Biology subjects

Schierup, M. H.

Publications and source records attributed to Schierup, M. H..

3 recordsLinked to original sources

bioRxiv2018

Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate

The human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother. The yearly trio-based mutation rate estimate of ~0.43x10-9 is markedly lower than prior indirect estimates of ~1x10-9 per year from phylogenetic comparisons of the great apes. This suggests either a slowdown over the past 10 million years or an inaccurate interpretation of the fossil record. Here we use sequencing of chimpanzee, gorilla and orangutan trios and find that each species has higher estimated mutation rates per year by factors of 1.67+/- 0.22, 1.54+/- 0.2 and 1.84+/- 0.19, respectively. These estimates suggest a very recent and appreciable slowdown in human mutation rate, and, if extrapolated over the great apes phylogeny, yields divergence estimates much more in line with the fossil record and the biogeography.

evolutionary biology↗

bioRxiv2018

Detecting archaic introgression without archaic reference genomes

Human populations out of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a small rate of false detection. Furthermore our approach is able to accurately infer admixture proportions and divergence time of human and archaic populations.\n\nWe apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and directly find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in West Eurasians, South East Asians and South Asians.

evolutionary biology↗

bioRxiv2017

Dynamic copy number evolution of X- and Y-linked ampliconic genes in human populations

Ampliconic genes are good candidates for speciation genes: they are testis-expressed, multicopy and localized on sex chromosomes. Moreover, copy number variation in a specific ampliconic gene pair (Slx and Sly) is involved in hybrid incompatibilities between M. musculus and M. domesticus. However, we know little about the distribution of the ampliconic genes copy number and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified less than 50,000 years ago. For the X chromosome, we also find high copy number and coding diversity within populations. While we cannot rule out that neutral processes are at the origin of this high diversity, this study gives insights on the distribution of copy number within human populations, and demonstrates an extremely fast turnover in copy number of these regions.

evolutionary biology↗