Category Archives: Evolutionary Genomics

A new paper on dingoes came out last winter which was in my “to-read” bookmarks, and I finally around to it. It’s open access, Genomic regions under selection in the feralization of the dingoes: Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the […]

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“Reader request”, what’s going on with this new crazy baleen whale paper, Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. First, putting “blue whale” in the title is genius, since blue whales are awesome and people will read the paper with that in the title (most people don’t […]

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In antiquity ostriches and lions roamed the Syrian desert. The cheetah even still clings to a tenuous existence in the fastness of the central Iranian desert. The point being that the new finding of African modern human remains on the southeast fringe of Arabia ~85,000 years ago shouldn’t be too surprising. Old modern(ish) looking humans date […]

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In the 1970s Richard C. Lewontin wrote about how the allozyme era finally allowed for the testing of theories which had long been perfected and refined but lay unused like elegant machines without a task. Almost immediately the empirical revolution that Lewontin began in the 1960s kickstarted debates about the nature of selection and neutrality […]

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As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.
Generalities:
– Life Technologies/Ion Torrent apparently hires d-bag bros to represent them…

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The Pith: Natural selection comes in different flavors in its genetic constituents. Some of those constituents are more elusive than others. That makes “reading the label” a non-trivial activity.
As you may know when you look at patterns of…

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A friend pointed me to the heated comment section of this article in Nature, Rebuilding the genome of a hidden ethnicity. The issue is that Nature originally stated that the Taino, the native people of Puerto Rico, were extinct. That resulted in an avalanche of angry comments, which one of the researchers, Carlos Bustamante, felt […]

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The Pith: The human X chromosome is subject to more pressure from natural selection, resulting in less genetic diversity. But, the differences in diversity of X chromosomes across human populations seem to be more a function of population history than …

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The Pith: In this post I review a paper which covers the evolutionary dimension of human childbirth. Specifically, the traits and tendencies peculiar to our species, the genes which may underpin those traits and tendencies, and how that …

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Credit: Karl Magnacca
The Pith: In this post I review some findings of patterns of natural selection within the Drosophila fruit fly genome. I relate them to very similar findings, though in the opposite direction, in human genomics. Different forms o…

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Does the chart above strike you as strange? What it shows is that the mean fitness of a population drops as you increase the rate of deleterious mutation (many more mutations are deleterious than favorable)…but at some point the fitness of the population bounces back, despite (or perhaps because of?) the deleterious mutations! This would […]

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The number 1 gets a lot more press than -1, and the concept of heterozygosity gets more attention than homozygosity. Concretely the difference between the latter two is rather straightforward. In diploid organisms the genes come in duplicates. If the alleles are the same, then they’re homozygous. If they’re different, then they’re heterozygous. Sex chromosomes […]

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Natural selection happens. It was hypothesized in copious detail by Charles Darwin, and has been confirmed in the laboratory, through observation, and also by inference via the methods of modern genomics. But science is more than broad brushes. We need to drill-down to a more fine-grained level to understand the dynamics with precision and detail, […]

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With all the justified concern about “missing heritability”, the age of human genomics hasn’t been a total bust. As I have observed before in 2005’s excellent book Mutants the evolutionary geneticist Armand M. Leroi asserted that we really didn’t have a good understanding of normal variation of human pigmentation. At the time I think it […]

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Over the past decade evolutionary geneticist Mike Lynch has been articulating a model of genome complexity which relies on stochastic factors as the primary motive force by which genome size increases. The argument is articulated in a 2003 paper, and further elaborated in his book The Origins of Genome Architecture. There are several moving parts […]

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Razib Khan