Query: https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=40674
-
2800 total genomes (= 264 RefSeq + 2,536 other assemblies)
-
754 unique taxa (includes species, subspecies, hybrids, no epithet)
- 168 chromoLevel unique taxa
- 489 scaffoldLevel unique taxa
- 254 contigLevel unique taxa
-
675 species after aligning with the mammal tree taxonomy and collapsing redundancy
- 76 chromoLevel species (= 68 + 8 more from the 'redundantOrNotUsing' category)
- 414 scaffoldLevel species (= 418 - 4 from above)
- 185 contigLevel species (= 189 - 4 from above)
| Higher taxon | GENOME SP | TOTAL SP | % SP |
|---|---|---|---|
| Afrotheria | 12 | 92 | 13% |
| Euarchontoglires | 208 | 2963 | 7% |
| Laurasiatheria | 277 | 2456 | 11% |
| Marsupialia | 168 ** | 362 | 46% |
| Monotremata | 2 | 5 | 40% |
| Xenarthra | 8 | 33 | 24% |
** There was only 7 marsupial genomes before 2021; then 11 + 148 + 2 added in 2021 (= 161 genomes) for the current total of 168
| Order | GENOME SP | TOTAL SP | % SP |
|---|---|---|---|
| AFROSORICIDA | 3 | 55 | 5% |
| ARTIODACTYLA | 128 | 348 | 37% |
| CARNIVORA | 74 | 298 | 25% |
| CHIROPTERA | 49 | 1287 | 4% |
| CINGULATA | 3 | 21 | 14% |
| DASYUROMORPHIA | 63 | 78 | 81% |
| DERMOPTERA | 2 | 2 | 100% |
| DIDELPHIMORPHIA | 3 | 106 | 3% |
| DIPROTODONTIA | 85 | 146 | 58% |
| EULIPOTYPHLA | 12 | 491 | 2% |
| HYRACOIDEA | 2 | 5 | 40% |
| LAGOMORPHA | 6 | 91 | 7% |
| MACROSCELIDEA | 1 | 19 | 5% |
| MICROBIOTHERIA | 1 | 1 | 100% |
| MONOTREMATA | 2 | 5 | 40% |
| OTORYCTEMORPHIA | 2 | 2 | 100% |
| PAUCITUBERCULATA | 0 ** | 7 | 0% |
| PERAMELEMORPHIA | 14 | 22 | 64% |
| PERISSODACTYLA | 10 | 24 | 42% |
| PHOLIDOTA | 4 | 8 | 50% |
| PILOSA | 5 | 12 | 42% |
| PRIMATES | 83 | 458 | 18% |
| PROBOSCIDEA | 2 | 7 | 29% |
| RODENTIA | 115 | 2392 | 5% |
| SCANDENTIA | 2 | 20 | 10% |
| SIRENIA | 3 | 5 | 60% |
| TUBULIDENTATA | 1 | 1 | 100% |
** Paucituberculata is the only extant mammal order yet without a genome! The extant marsupial family Caenolestidae (shrew-opossums) is represented by 7 species in the Andes mountains of South America.
- body size (adult average body mass of sequenced species, log kg; modified from Faurby and Svenning 2016 http://www.journals.uchicago.edu/doi/10.1086/686268)
- latitude (absolute value of centroid of species geographic range polygon; modified from IUCN 2016 https://www.iucnredlist.org/resources/spatial-data-download)
| variable | med | low95 | up95 | low50 | up50 |
|---|---|---|---|---|---|
| Body mass (all) | 0.08 | 0.00 | 180.39 | 0.02 | 0.63 |
| Body mass (genome) | 2.07 | 0.01 | 2392.26 | 0.08 | 22.42 |
| Latitude (all) | 15.35 | 0.52 | 52.44 | 5.87 | 28.06 |
| Latitude (genome) | 22.30 | 0.64 | 58.69 | 8.39 | 34.90 |
- Wilcoxon rank sum tests with continuity correction:
- Body mass: W = 1150239, p-value < 2.2e-16
- Latitude: W = 1404678, p-value = 3.09e-14
- 239 species (241 taxa) in the Zoonomia Consortium alignment
- "A total of 242 genome assemblies, representing 240 species, are included in the Zoonomia Cactus alignment. We included all non-redundant, high-quality assemblies posted on NCBI for >6 months as of March 3, 2018, or for a shorter time if an associated publication was available. One species (dog) is represented by two genomes. Due to a technical error, one genome available on NCBI (Tarsius_syrichta-2.0.1) was not included in this initial alignment, and the genome for Dipodomys stephensi was represented twice."
- So, 241 species in the alignment V2 on UCSC: https://cglgenomics.ucsc.edu/data/cactus/
- Of these, 2 are redundant at the species level (Canis lupus dingo, Ceratotherium simum cottoni) == 239 species
- 121 species were newly generated by Zoonomia, published in 2019
- 118 species were aligned from RefSeq
