Population Genetics

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Category archives for Population Genetics

All those types of speciation

Over at Wilkins’ cabana, there’s a post (Some new work on speciation and species) on a paper by Nitin Phadnis and Allen Orr (doi:10.1126/science.1163934). Phadnis and Orr isolated a gene responsible for both reproductive isolation and sex-ratio distortion between two populations of Drosophila pseudoobscura. Wilkins doesn’t like speciation genes, and he’s rails on the concept…

Is Nested Clade Analysis Worthwhile?

Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.…

Slightly Deleterious in Trans

One of the hot topics in evolutionary biology concerns the relative contributions of protein coding sequence changes and non-coding changes that lead to differences in the expression of protein coding genes. A subset of this debate can be summarized as cis versus trans. Non-coding sequences that regulate gene expression are known as cis regulatory elements…

How do you really feel, Dr. Wakeley?

I’m currently working my way through John Wakeley’s book on Coalescent Theory. (The website has a few pre-publication chapters if you want to take a peek.) In his introductory chapter, Wakeley introduces the concept of gene genealogies. He’s careful to point out that, unlike the phylogenies we construct using inter-specific data, we don’t actually use…

A Neutral Theory of Memetics

In his classic book from 1976, The Selfish Gene, Richard Dawkins introduced the concept of the meme. Basically, a meme can be thought of as a cultural gene — an idea that is transmitted in a population. This being Dawkins, memetics has a certain adaptationist flavor to it. The Selfish Gene introduces evolution from the…

Brian Charlesworth wrote a review of Mike Lynch’s The Origins of Genome Architecture, in which Charlesworth argues that sexual reproduction can explain many of the features Lynch claims evolved under nearly neutral processes (doi:10.1016/j.cub.2008.01.008). Not to be left out of the party, Deborah Charlesworth has chimed in with her opinion, and it’s much more critical…

Charlesworth on Lynch

Brian Charlesworth has reviewed Michael Lynch’s The Origins of Genome Architecture for Current Biology. Charlesworth’s review is generally positive, and he agrees that population size may be an important factor in genome evolution. However, he thinks that Lynch overplays the role relaxed selective constraint in small populations plays in the evolution of genomic complexity. Charlesworth…

One of the drums I beat around here pertains to inferring demographic history using molecular markers (i.e., DNA data). I’ve been known to go off on people who make claims about ancestral population sizes based on studies of a single locus or gene. You see, studying a single locus only gives you the evolutionary history…

Competitive Release and Antibiotic Resistance

While much of the research in evolutionary biology is purely academic in nature — designed for the purpose of understanding the biology of a system rather than for immediate human benefit — there is some research that yields immediate practical uses. One research area that is particular fruitful in this regard involves applying evolutionary theory…

Accelerated Evolution — yet again

Can positive selection drown out neutral evolution? That’s what John Hawks claims in response to my post on accelerated evolution. Hawks points out that, rather than looking at the neutral fixation rate (which is equal to the mutation rate, u), we should be more interested in the average time to fixation of a neutral mutation…