Molecular Evolution

evolgen

Category archives for Molecular Evolution

Genomfart

Massimo Pigliucci has reviewed Mike Lynch’s book on genome evolution for Science [Postgenomic Musings]. In his review, Pigliucci writes the following: One of the central theses of the book is that natural selection is not necessarily the central evolutionary mechanism, as quite a bit of the details of genomic structures and evolution can be accounted…

Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the host, but there are also transposable elements (TEs), sequences from mitochondria (numts), and endogenous retroviruses (ERVs). In addition to those examples, other symbionts also infect eukaryotes and leave traces of their presence in the…

Sorting the Pancakes that Make up a Genome

Genome rearrangements are fast becoming one of the most interesting aspects of comparative genomics (I may be slightly biased in my perspective). We have known for quite some time that genomes of different species (and even within species) differ by inversions of their chromosomes (this was first studied in Drosophila). In fact, some of the…

In Vino (Genome) Veritas

A group of researchers from France and Italy have sequenced the genome of the finest grape varietal, Pinot Noir. The genome has hallmarks of ancient triploidization, shared by other dicotyledons, but there is no evidence for recent polyploidization. That meant sequencing and assembling this genome is easier than doing so for other agricultural plants that…

Junk on Cancer

The University of Michigan has put out a press release entitled: Bits of ‘junk’ RNA aid master tumor-suppressor gene With a title like that, how could I not blog the hell out of this bastard? I mean, they even put the scare quotes around “junk”. Like that — like I just did. Amazing! The story…

Score One for King & Wilson?

King and Wilson are the bee’s knees for all the kids who want to hype the effect of gene expression divergence between humans and chimps. The argument boils down to a few points: humans and chimps are mad different, their protein sequences are mad similar, therefore expression of the proteins must be important for those…

Is Sean Carroll Wrong?

One of the primary hypotheses of Sean Carroll’s model of evo-devo is that cis-regulatory elements (CREs) are the primary drivers of morphological evolution (see here). This hypothesis is controversial in the evolutionary genetics community. Because it’s hard to examine the effect of CREs on phenotypes at a genome-wide scale, the problem must be reduced into…

The Frailty of Nearly Neutral Hypotheses

Mike Lynch has been getting a fair bit of hype recently for his nearly neutral model of genome evolution (see here and here). The nearly neutral theory riffs off the idea that the ability of natural selection to purge deleterious mutations and fix advantageous mutations depends on the effective population size of the population in…

Junk on Junk

I’ve recently come across two articles on junk DNA. The first one, from New Scientist, includes a pretty thorough coverage of recent studies that have identified functions for non-protein-coding regions of the human genome (“Why ‘junk DNA’ may be useful after all”). The article is set up as if it will present the demise of…

Evo-Devo Revisited

I thought I had come to grips with evo-devo. Then along come Hopi Hoekstra and Jerry Coyne to call shenanigans on Sean Carroll’s model of evo-devo. This is nothing new for Coyne, but I can’t recall Hoekstra ever getting involved in the debate before now. Before we get to Hoekstra and Coyne, let’s allow Carroll…