Using genomic data to infer historic population dynamics of nonmodel organisms

AC Beichman, E Huerta-Sanchez… - Annual Review of …, 2018 - annualreviews.org
Genome sequence data are now being routinely obtained from many nonmodel organisms.
These data contain a wealth of information about the demographic history of the populations …

A survey of methods and tools to detect recent and strong positive selection

P Pavlidis, N Alachiotis - Journal of Biological Research-Thessaloniki, 2017 - Springer
Positive selection occurs when an allele is favored by natural selection. The frequency of the
favored allele increases in the population and due to genetic hitchhiking the neighboring …

Long-read sequence assembly of the gorilla genome

D Gordon, J Huddleston, MJP Chaisson, CM Hill… - Science, 2016 - science.org
INTRODUCTION The accurate sequence and assembly of genomes is critical to our
understanding of evolution and genetic variation. Despite advances in short-read …

Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples

BY Kim, CD Huber, KE Lohmueller - Genetics, 2017 - academic.oup.com
The distribution of fitness effects (DFE) has considerable importance in population genetics.
To date, estimates of the DFE come from studies using a small number of individuals. Thus …

Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

F Pouyet, S Aeschbacher, A Thiéry, L Excoffier - Elife, 2018 - elifesciences.org
Disentangling the effect on genomic diversity of natural selection from that of demography is
notoriously difficult, but necessary to properly reconstruct the history of species. Here, we …

[图书][B] Divergence with genetic exchange

ML Arnold - 2016 - books.google.com
The study of genetic exchange resulting from natural hybridization, horizontal gene transfer,
and viral recombination has long been marked by controversy between researchers holding …

Complete sequencing of ape genomes

DA Yoo, A Rhie, P Hebbar, F Antonacci… - BioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
We present haplotype-resolved reference genomes and comparative analyses of six ape
species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan …

Ecology, not host phylogeny, shapes the oral microbiome in closely related species

M Moraitou, A Forsythe, JA Fellows Yates… - Molecular biology …, 2022 - academic.oup.com
Host-associated microbiomes are essential for a multitude of biological processes. Placed at
the contact zone between external and internal environments, the little-studied oral …

The time scale of recombination rate evolution in great apes

LS Stevison, AE Woerner, JM Kidd… - Molecular biology …, 2016 - academic.oup.com
We present three linkage-disequilibrium (LD)-based recombination maps generated using
whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western …

Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions

M Weldenegodguad, R Popov, K Pokharel… - Frontiers in …, 2019 - frontiersin.org
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the
northernmost regions on Earth where cattle farming has been traditionally practiced. In this …