Login

Recent searches

No recent searches

Search options

Not available on mastodon.xyz.
mastodon.xyz is one of the many independent Mastodon servers you can use to participate in the fediverse.
A Mastodon instance, open to everyone, but mainly English and French speaking.

Administered by:

Server stats:

788
active users

mastodon.xyz: AboutProfiles directoryPrivacy policy

Mastodon: AboutGet the appKeyboard shortcutsView source codev4.3.4

#popgen

0 posts0 participants0 posts today
Replied in thread
Public
Arlin Stoltzfus

@chasewnelson, some #popgen papers about this:

Kryazhimskiy and Plotkin, 2008, The Population Genetics of dN/dS

doi.org/10.1371/journal.pgen.1

Wolf, et al. 2009. Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol 1:308-319.

ncbi.nlm.nih.gov/pubmed/203332

doi.orgThe Population Genetics of dN/dSAuthor Summary Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two cases. In particular, when applied to sequences from a single population, the dN/dS ratio is relatively insensitive to the strength of natural selection, and the anticipated signature of adaptive evolution, dN/dS>1, is violated. These results have implications for the interpretation of genetic variation sampled from a population. In particular, these results suggest that microbes may experience substantially stronger selective forces than previously thought.
Public
Matt Osmond

3 years (and 2 kids) later, I finally revised the manuscript:

biorxiv.org/content/10.1101/20

we develop a #popgen method to locate genetic ancestors from tree sequences and apply it to arabidopsis thaliana.

software is ready to be applied to any dataset with Relate trees:
github.com/osmond-lab/spacetre

check out our video to learn more: youtube.com/watch?v=4itER1uEKb

thanks for your patience @gcbias !

Public
Jason H. Moore, Ph.D.

Population genetics: an introduction for physicists arxiv.org/abs/2408.02650 #genetics #physics #popgen

arXiv.orgPopulation genetics: an introduction for physicistsPopulation genetics lies at the heart of evolutionary theory. This topic forms part of many biological science curricula but is rarely taught to physics students. Since physicists are becoming increasingly interested in biological evolution, we aim to provide a brief introduction to population genetics, written for physicists. We start with two background chapters: chapter 1 provides a brief historical introduction to the topic, while chapter 2 provides some essential biological background. We begin our main content with chapter 3 which discusses the key concepts behind Darwinian natural selection and Mendelian inheritance. Chapter 4 covers the basics of how variation is maintained in populations, while chapter 5 discusses mutation and selection. In chapter 6 we discuss stochastic effects in population genetics using the Wright-Fisher model as our example, and finally we offer concluding thoughts and references to excellent textbooks in chapter 7.
Public *
Julien JOSEPH

Hi everybody,

I am pleased to share with you my latest work in collaboration with Augustin Cléssin and Nicolas Lartillot:

biorxiv.org/content/10.1101/20

GC-biased gene conversion (gBGC) is a process that distorts the segregation of heterozygous AT:GC polymorphisms during meiotic #recombination. This genome-wide non-Mendelian segregation has been shown to be a major source of #genetic load, earning the nickname of “Achille’s heel” of #genomes. (1/2)

#PopGen
#Evolution

Public *
Julien JOSEPH

Hello everyone,

I'm glad to share this preprint:

biorxiv.org/content/10.1101/20

PRDM9 is a gene that determines the location of most meiotic #recombination events through local histone methylation in humans and mice. It is also one of the fastest evolving gene in mammals.

In this preprint, we show that its molecular function in #meiosis is the same in salmonids!

This suggests that PRDM9's rapid #evolution has been going on for hundreds of Mys.

#PopGen
Public
Julien JOSEPH

Hello Mastodon people,

I wanted to mention that I have a new preprint out on bioRxiv:

biorxiv.org/content/10.1101/20

I think it could be really useful for people interested in the consequences of #Recombination on #Genome #Evolution, but more generally in interpreting DFEs, positive selection and dN/dS.

I will take the time to make a thread once the final paper is published (I hope it will).

For those who will take the time to read it, don't hesitate to give me feedback 😊

#Popgen
ExploreLive feeds
About