
 	
 	// create the permanent m2 mutation objects we will use
-	target = p1.genomes[0];
+	target = p1.haplosomes[0];
 	target.addNewDrawnMutation(m2, 0:99);
 	defineConstant("MUT", target.mutations);
 	
@@ -37,7 +37,7 @@ initialize() {
 mutation(m3) {
 	// if we already have an m2 mutation at the site, allow
 	// the new m3 mutation; we will remove the stack below
-	if (genome.containsMarkerMutation(m2, mut.position))
+	if (haplosome.containsMarkerMutation(m2, mut.position))
 		return T;
 	
 	// no m2 mutation is present, so unique down
@@ -51,18 +51,18 @@ late() {
 	// if so, we have m2/m3 stacked mutations to remove
 	if (m3muts.length() > 0)
 	{
-		genomes = sim.subpopulations.genomes;
-		counts = genomes.countOfMutationsOfType(m3);
-		hasStacked = genomes[counts > 0];
+		haplosomes = sim.subpopulations.haplosomes;
+		counts = haplosomes.countOfMutationsOfType(m3);
+		hasStacked = haplosomes[counts > 0];
 		
-		for (genome in hasStacked)
+		for (haplosome in hasStacked)
 		{
-			stacked_m3 = genome.mutationsOfType(m3);
+			stacked_m3 = haplosome.mutationsOfType(m3);
 			stackPositions = stacked_m3.position;
-			all_m2 = genome.mutationsOfType(m2);
+			all_m2 = haplosome.mutationsOfType(m2);
 			s = (match(all_m2.position, stackPositions) >= 0);
 			stacked_m2 = all_m2[s];
-			genome.removeMutations(c(stacked_m3, stacked_m2));
+			haplosome.removeMutations(c(stacked_m3, stacked_m2));
 		}
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt b/SLiMgui/Recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt
index ce7b702fe..d1852a5d5 100644
--- a/SLiMgui/Recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt	
+++ b/SLiMgui/Recipes/Recipe 14.3 - Reading initial simulation state from an MS output file II.txt	
@@ -38,15 +38,15 @@ initialize() {
 	if (parts[0] != "positions:") stop("Missing positions.");
 	positions = asFloat(parts[1:(size(parts)-1)]);
 	
-	// create all mutations in a genome in a dummy subpopulation
+	// create all mutations in a haplosome in a dummy subpopulation
 	sim.addSubpop("p2", 1);
-	g = p2.genomes[0];
-	L = sim.chromosome.lastPosition;
+	g = p2.haplosomes[0];
+	L = sim.chromosomes.lastPosition;
 	intPositions = asInteger(round(positions * L));
 	muts = g.addNewMutation(m1, 0.0, intPositions);
 	
-	// add the appropriate mutations to each genome
-	for (g in p1.genomes)
+	// add the appropriate mutations to each haplosome
+	for (g in p1.haplosomes)
 	{
 		f = asLogical(asInteger(strsplit(lines[index], "")));
 		index = index + 1;
diff --git a/SLiMgui/Recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt b/SLiMgui/Recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt
index 91ec540e2..a63474a02 100644
--- a/SLiMgui/Recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt	
+++ b/SLiMgui/Recipes/Recipe 14.4 - Modeling chromosomal inversions with a recombination() callback.txt	
@@ -21,8 +21,8 @@ initialize() {
 1 late() {
 	sim.addSubpop("p1", N);
 
-	// give some genomes an inversion
-	inverted = sample(p1.genomes, 100);
+	// give some haplosomes an inversion
+	inverted = sample(p1.haplosomes, 100);
 	inverted.addNewDrawnMutation(m2, INV_START);
 	inverted.addNewDrawnMutation(m3, INV_END);
 }
@@ -41,8 +41,8 @@ mutationEffect(m2) {
 }
 
 recombination() {
-	gm1 = genome1.containsMarkerMutation(m2, INV_START);
-	gm2 = genome2.containsMarkerMutation(m2, INV_START);
+	gm1 = haplosome1.containsMarkerMutation(m2, INV_START);
+	gm2 = haplosome2.containsMarkerMutation(m2, INV_START);
 	if (!(gm1 | gm2)) {
 		// homozygote non-inverted
 		return F;
@@ -61,7 +61,7 @@ recombination() {
 	} else {
 		// heterozygote inverted: resample to get an even number of breakpoints
 		// this is *recursive*: it calls this recombination callback again!
-		breakpoints = sim.chromosome.drawBreakpoints(individual);
+		breakpoints = sim.chromosomes.drawBreakpoints(individual);
 	}
 	return T;
 }
diff --git a/SLiMgui/Recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt b/SLiMgui/Recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt
index f115ac350..f7cd2ade8 100644
--- a/SLiMgui/Recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt	
+++ b/SLiMgui/Recipes/Recipe 14.5 - Modeling both X and Y Chromosomes with a Pseudo-Autosomal Region (PAR).txt	
@@ -25,15 +25,15 @@ initialize()
 	// initialize the pop, with a Y marker for each male
 	sim.addSubpop("p1", 1000);
 	i = p1.individuals;
-	i[i.sex == "M"].genome2.addNewMutation(m3, 0.0, 5999999);
+	i[i.sex == "M"].haplosomesFromParent2.addNewMutation(m3, 0.0, 5999999);
 }
 
 modifyChild() {
 	// females should not have a Y, males should have a Y
 	if (child.sex == "F")
-		return !child.genome2.containsMarkerMutation(m3, 5999999);
+		return !child.haplosomesFromParent2.containsMarkerMutation(m3, 5999999);
 	else
-		return child.genome2.containsMarkerMutation(m3, 5999999);
+		return child.haplosomesFromParent2.containsMarkerMutation(m3, 5999999);
 }
 
 1:10000 late() {
@@ -46,7 +46,7 @@ modifyChild() {
 		// look at the mutations in a single Y chromosome
 		// to find mutations that are fixed in all Y's
 		firstMale = p1.individuals[p1.individuals.sex == "M"][0];
-		fMG = firstMale.genomes;
+		fMG = firstMale.haplosomes;
 		
 		if (fMG[0].containsMarkerMutation(m3, 5999999)) {
 			firstY = fMG[0];
@@ -70,7 +70,7 @@ modifyChild() {
 		cat(removeX.size() + "/" + removeY.size() + " on X/Y\n");
 		
 		removes = c(removeY, removeX);
-		sim.subpopulations.genomes.removeMutations(removes, T);
+		sim.subpopulations.haplosomes.removeMutations(removes, T);
 	}
 }
 
diff --git a/SLiMgui/Recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt b/SLiMgui/Recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt
index f7117ae64..169595234 100644
--- a/SLiMgui/Recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt	
+++ b/SLiMgui/Recipes/Recipe 14.7 - Tracking local ancestry along the chromosome.txt	
@@ -30,11 +30,11 @@ initialize() {
 	     muttype in c(m1,m2,m3),
 	     symbol in c("M1","M2","M3"))
 	{
-		genomes = subpop.genomes;
-		muts = genomes.addNewDrawnMutation(muttype, positions);
+		haplosomes = subpop.haplosomes;
+		muts = haplosomes.addNewDrawnMutation(muttype, positions);
 		defineConstant(symbol, muts);
 		
-		mut = genomes.addNewDrawnMutation(m4, integerDiv(Z, 2));
+		mut = haplosomes.addNewDrawnMutation(m4, integerDiv(Z, 2));
 		catn("Beneficial mutation: s == " + mut.selectionCoeff);
 	}
 	
diff --git a/SLiMgui/Recipes/Recipe 14.9 - Modeling haploid organisms.txt b/SLiMgui/Recipes/Recipe 14.9 - Modeling haploid organisms.txt
index a29f44e5c..faff72216 100644
--- a/SLiMgui/Recipes/Recipe 14.9 - Modeling haploid organisms.txt	
+++ b/SLiMgui/Recipes/Recipe 14.9 - Modeling haploid organisms.txt	
@@ -12,14 +12,14 @@ initialize() {
 	p1.setCloningRate(1.0);
 }
 late() {
-	// remove any new mutations added to the disabled diploid genomes
-	sim.subpopulations.individuals.genome2.removeMutations();
+	// remove any new mutations added to the disabled diploid haplosomes
+	sim.subpopulations.individuals.haplosomesFromParent2.removeMutations();
 	
-	// remove mutations in the haploid genomes that have fixed
+	// remove mutations in the haploid haplosomes that have fixed
 	muts = sim.mutationsOfType(m1);
 	freqs = sim.mutationFrequencies(NULL, muts);
 	if (any(freqs == 0.5))
-		sim.subpopulations.genomes.removeMutations(muts[freqs == 0.5], T);
+		sim.subpopulations.haplosomes.removeMutations(muts[freqs == 0.5], T);
 }
 200000 late() {
 	sim.outputFixedMutations();
diff --git a/SLiMgui/Recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt b/SLiMgui/Recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt
index 488f598b4..3568a6cb2 100644
--- a/SLiMgui/Recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt	
+++ b/SLiMgui/Recipes/Recipe 15.11 - Modeling clonal haploids in a nonWF model with addRecombinant().txt	
@@ -11,7 +11,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 reproduction() {
-	subpop.addRecombinant(individual.genome1, NULL, NULL, NULL, NULL, NULL);
+	subpop.addRecombinant(individual.haplosomesFromParent1, NULL, NULL, NULL, NULL, NULL);
 }
 1 early() {
 	sim.addSubpop("p1", 500, haploid=T);
diff --git a/SLiMgui/Recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt b/SLiMgui/Recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt
index 00df94d7d..9f2c6c859 100644
--- a/SLiMgui/Recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt	
+++ b/SLiMgui/Recipes/Recipe 15.12 - Modeling clonal haploid bacteria with horizontal gene transfer.txt	
@@ -16,7 +16,7 @@ reproduction() {
 	if (runif(1) < H)
 	{
 		// horizontal gene transfer from a randomly chosen individual
-		HGTsource = p1.sampleIndividuals(1, exclude=individual).genome1;
+		HGTsource = p1.sampleIndividuals(1, exclude=individual).haplosomesFromParent1;
 		
 		// draw two distinct locations; redraw if we get a duplicate
 		do breaks = rdunif(2, max=L-1);
@@ -26,12 +26,12 @@ reproduction() {
 		if (breaks[0] > breaks[1])
 			breaks = c(0, breaks[1], breaks[0]);
 		
-		subpop.addRecombinant(individual.genome1, HGTsource, breaks, NULL, NULL, NULL);
+		subpop.addRecombinant(individual.haplosomesFromParent1, HGTsource, breaks, NULL, NULL, NULL);
 	}
 	else
 	{
 		// no horizontal gene transfer; clonal replication
-		subpop.addRecombinant(individual.genome1, NULL, NULL, NULL, NULL, NULL);
+		subpop.addRecombinant(individual.haplosomesFromParent1, NULL, NULL, NULL, NULL, NULL);
 	}
 }
 1 early() {
@@ -39,7 +39,7 @@ reproduction() {
 	sim.addSubpop("p1", 2, haploid=T);
 	
 	// add beneficial mutations to each bacterium, but at different loci
-	g = p1.individuals.genome1;
+	g = p1.individuals.haplosomesFromParent1;
 	g[0].addNewDrawnMutation(m2, asInteger(L * 0.25));
 	g[1].addNewDrawnMutation(m2, asInteger(L * 0.75));
 }
diff --git a/SLiMgui/Recipes/Recipe 15.14 - Alternation of generations.txt b/SLiMgui/Recipes/Recipe 15.14 - Alternation of generations.txt
index 1b677fb11..9f28ad51b 100644
--- a/SLiMgui/Recipes/Recipe 15.14 - Alternation of generations.txt	
+++ b/SLiMgui/Recipes/Recipe 15.14 - Alternation of generations.txt	
@@ -23,24 +23,24 @@ initialize()
 }
 reproduction(p1)
 {
-	g_1 = individual.genome1;
-	g_2 = individual.genome2;
+	g_1 = individual.haplosomesFromParent1;
+	g_2 = individual.haplosomesFromParent2;
 	
 	for (meiosisCount in 1:5)
 	{
 		if (individual.sex == "M")
 		{
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			s_1 = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "M");
 			s_2 = p2.addRecombinant(g_2, g_1, breaks, NULL, NULL, NULL, "M");
 			
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			s_3 = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "M");
 			s_4 = p2.addRecombinant(g_2, g_1, breaks, NULL, NULL, NULL, "M");
 		}
 		else if (individual.sex == "F")
 		{
-			breaks = sim.chromosome.drawBreakpoints(individual);
+			breaks = sim.chromosomes.drawBreakpoints(individual);
 			e = p2.addRecombinant(g_1, g_2, breaks, NULL, NULL, NULL, "F",
 				randomizeStrands=T);
 		}
@@ -51,8 +51,8 @@ reproduction(p2, "F")
 	mate = p2.sampleIndividuals(1, sex="M", tagL0=F);
 	mate.tagL0 = T;
 	
-	child = p1.addRecombinant(individual.genome1, NULL, NULL,
-		mate.genome1, NULL, NULL);
+	child = p1.addRecombinant(individual.haplosomesFromParent1, NULL, NULL,
+		mate.haplosomesFromParent1, NULL, NULL);
 }
 early()
 {
@@ -60,13 +60,13 @@ early()
 	{
 		p1.fitnessScaling = 0.0;
 		p2.individuals.tagL0 = F;
-		sim.chromosome.setMutationRate(0.0);
+		sim.chromosomes.setMutationRate(0.0);
 	}
 	else
 	{
 		p2.fitnessScaling = 0.0;
 		p1.fitnessScaling = K / p1.individualCount;
-		sim.chromosome.setMutationRate(MU);
+		sim.chromosomes.setMutationRate(MU);
 	}
 }
 10000 late()
diff --git a/SLiMgui/Recipes/Recipe 15.15 - Meiotic drive.txt b/SLiMgui/Recipes/Recipe 15.15 - Meiotic drive.txt
index 0b133755c..90b28c351 100644
--- a/SLiMgui/Recipes/Recipe 15.15 - Meiotic drive.txt	
+++ b/SLiMgui/Recipes/Recipe 15.15 - Meiotic drive.txt	
@@ -1,11 +1,11 @@
 // Keywords: nonWF, non-Wright-Fisher, meiotic drive, segregation distortion, intragenomic conflict
 
-function (i)driveBreakpoints(o<Genome>$ gen1, o<Genome>$ gen2)
+function (i)driveBreakpoints(o<Haplosome>$ gen1, o<Haplosome>$ gen2)
 {
 	// start with default breakpoints generated by the chromosome
-	breaks = sim.chromosome.drawBreakpoints();
+	breaks = sim.chromosomes.drawBreakpoints();
 	
-	// if both genomes have the drive, or neither, then just return
+	// if both haplosomes have the drive, or neither, then just return
 	gen1has = gen1.containsMarkerMutation(m2, D_pos);
 	gen2has = gen2.containsMarkerMutation(m2, D_pos);
 	if (gen1has == gen2has)
@@ -42,9 +42,9 @@ initialize() {
 }
 reproduction() {
 	m = subpop.sampleIndividuals(1);
-	b1 = driveBreakpoints(individual.genome1, individual.genome2);
-	b2 = driveBreakpoints(m.genome1, m.genome2);
-	subpop.addRecombinant(individual.genome1, individual.genome2, b1, m.genome1, m.genome2, b2);
+	b1 = driveBreakpoints(individual.haplosomesFromParent1, individual.haplosomesFromParent2);
+	b2 = driveBreakpoints(m.haplosomesFromParent1, m.haplosomesFromParent2);
+	subpop.addRecombinant(individual.haplosomesFromParent1, individual.haplosomesFromParent2, b1, m.haplosomesFromParent1, m.haplosomesFromParent2, b2);
 }
 1 early() {
 	sim.addSubpop("p1", 10);
@@ -53,7 +53,7 @@ early() {
 	p1.fitnessScaling = K / p1.individualCount;
 }
 100 early() {
-	target = sample(p1.genomes, 10);
+	target = sample(p1.haplosomes, 10);
 	target.addNewDrawnMutation(m2, D_pos);
 }
 100:1000 late() {
diff --git a/SLiMgui/Recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt b/SLiMgui/Recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt
index 10a784b85..194a9c859 100644
--- a/SLiMgui/Recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt	
+++ b/SLiMgui/Recipes/Recipe 15.21 - Modeling haplodiploidy with addRecombinant().txt	
@@ -14,26 +14,26 @@ initialize() {
 	initializeSex("A");
 }
 reproduction(NULL, "F") {
-	gen1 = individual.genome1;
-	gen2 = individual.genome2;
-	breaks = sim.chromosome.drawBreakpoints(individual);
+	gen1 = individual.haplosomesFromParent1;
+	gen2 = individual.haplosomesFromParent2;
+	breaks = sim.chromosomes.drawBreakpoints(individual);
 	
 	// decide whether we're generating a haploid male or a diploid female
 	if (rbinom(1, 1, P_OFFSPRING_MALE))
 	{
 		// didn't find a mate; make a haploid male from an unfertilized egg:
-		//		- one genome comes from recombination of the female's genomes
-		//		- the other genome is a null genome (a placeholder)
+		//		- one haplosome comes from recombination of the female's haplosomes
+		//		- the other haplosome is a null haplosome (a placeholder)
 		subpop.addRecombinant(gen1, gen2, breaks, NULL, NULL, NULL, "M",
 			randomizeStrands=T);
 	}
 	else
 	{
 		// found a mate; make a diploid female from a fertilized egg:
-		//		- one genome comes from recombination of the female's genomes
-		//		- the other genome comes from the mate (a haploid male)
+		//		- one haplosome comes from recombination of the female's haplosomes
+		//		- the other haplosome comes from the mate (a haploid male)
 		mate = subpop.sampleIndividuals(1, sex="M");
-		subpop.addRecombinant(gen1, gen2, breaks, mate.genome1, NULL, NULL, "F",
+		subpop.addRecombinant(gen1, gen2, breaks, mate.haplosomesFromParent1, NULL, NULL, "F",
 			randomizeStrands=T);
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt b/SLiMgui/Recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt
index 35bf5f83e..c9ba9f74d 100644
--- a/SLiMgui/Recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt	
+++ b/SLiMgui/Recipes/Recipe 15.4 - Beneficial mutations and absolute fitness.txt	
@@ -21,7 +21,7 @@ reproduction() {
 	sim.addSubpop("p1", 10);
 }
 100 early() {
-	mutant = sample(p1.individuals.genomes, 10);
+	mutant = sample(p1.individuals.haplosomes, 10);
 	mutant.addNewDrawnMutation(m2, 10000);
 }
 early() {
diff --git a/SLiMgui/Recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt b/SLiMgui/Recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt
index 2a3208754..8b55068a1 100644
--- a/SLiMgui/Recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt	
+++ b/SLiMgui/Recipes/Recipe 17.10 - Adding a neutral burn-in after simulation with recapitation I.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 1e5);
 }
 100 late() {
-	sample(p1.genomes, 1).addNewDrawnMutation(m2, 5e5);
+	sample(p1.haplosomes, 1).addNewDrawnMutation(m2, 5e5);
 }
 100:10000 late() {
 	mut = sim.mutationsOfType(m2);
diff --git a/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt b/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt
index d274adcaa..dd06e056d 100644
--- a/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt	
+++ b/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry I.txt	
@@ -14,7 +14,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
 	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
 	sim.outputFull(PATH);
diff --git a/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt b/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt
index a5107673f..2813e6f93 100644
--- a/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt	
+++ b/SLiMgui/Recipes/Recipe 17.3 - Simulation conditional upon fixation of a sweep, preserving ancestry II.txt	
@@ -23,7 +23,7 @@ initialize() {
 	// record tag values and pedigree IDs in metadata
 	metadataDict = Dictionary("tags", tags, "ids", inds.pedigreeID);
 	
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m3, 10000);
 	defineConstant("PATH", tempdir() + "slim_" + simID + ".trees");
 	sim.treeSeqOutput(PATH, metadata=metadataDict);
diff --git a/SLiMgui/Recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt b/SLiMgui/Recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt
index b78423641..94ba44755 100644
--- a/SLiMgui/Recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt	
+++ b/SLiMgui/Recipes/Recipe 17.5 - Mapping admixture (analyzing ancestry in Python) I.txt	
@@ -14,8 +14,8 @@ initialize() {
 	sim.addSubpop("p2", 500);
 	sim.treeSeqRememberIndividuals(sim.subpopulations.individuals);
 	
-	p1.genomes.addNewDrawnMutation(m1, asInteger(L * 0.2));
-	p2.genomes.addNewDrawnMutation(m1, asInteger(L * 0.8));
+	p1.haplosomes.addNewDrawnMutation(m1, asInteger(L * 0.2));
+	p2.haplosomes.addNewDrawnMutation(m1, asInteger(L * 0.8));
 	
 	sim.addSubpop("p3", 1000);
 	p3.setMigrationRates(c(p1, p2), c(0.5, 0.5));
diff --git a/SLiMgui/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt b/SLiMgui/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt
index d35988776..9e3533fde 100644
--- a/SLiMgui/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt	
+++ b/SLiMgui/Recipes/Recipe 17.8 - Starting a hermaphroditic WF model with a coalescent history II.txt	
@@ -14,7 +14,7 @@ initialize() {
 }
 1 late() {
 	sim.readFromPopulationFile("coalasex.trees");
-	target = sample(sim.subpopulations.genomes, 1);
+	target = sample(sim.subpopulations.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1: late() {
diff --git a/SLiMgui/Recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt b/SLiMgui/Recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt
index 4c60bf89e..97d34d8c5 100644
--- a/SLiMgui/Recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt	
+++ b/SLiMgui/Recipes/Recipe 18.11 - Modeling GC-biased gene conversion (gBGC).txt	
@@ -18,6 +18,6 @@ initialize() {
 1:500001 early() {
 	if (sim.cycle % 1000 == 1) {
 		cat(sim.cycle + ": ");
-		print(nucleotideFrequencies(sim.chromosome.ancestralNucleotides()));
+		print(nucleotideFrequencies(sim.chromosomes.ancestralNucleotides()));
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt b/SLiMgui/Recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt
index 7b9547f9c..4ae6ee7d6 100644
--- a/SLiMgui/Recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt	
+++ b/SLiMgui/Recipes/Recipe 18.12 - Reading VCF files to create nucleotide-based SNPs.txt	
@@ -14,7 +14,7 @@ initialize() {
 }
 1 late() {
 	sim.addSubpop("p1", 99);
-	p1.genomes.readFromVCF("chr22_filtered.recode.vcf", m1);
+	p1.haplosomes.readFromVCF("chr22_filtered.recode.vcf", m1);
 	p1.setSubpopulationSize(1000);
 }
 5 late() {
diff --git a/SLiMgui/Recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt b/SLiMgui/Recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt
index 5591e40f6..ea2f7c1b0 100644
--- a/SLiMgui/Recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt	
+++ b/SLiMgui/Recipes/Recipe 18.15 - Modeling identity by state (IBS) (uniquing back-mutations to the ancestral state).txt	
@@ -25,18 +25,18 @@ late() {
 	for (mut in new_muts)
 	{
 		pos = mut.position;
-		if (mut.nucleotide == sim.chromosome.ancestralNucleotides(pos, pos))
+		if (mut.nucleotide == sim.chromosomes.ancestralNucleotides(pos, pos))
 			back_muts = c(back_muts, mut);
 	}
 	if (size(back_muts))
-		sim.subpopulations.genomes.removeMutations(back_muts);
+		sim.subpopulations.haplosomes.removeMutations(back_muts);
 }
 1000 late() {
 	for (pos in 0:99)
 	{
 		muts = sim.subsetMutations(position=pos);
 		nucs = muts.nucleotide;
-		ancestral = sim.chromosome.ancestralNucleotides(pos, pos);
+		ancestral = sim.chromosomes.ancestralNucleotides(pos, pos);
 		cat(pos + " : " + paste(nucs));
 		if (size(nucs) != size(unique(nucs)))
 			cat("     DUPLICATES!");
diff --git a/SLiMgui/Recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt b/SLiMgui/Recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt
index 2efc9654d..5a31b6ce6 100644
--- a/SLiMgui/Recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt	
+++ b/SLiMgui/Recipes/Recipe 18.3 - Sequence output from nucleotide-based models.txt	
@@ -10,7 +10,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	c = sim.chromosome;
+	c = sim.chromosomes;
 	catn("Ancestral: " + c.ancestralNucleotides());
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="char")));
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="integer")));
@@ -25,14 +25,14 @@ initialize() {
 	catn("positions: " + paste(sim.substitutions.position));
 	catn();
 	
-	c = sim.chromosome;
+	c = sim.chromosomes;
 	catn("Ancestral: " + c.ancestralNucleotides());
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="char")));
 	catn("Ancestral: " + paste(c.ancestralNucleotides(format="integer")));
 	catn("positions: " + paste(0:(L-1)));
 	catn();
 	
-	g = p1.genomes[0];
+	g = p1.haplosomes[0];
 	
 	catn("SNPs:      " + paste(g.mutations.nucleotide));
 	catn("SNPs:      " + paste(g.mutations.nucleotideValue));
diff --git a/SLiMgui/Recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt b/SLiMgui/Recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt
index 67b7aef5e..c10085da0 100644
--- a/SLiMgui/Recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt	
+++ b/SLiMgui/Recipes/Recipe 18.4 - Back-mutations, independent mutational lineages, and VCF output.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 5000 late() {
-	g = p1.sampleIndividuals(5).genomes;
+	g = p1.sampleIndividuals(5).haplosomes;
 	g.outputVCF(simplifyNucleotides=F);
 	g.outputVCF(simplifyNucleotides=T);
 }
diff --git a/SLiMgui/Recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt b/SLiMgui/Recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt
index c9c84d0a1..ad59d357c 100644
--- a/SLiMgui/Recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt	
+++ b/SLiMgui/Recipes/Recipe 18.5 - Modeling elevated CpG mutation rates and equilibrium nucleotide frequencies.txt	
@@ -26,6 +26,6 @@ initialize() {
 1:10000000 early() {
 	if (sim.cycle % 10000 == 1) {
 		cat(sim.cycle + ": ");
-		print(nucleotideFrequencies(sim.chromosome.ancestralNucleotides()));
+		print(nucleotideFrequencies(sim.chromosomes.ancestralNucleotides()));
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt b/SLiMgui/Recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt
index 5891977d6..79a80ef33 100644
--- a/SLiMgui/Recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt	
+++ b/SLiMgui/Recipes/Recipe 18.6 - A nucleotide-based model with introduced non-nucleotide-based mutations.txt	
@@ -15,7 +15,7 @@ initialize() {
 }
 1 late() {
 	sim.addSubpop("p1", 500);
-	sample(p1.genomes, 10).addNewDrawnMutation(m2, 20000);
+	sample(p1.haplosomes, 10).addNewDrawnMutation(m2, 20000);
 }
 2000 late() {
 	print(sim.mutationsOfType(m2));
diff --git a/SLiMgui/Recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt b/SLiMgui/Recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt
index 8d0435bdf..63f5c3178 100644
--- a/SLiMgui/Recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt	
+++ b/SLiMgui/Recipes/Recipe 18.8 - Defining sequence-based fitness effects at the nucleotide level.txt	
@@ -21,8 +21,8 @@ late() {
 		s1.active = 0;
 }
 s1 fitnessEffect() {
-	nuc1 = individual.genome1.nucleotides(100, 100, format="integer");
-	nuc2 = individual.genome2.nucleotides(100, 100, format="integer");
+	nuc1 = individual.haplosomesFromParent1.nucleotides(100, 100, format="integer");
+	nuc2 = individual.haplosomesFromParent2.nucleotides(100, 100, format="integer");
 	return EFF[nuc1] * EFF[nuc2];
 }
 10000 late() {
diff --git a/SLiMgui/Recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt b/SLiMgui/Recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt
index e158f8641..a2446caa5 100644
--- a/SLiMgui/Recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt	
+++ b/SLiMgui/Recipes/Recipe 18.9 - Defining sequence-based fitness effects at the amino acid level.txt	
@@ -28,7 +28,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 fitnessEffect() {
-	for (g in individual.genomes)
+	for (g in individual.haplosomes)
 	{
 		seq = g.nucleotides(253, 670) + g.nucleotides(871, 1034);
 		codons = nucleotidesToCodons(seq);
@@ -41,8 +41,8 @@ fitnessEffect() {
 100000 late() {
 	catn(sim.substitutions.size() + " fixed mutations.");
 	
-	as1 = sim.chromosome.ancestralNucleotides(253, 670, "integer");
-	as2 = sim.chromosome.ancestralNucleotides(871, 1034, "integer");
+	as1 = sim.chromosomes.ancestralNucleotides(253, 670, "integer");
+	as2 = sim.chromosomes.ancestralNucleotides(871, 1034, "integer");
 	as = c(as1, as2);
 	codons = nucleotidesToCodons(as);
 	catn("Final AA sequence: " + codonsToAminoAcids(codons));
diff --git a/SLiMgui/Recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt b/SLiMgui/Recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt
index 3f77b3f7c..45861183f 100644
--- a/SLiMgui/Recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt	
+++ b/SLiMgui/Recipes/Recipe 19.7 - A coevolutionary host-parasite matching-allele model.txt	
@@ -27,7 +27,7 @@ species parasite initialize() {
 }
 
 function (float$)nucleotideFreq(o<Species>$ species, s$ nuc) {
-	nucs = species.subpopulations.individuals.genomes.nucleotides();
+	nucs = species.subpopulations.individuals.haplosomes.nucleotides();
 	return mean(nucs == nuc);
 }
 
@@ -55,7 +55,7 @@ ticks all late() {
 	for (p in parasites, h in chosen_hosts)
 	{
 		// infection depends upon a match (diploid matching-allele model)
-		all_nucleotides = c(p.genomes.nucleotides(), h.genomes.nucleotides());
+		all_nucleotides = c(p.haplosomes.nucleotides(), h.haplosomes.nucleotides());
 		
 		if (size(unique(all_nucleotides, preserveOrder=F)) == 1)
 		{
diff --git a/SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt b/SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt
similarity index 93%
rename from SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt
rename to SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt
index 0a54862db..72f1edbb7 100644
--- a/SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than genomes.txt	
+++ b/SLiMgui/Recipes/Recipe 4.2.3 - Basic output, Sampling individuals rather than haplosomes.txt	
@@ -18,5 +18,5 @@ initialize() {
 	allIndividuals = sim.subpopulations.individuals;
 	w = asFloat(allIndividuals.countOfMutationsOfType(m2) + 1);
 	sampledIndividuals = sample(allIndividuals, 10, weights=w);
-	sampledIndividuals.genomes.output();
+	sampledIndividuals.haplosomes.output();
 }
diff --git a/SLiMgui/Recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt b/SLiMgui/Recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt
index b68038630..9da5273c7 100644
--- a/SLiMgui/Recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt	
+++ b/SLiMgui/Recipes/Recipe 4.2.5 - Basic output, Automatic logging with LogFile.txt	
@@ -14,6 +14,6 @@ initialize() {
 	p2.setMigrationRates(p1, 0.001);
 	log = community.createLogFile("sim_log.txt", logInterval=10);
 	log.addCycle();
-	log.addCustomColumn("FST", "calcFST(p1.genomes, p2.genomes);");
+	log.addCustomColumn("FST", "calcFST(p1.haplosomes, p2.haplosomes);");
 }
 20000 late() { }
diff --git a/SLiMgui/Recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt b/SLiMgui/Recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt
index 2cb99a3fd..bb9e6afcf 100644
--- a/SLiMgui/Recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt	
+++ b/SLiMgui/Recipes/Recipe 4.2.6 - Basic output, Custom output with Eidos.txt	
@@ -14,8 +14,8 @@ initialize() {
 
 // custom MS-style output from a multi-subpop sample
 2000 late() {
-	// obtain a random sample of genomes from the whole population
-	g = sample(sim.subpopulations.genomes, 10, T);
+	// obtain a random sample of haplosomes from the whole population
+	h = sample(sim.subpopulations.haplosomes, 10, T);
 	
 	// get the unique mutations in the sample, sorted by position
 	m = sortBy(unique(g.mutations), "position");
@@ -24,13 +24,13 @@ initialize() {
 	cat("\n\nsegsites: " + size(m) + "\n");
 	
 	// print the positions
-	positions = format("%.6f", m.position / sim.chromosome.lastPosition);
+	positions = format("%.6f", m.position / sim.chromosomes.lastPosition);
 	cat("positions: " + paste(positions, sep=" ") + "\n");
 	
-	// print the sampled genomes
-	for (genome in g)
+	// print the sampled haplosomes
+	for (haplosome in h)
 	{
-		hasMuts = (match(m, genome.mutations) >= 0);
+		hasMuts = (match(m, haplosome.mutations) >= 0);
 		cat(paste(asInteger(hasMuts), sep="") + "\n");
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt b/SLiMgui/Recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt
index 23913ec76..6c01133a2 100644
--- a/SLiMgui/Recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt	
+++ b/SLiMgui/Recipes/Recipe 5.3.4 - Migration and admixture, A random, sparse spatial metapopulation.txt	
@@ -39,6 +39,6 @@ initialize() {
 	
 	// introduce a beneficial mutation
 	target_subpop = sample(sim.subpopulations, 1);
-	sample(target_subpop.genomes, 10).addNewDrawnMutation(m2, 20000);
+	sample(target_subpop.haplosomes, 10).addNewDrawnMutation(m2, 20000);
 }
 10000 late() { sim.outputFixedMutations(); }
diff --git a/SLiMgui/Recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt b/SLiMgui/Recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt
index 44a2b547e..19f222911 100644
--- a/SLiMgui/Recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt	
+++ b/SLiMgui/Recipes/Recipe 7.4 - Genomic structure, Part IV (Custom display colors in SLiMgui).txt	
@@ -59,7 +59,7 @@ initialize() {
 	initializeRecombinationRate(1e-8);
 }
 1 early() {
-	sim.chromosome.colorSubstitution = "";
+	sim.chromosomes.colorSubstitution = "";
 	sim.addSubpop("p1", 5000);
 }
 10000 early() { sim.simulationFinished(); }
diff --git a/SLiMgui/Recipes/Recipe 9.1 - Introducing adaptive mutations.txt b/SLiMgui/Recipes/Recipe 9.1 - Introducing adaptive mutations.txt
index 992eb4e61..f3a952b01 100644
--- a/SLiMgui/Recipes/Recipe 9.1 - Introducing adaptive mutations.txt	
+++ b/SLiMgui/Recipes/Recipe 9.1 - Introducing adaptive mutations.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:100000 late() {
diff --git a/SLiMgui/Recipes/Recipe 9.10 - Tracking the fate of background mutations.txt b/SLiMgui/Recipes/Recipe 9.10 - Tracking the fate of background mutations.txt
index 0ecfdadaa..32eda7b8a 100644
--- a/SLiMgui/Recipes/Recipe 9.10 - Tracking the fate of background mutations.txt	
+++ b/SLiMgui/Recipes/Recipe 9.10 - Tracking the fate of background mutations.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 500);
 }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	defineConstant("BACKGROUND", target.mutations);
 	mut = target.addNewDrawnMutation(m2, asInteger(L/2));
 	defineConstant("SWEEP", mut);
diff --git a/SLiMgui/Recipes/Recipe 9.11 - Effective population size versus census population size.txt b/SLiMgui/Recipes/Recipe 9.11 - Effective population size versus census population size.txt
index 2308b719c..a29b0d99a 100644
--- a/SLiMgui/Recipes/Recipe 9.11 - Effective population size versus census population size.txt	
+++ b/SLiMgui/Recipes/Recipe 9.11 - Effective population size versus census population size.txt	
@@ -32,7 +32,7 @@ initialize() {
 	p1.setValue("previous_N", p1.individualCount);
 }
 10000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, integerDiv(L, 2));
 }
 20000 late() {
@@ -49,7 +49,7 @@ function (float)mutTypeFrequency(o<MutationType>$ mutType)
 
 function (float)estimateNe_Heterozygosity(o<Subpopulation>$ subpop)
 {
-	pi = calcHeterozygosity(p1.genomes);
+	pi = calcHeterozygosity(p1.haplosomes);
 	return pi / (4 * MU);
 }
 
diff --git a/SLiMgui/Recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt b/SLiMgui/Recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt
index bf7859af5..0dbb0f2f8 100644
--- a/SLiMgui/Recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt	
+++ b/SLiMgui/Recipes/Recipe 9.2 - Making sweeps conditional on fixation.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:100000 late() {
@@ -43,7 +43,7 @@ initialize() {
 			setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 			
 			// re-introduce the sweep mutation
-			target = sample(p1.genomes, 1);
+			target = sample(p1.haplosomes, 1);
 			target.addNewDrawnMutation(m2, 10000);
 		}
 	}
diff --git a/SLiMgui/Recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt b/SLiMgui/Recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt
index b149a22c6..df1086fe7 100644
--- a/SLiMgui/Recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt	
+++ b/SLiMgui/Recipes/Recipe 9.3 - Making sweeps conditional on establishment.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000: late() {
@@ -44,7 +44,7 @@ initialize() {
 		setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 		
 		// re-introduce the sweep mutation
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		target.addNewDrawnMutation(m2, 10000);
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 9.4 - Partial sweeps.txt b/SLiMgui/Recipes/Recipe 9.4 - Partial sweeps.txt
index f192d43e3..c625551e1 100644
--- a/SLiMgui/Recipes/Recipe 9.4 - Partial sweeps.txt	
+++ b/SLiMgui/Recipes/Recipe 9.4 - Partial sweeps.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000:10000 late() {
diff --git a/SLiMgui/Recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt b/SLiMgui/Recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt
index d5ca891e3..f98614b2a 100644
--- a/SLiMgui/Recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt	
+++ b/SLiMgui/Recipes/Recipe 9.5.1 - A soft sweep from recurrent de novo mutations in a large population.txt	
@@ -13,7 +13,7 @@ initialize() {
 	sim.addSubpop("p1", 100000);
 }
 1:10000 early() {
-	counts = p1.genomes.countOfMutationsOfType(m1);
+	counts = p1.haplosomes.countOfMutationsOfType(m1);
 	freq = mean(counts > 0);
 	
 	if (freq == 1.0)
@@ -22,7 +22,7 @@ initialize() {
 		
 		for (mut in sortBy(sim.mutations, "originTick"))
 		{
-			mutFreq = mean(p1.genomes.containsMutations(mut));
+			mutFreq = mean(p1.haplosomes.containsMutations(mut));
 			cat("Origin " + mut.originTick + ": " + mutFreq + "\n");
 		}
 		
diff --git a/SLiMgui/Recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt b/SLiMgui/Recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt
index f7692ae87..791d93928 100644
--- a/SLiMgui/Recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt	
+++ b/SLiMgui/Recipes/Recipe 9.5.2 - A soft sweep with a fixed de novo mutation schedule.txt	
@@ -15,7 +15,7 @@ initialize() {
 1000:1100 late() {
 	if (sim.cycle % 10 == 0)
 	{
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		if (target.countOfMutationsOfType(m2) == 0)
 			target.addNewDrawnMutation(m2, 10000);
 	}
@@ -36,7 +36,7 @@ initialize() {
 			}
 		}
 	}
-	if (all(p1.genomes.countOfMutationsOfType(m2) > 0)) {
+	if (all(p1.haplosomes.countOfMutationsOfType(m2) > 0)) {
 		cat("Soft sweep ended in cycle " + sim.cycle + "\n");
 		cat("Frequencies:\n");
 		print(sim.mutationFrequencies(p1, sim.mutationsOfType(m2)));
diff --git a/SLiMgui/Recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt b/SLiMgui/Recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt
index e2e94b0b3..8ed98b152 100644
--- a/SLiMgui/Recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt	
+++ b/SLiMgui/Recipes/Recipe 9.5.3 - A soft sweep with a random de novo mutation schedule.txt	
@@ -21,7 +21,7 @@ initialize() {
 	community.deregisterScriptBlock(s1);
 }
 s1 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	mut = sim.mutationsOfType(m2);
 	if (mut.size() > 0)
 		target.addMutations(mut);
diff --git a/SLiMgui/Recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt b/SLiMgui/Recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt
index d966f98e7..b23841f9c 100644
--- a/SLiMgui/Recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt	
+++ b/SLiMgui/Recipes/Recipe 9.6.2 - A sweep from standing variation at a predetermined locus.txt	
@@ -19,7 +19,7 @@ initialize() {
 	sim.outputFull(tempdir() + "slim_" + simID + ".txt");
 	
 	// introduce the sweep mutation
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 1000: late() {
@@ -45,7 +45,7 @@ initialize() {
 		setSeed(rdunif(1, 0, asInteger(2^62) - 1));
 		
 		// re-introduce the sweep mutation
-		target = sample(p1.genomes, 1);
+		target = sample(p1.haplosomes, 1);
 		target.addNewDrawnMutation(m2, 10000);
 	}
 }
diff --git a/SLiMgui/Recipes/Recipe 9.7 - Adaptive introgression.txt b/SLiMgui/Recipes/Recipe 9.7 - Adaptive introgression.txt
index 76f6f3d95..bdb9ffa52 100644
--- a/SLiMgui/Recipes/Recipe 9.7 - Adaptive introgression.txt	
+++ b/SLiMgui/Recipes/Recipe 9.7 - Adaptive introgression.txt	
@@ -18,7 +18,7 @@ initialize() {
 		sim.subpopulations[i-1].setMigrationRates(i+1, 0.2);
 }
 100 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	target.addNewDrawnMutation(m2, 10000);
 }
 100:100000 late() {
diff --git a/SLiMgui/Recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt b/SLiMgui/Recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt
index b6694b10c..2494f90d6 100644
--- a/SLiMgui/Recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt	
+++ b/SLiMgui/Recipes/Recipe 9.9 - Keeping a reference to a sweep mutation.txt	
@@ -10,7 +10,7 @@ initialize() {
 }
 1 early() { sim.addSubpop("p1", 500); }
 1000 late() {
-	target = sample(p1.genomes, 1);
+	target = sample(p1.haplosomes, 1);
 	mut = target.addNewDrawnMutation(m2, 10000);
 	defineConstant("SWEEP", mut);
 }
diff --git a/VERSIONS b/VERSIONS
index 1f36817b6..64910016e 100644
--- a/VERSIONS
+++ b/VERSIONS
@@ -50,12 +50,15 @@ development head (in the master branch):
 				method: (object<Chromosome>)chromosomesWithSymbols(string symbols)
 			Individual class:
 				method: (object<Haplosome>)haplosomesForChromosomes([Niso<Chromosome> chromosomes = NULL], [Ni index = NULL], [logical$ includeNulls = T])
-			Mutation class:
-				property: chromosome => (object<Chromosome>$)
+		x	Mutation class:
+		x		property: chromosome => (object<Chromosome>$)
 			Subpopulation class:
 				method: (object<Haplosome>)haplosomesForChromosomes([Niso<Chromosome> chromosomes = NULL], [Ni index = NULL], [logical$ includeNulls = T])
 				method: (object<Individual>)addMultiRecombinant(object<Dictionary>$ pattern, [Nfs$ sex = NULL], [No<Individual>$ parent1 = NULL],
 							[No<Individual>$ parent2 = NULL], [logical$ randomizeStrands = F], [integer$ count = 1], [logical$ defer = F])
+		add autofixes in SLiMgui for the above API changes
+		revise recipes for new terminology (but they will require more revision downstream)
+		fix calc...() functions for new terminology (but they will require more revision downstream)
 
 
 version 4.3 (Eidos version 3.3):
diff --git a/core/slim_functions.cpp b/core/slim_functions.cpp
index a9270ae04..535ab831f 100644
--- a/core/slim_functions.cpp
+++ b/core/slim_functions.cpp
@@ -186,7 +186,7 @@ R"V0G0N({
 	
 	muts1 = haplosome1.mutations;
 	muts2 = haplosome2.mutations;
-	length = species.chromosome.lastPosition + 1;
+	length = species.chromosomes.lastPosition + 1;
 
 	// handle windowing
 	if (!isNULL(start) & !isNULL(end))
@@ -231,7 +231,7 @@ R"V0G0N({
 		species = community.allSpecies;
 	}
 	
-	length = species.chromosome.lastPosition + 1;
+	length = species.chromosomes.lastPosition + 1;
 
 	// handle windowing
 	if (!isNULL(start) & !isNULL(end))
@@ -274,7 +274,7 @@ R"V0G0N({
 		species = community.allSpecies;
 	}
 	
-	length = species.chromosome.lastPosition + 1;
+	length = species.chromosomes.lastPosition + 1;
 	
 	if (isNULL(muts))
 		muts = species.mutations;
@@ -375,7 +375,7 @@ R"V0G0N({
 		species = community.allSpecies;
 	}
 	
-	length = species.chromosome.lastPosition + 1;
+	length = species.chromosomes.lastPosition + 1;
 	
 	if (isNULL(muts))
 		muts = species.mutations;
@@ -432,7 +432,7 @@ R"V0G0N({
 		species = community.allSpecies;
 	}
 	
-	length = species.chromosome.lastPosition + 1;
+	length = species.chromosomes.lastPosition + 1;
 	
 	if (isNULL(muts))
 		muts = species.mutations;