evolutionary genetics
razib | March 1, 2010I have pointed to the fact that mtDNA genetics has suggested that the polar bear is actually a derived lineage of brown bears. And, more specifically, that some extant lineages of brown bears share a more recent common ancestor with polar bears than other brown bears. In other words, brown bears are paraphyletic. Apparently there has been dispute of when the polar bear morph emerged from the brown bears. Luckily polar bears have been resident in a region where the likelihood of preservation of ancient DNA is relatively high. PNAS has a new paper which reports on the extraction of genetic…
razib | March 1, 2010A few days ago I pointed to a paper which suggests the possible utility of looking at selection on standing genetic variation on quantitative traits to get a sense of the role of adaptation in the human genome. We humans like to think we're a complex species, so I see no a priori reason why our evolutionary history should be easily reducible to spare compact dynamics. Granted, we can start with the assumption that on the order of 50,000 years before the present there was a rapid demographic expansion of anatomically modern humans out of the continent of Africa. This story is simple, and is…
razib | November 11, 2009There are many ways one can model population genetic dynamics. A simple avenue is to imagine a deme, a group of breeding individuals, subject to a few major parameters which are modulating genetic variation. Mutation, migration, random drift and selection. A model being what a model is, one's goal is to simplify, utilize approximations, and still manage to extract insight as to the relevant aspects of the dynamics one is focusing on (unless you're Stephen Wolfram). One of the major upsides of the Price Equation is that it makes no compromises, rather, it starts from first principles and…
razib | November 11, 2009In the post below on the Price Equation I stayed true to George Price's original notation in his 1970 paper where he introduced his formalism. But here is a more conventional form, the "Full Price Equation," which introduces a second element on the right-side.
Δz = Cov(w, z) / w
One can specifically reformulate this verbally for a biological context:
Change in trait = Change due to selection on individuals + Change due to individual transmission
The first element on the right-side is explicable as selection upon a heritable trait. w is the conventional letter used for "fitness," so w is…
razib | November 10, 2009In the comments below I referred to the "Price Equation." Here is what William D. Hamilton had to say about George Price's formalism in Narrow Roads of Gene Land:
A manuscript did eventually come from him but what I found set out was not any sort of new derivation or correction of my 'kin selection' but rather a strange new formalism that was applicable to every kind of natural selection. Central to Price's approach was a covariance formula the like of which I had never seen...Price had not like the rest of us looked up the work of the pioneers when he first became interested in selection;…
razib | October 22, 2009If you have more than a marginal interest in evolutionary biology you will no doubt have stumbled upon the conundrum of sex & sexes. Matt Ridley's most prominent work, The Red Queen: Sex and the Evolution of Human Nature, covered both the theoretical framework and applied implications of the subject. Ridley leaned heavily upon William D. Hamilton's scientific work, which extended upon Leigh Van Valen's concept of the book's titular Red Queen. The complex interplay between pathogens & multicelluar organisms across the eons is a topic of such breadth and depth that a substantial…
razib | October 21, 2009One of the banes of modern life is the stack of papers in one's "to-read" list. I guess that goes to show how cushy modern life is, as what sort of complaint is that? In any case, I began to consider this after reading Joe Thornton's magisterial response to Michael Behe's giddy excitement over his most recent paper, An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Thornton dispatches Behe's muddled misconceptions with economy and precision, but after reading the paper, as opposed to cogent summaries such as Carl Zimmer's in The New York Times I'm even more…
razib | October 20, 2009Evolutionary ideas have been around a long time, at least since the Greeks, and likely longer. I accept the arguments of researchers who suggest that humans are predisposed to Creationist thinking; after all, cross-cultural data shows the dominance of this model before the rise of modern evolutionary biology. But this does not mean that the possibility of evolution would be totally mystifying to the human race before Charles Darwin's time. After all, it may be that humans as a species have a predisposition toward theism as well, and yet all complex societies produce atheistic movements as…
dgmacarthur | June 3, 2009Razib from Gene Expression has a frankly heroic post up dissecting a recent paper on genetic variation around the FUT2 gene, which encodes a cell surface protein involved in the pathway that produces the ABO blood group antigens.
The story illustrates some of the difficulties associated with extracting information about human evolution from genetic sequence data. There is fairly compelling a priori evidence for natural selection having a strong effect on this gene during recent human evolution, but even with data on genetic variation from a large sample of worldwide populations it is…
razib | May 27, 2009Scientific American has a long piece reviewing the recent genetic insights into the origins and development of the most awesome pets of all:
It is by turns aloof and affectionate, serene and savage, endearing and exasperating. Despite its mercurial nature, however, the house cat is the most popular pet in the world. A third of American households have feline members, and more than 600 million cats live among humans worldwide. Yet as familiar as these creatures are, a complete understanding of their origins has proved elusive. Whereas other once wild animals were domesticated for their milk,…
razib | May 26, 2009On this week's Science Saturday John Horgan interviews Richard Wrangham. The second half of the conversation focuses on Wrangham's new book, Catching Fire: How Cooking Made Us Human. I've heard pieces of the arguments mooted in the back & forth before, but it looks like in this book they're all brought together. Humans are a large animal with a very small gut, so we need to maximize the bang-for-the buck when it comes to what we eat. Unlike gorillas and to a lesser extent chimpanzees we just aren't able to process enough low quality vegetable matter to keep ourselves going. Part of this…
razib | May 11, 2009Dienekes reports on an abstracts for paper presentations at the ESHG 2009. This was is particularly interesting:
European Lactase Persistence Allele is Associated With Increase in Body Mass Index
J. A. Kettunen et al.
The global prevalence of obesity, usually indexed by body mass index (BMI) cut-offs, has increased significantly in the recent decades, mainly due to positive energy balance. However, the impact of a selection for specific genes cannot be excluded. Here we have tested the association between BMI and one of the best known genetic variants showing strong selective pressure: the…
razib | April 30, 2009I've been fine tuning Ubuntu all day with goodies and getting drivers to work right, so I missed this paper on African genetics:
Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, 4 African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared…
dgmacarthur | April 30, 2009This is a profoundly impressive paper - a study of the patterns of genetic variation in 2,400 individuals from 113 African populations, by far the most comprehensive analysis of African genetic diversity ever performed.
I had heard that Sarah Tishkoff's group had assembled a large
collection of African DNA samples, a daunting achievement in itself
given the logistical, ethical and social challenges involved (New Scientist
notes that "the researchers often had to use their vehicle batteries to
power the
centrifuges used to separate out white blood cells from their samples")
- but the breadth…
razib | April 29, 2009Haplotypic Background of a Private Allele at High Frequency in the Americas:
Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these…
razib | April 27, 2009On the order of ~1 million years ago humans seem to have evolved dark skin. While light skin evolved several times, it looks like dark skin exhibits an "consensus sequence," so that all dark skinned peoples seem to have the same genetic architecture.
This chart (from Signatures of Positive Selection in Genes Associated with Human Skin Pigmentation as Revealed from Analyses of Single Nucleotide Polymorphisms) shows that when it comes to skin color related genes the populations of Bougainville Island (off the eastern coast of Papua New Guinea) and Sub-Saharan Africa are far closer than you…
razib | April 23, 2009There are some papers out on the genome of the domestic cow out right now. ScienceNews has an overview:
Two competing research teams have cataloged the "essence of bovinity" found in the DNA of cattle, but not without disagreement on some essential points.
Reporting online April 23 in Science and April 24 in Genome Biology, the two groups compiled drafts of the bovine genome, identifying genes important for fighting disease, digesting food and producing milk.
I don't see the Genome Biology paper on the site yet, but there are two in Science. First, The Genome Sequence of Taurine Cattle: A…
razib | April 16, 2009Another response by Etienne Patin, lead author of Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set, to a follow up post:
As to your hypothesis represented by the cladogram, this is a quite reasonable and interesting idea. Actually, the only method that we could use to prove it is to find human remains of Pygmies dating back to Bantu expansions, in regions that were colonized by Bantus. Population genetics cannot infer the presence of extinct populations. However, as stated in our article, Western and Eastern Pygmies may…
razib | April 14, 2009Accelerated Adaptive Evolution on a Newly Formed X Chromosome:
Sex chromosomes originated from ordinary autosomes, and their evolution is characterized by continuous gene loss from the ancestral Y chromosome. Here, we document a new feature of sex chromosome evolution: bursts of adaptive fixations on a newly formed X chromosome. Taking advantage of the recently formed neo-X chromosome of Drosophila miranda, we compare patterns of DNA sequence variation at genes located on the neo-X to genes on the ancestral X chromosome. This contrast allows us to draw inferences of selection on a newly…
razib | April 11, 2009The leader author of the PLoS Genetics paper Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set, which I blogged a few days ago left a clarifying comment:
I just have few remarks. I do not expect that the Bantu expansions are responsible for the separation of Western and Eastern Pygmies. In a recent article in Current Biology, Paul Verdu and colleagues showed that the separation of Pygmy groups, but only those from the Western part of sub-Saharan Africa, diverged concomitantly with Bantu expansions (3,000-5,000 years ago…