Wednesday, June 24, 2020

Calibrating Mutation Rates

Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.73 × 10−8 de novo mutations per site per generation (95 % CI: 0.65 × 10−8 - 0.81 × 10−8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 80 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 1.9 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular divergence dated at 54 Mya using our new estimate of the yearly mutation rate.
Lucie A. Bergerson, et al., "The germline mutational process in rhesus macaque and its implications for phylogenetic dating" bioRxiv (June 23, 2020). doi:


neo said...

coronavirus Mutation Rates

andrew said...

Not really comparable to primate mutation rates.

DDeden said...

They claim OWMonkeys split from hominoids 54ma?? I thought it was about 30ma.

DDeden said...

OT but related

Parallel convergence in Great Apes

1) Laryngeal air sacs enlarged
2) Knuckle/fist quadrupedalism
3) Short stiff back

Hylobatids & Homo OTOH retain ancestral traits (cf Miocene quasi-hylobatids)

Journal of Human Evolution
Volume 144, July 2020, 102791

Great apes and humans evolved from a long-backed ancestor

Author Allison L.Machnickia
Philip L.Renob

There is current debate whether the Homo/Pan last common ancestor (LCA) had a short, stiff lumbar column like great apes or a longer, flexible column observed in generalized Miocene hominoids. Beyond having only four segments, three additional features contribute to lumbar stiffening: the position of the transitional vertebra (TV), orientation of the lumbar spinous processes, and entrapment of lumbar vertebrae between the iliac blades. For great apes, these features would be homologous if inherited from a short-backed LCA but likely functionally convergent through dissimilar phenotypes if evolved from a long-backed LCA. We quantitatively and qualitatively analyzed human, ape, and monkey thoracic and lumbar vertebrae using 3D surface scanning and osteological measurements to compare spinous process morphology and sacral depth. We also used a large sample of hominoid vertebral counts to assess variation in the position of the TV and lumbosacral boundary. All extant hominoids modally place the TV at the ultimate thoracic. However, humans and orangutans place the TV at the 19th postcranial vertebral segment, whereas other apes place the TV at the 20th. Furthermore, chimpanzees, gorillas, and orangutans each have distinct patterns of spinous process angulation and morphology associated with lumbar stiffening, while human spinous process morphology is similar to that of longer backed gibbons, monkeys, and Miocene hominoids Morotopithecus and Pierolapithecus.


DDeden said...

That claim of the split being 54ma is really questionable IMO.

2009 paper

Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA.