Population Genetics
razib | March 4, 2010A new paper in PLoS, Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples:
Many association studies have been published looking for genetic variants contributing to a variety of human traits such as obesity, diabetes, and height. Because the frequency of genetic variants can differ across populations, it is important to have estimates of genetic ancestry in the individuals being studied. In this study, we were able to measure genetic ancestry in populations of mixed ancestry by genotyping pooled, rather than individual, DNA samples…
sporte | January 4, 2010An NSF post on Twitter this morning described an interesting study from the University of Pennsylanvia and Cornell University, that found that some people who call themselves "African Americans" may only be 1% West African, according to their DNA.
The University of Pennsylvania press release contains other interesting findings as well. 365 individuals were studied and 300,000 genetic markers were examined.
Some of the findings were:
If you're African American, the genes most likely to have an African origin are those on your X chromosome. The article didn't mention it, but I would guess…
razib | November 25, 2009The state of China has 1/5 of humanity within its borders, so it's genetic structure is of interest. It is obviously important for medical reasons to clarify issues of population structure so that disease susceptibility among the Han is well characterized, in particular with the heightened medical needs of an aging population in the coming generation. And of course, there are the nationalistic concerns. About 20 years ago L. L. Cavalli-Sforza reported that his South Chinese samples were genetically closer to Southeast Asians than North Chinese in The History and Geography of Human Genes.…
razib | November 24, 2009
Since The Origin of Species was published 150 years ago many articles on evolution are seeing the light of day today. Normally I'm all in favor of this, I ♥ evolution. But it also means that woolly thinking is put out there as conventional wisdom as journalists simply act as stenographers for any scientist who's in their rolodex. Some of the quotes in this National Geographic article make me want to tear my hair out. Ian Tattersall, a paleoanthropologist, decides to offer up his opinions as a population geneticist:
"Everything we know about evolutionary change suggests that genetic…
razib | October 25, 2009When Mendelism reemerged in the early 20th century to become what we term genetics no doubt the early practitioners of the nascent field would have been surprised to see where it went. The centrality of of DNA as the substrate which encodes genetic information in the 1950s opened up molecular biology and led to the biophysical strain which remains prominent in genetics. Later, in the 1970s Alan Wilson and Vincent Sarich used crude measures of genetic distance to resolve controversies in paleontology, specifically, the date of separation between the human and ape lineage. Genetics spans the…
razib | October 13, 2009I'm talking about coeliac disease:
Coeliac disease is caused by a reaction to gliadin, a gluten protein found in wheat (and similar proteins of the tribe Triticeae, which includes other cultivars such as barley and rye). Upon exposure to gliadin, the enzyme tissue transglutaminase modifies the protein, and the immune system cross-reacts with the small-bowel tissue, causing an inflammatory reaction. That leads to a truncating of the villi lining the small intestine (called villous atrophy). This interferes with the absorption of nutrients, because the intestinal villi are responsible for…
razib | October 10, 2009Dienekes points to a new paper which attempts to quantify the genetic ancestry of South Asian Muslims into indigenous and exogenous components:
Islam is the second most practiced religion in India, next to Hinduism. It is still unclear whether the spread of Islam in India has been only a cultural transformation or is associated with detectable levels of gene flow. To estimate the contribution of West Asian and Arabian admixture to Indian Muslims, we assessed genetic variation in mtDNA, Y-chromosomal and LCT/MCM6 markers in 472, 431 and 476 samples, respectively, representing six Muslim…
razib | August 29, 2009Dienekes points me to a new paper, European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups. You've seen this song & dance before:
Population substructure in Japan
Population substructure of Mexican Mestizos
European population substructure
Genetic Map of East Asia
The genetics of Fenno-Scandinavia
Finns as European outliers
Uyghurs are hybrids
Genetic structure of Eastern European populations
Genetic map of Europe; genes vary as a function of distance
More genetic maps of Europe
Human population…
razib | July 7, 2009Blogger Thomas Mailund is an author on a new paper, Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach:
With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the number of generations between speciation events. We use a hidden Markov model parametrized according to coalescent theory in order to infer the genealogy along a four-species genome alignment of closely related species…
razib | May 24, 2009Waves of stationary shape:
Over at Scienceblogs, people are talking about waves. Of course, everyone thinks that waves are in the domain of physics, and people always forget about one of my favorite subjects: waves of advance. Way back in the day, RA Fisher wondered what might happen if genes had to spread not just locally but across space, and he published his findings in a landmark article called The Wave of Advance of Advantageous Genes. This paper was not just important for its contributions to population genetics, but because of fundamental contributions to applied mathematics. As far as…
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…
evolgen | December 16, 2008Over 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 in his post.
What I'm interested in are the comments on Wilkins' post -- primarily the confusion over what the speciation gene hunters mean when they talk about different flavors of speciation. Most population geneticists…
sb admin | November 16, 2008
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.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of…
evolgen | November 16, 2008
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.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of…
sporte | October 21, 2008Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it.
And now that a genome is no longer an entirely personal bit of information, you may be in for a surprise meeting someday, with the end result.
That's right.
Male adoptees are getting their DNA tested and getting information about their possible surnames.
According to the BBC news:
At least 30 men registered with US consumer genetic testing firm Family Tree DNA have found their…
evolgen | October 7, 2008One 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 (CREs). The protein coding genes that bind to CREs and control the expression of genes act in trans.
That's the background,and here are some more details. The poster boy for the importance of CREs is Sean Carroll, who argues that the…
evolgen | September 15, 2008
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 intra-specific gene genealogies to infer the relationships of the sequences we've sampled:
Readers used to "tree thinking," which is the subject of Section 1.1, will have little trouble seeing the close connection between gene genealogies and…
evolgen | May 27, 2008
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 gene's eye view. But Dawkins is a staunch advocate of natural selection as the primary driving force behind evolution. The debate over the role of natural selection in evolution has been carried out using empirical data, theoretical modeling, and philosophical arguments. I…
evolgen | April 23, 2008Brian 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 of Lynch than her husband's (doi:10.1017/S0016672308009282). The main thesis that Lynch has been presenting in both this book and some of his recent papers is that many features of eukaryotic genomes (introns, complicated cis…
sporte | April 9, 2008You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz.