The genetic ancestry of modern lions
Marc de Manuel and coworkers have a new paper in PNAS that presents some new findings about lion population history from whole-genome sequencing. The paper h...
All posts tagged with population structure
An archaic human from the bed of the Taiwan Strait
From the bottom of the sea this week comes another new fossil hominin. The specimen is a partial mandible, described in Nature Communications, by Chun-Hsiang...
Notable: Gorilla genomes illuminate phylogeography
Notable paper: Kimberly F. McManus, Joanna L. Kelley, Shiya Song, et al. 2015. Inference of Gorilla demographic and selective history from whole genome seque...
Ghost populations and ancient DNA
The rapidly changing field of ancient DNA has settled into a kind of normal science, as several teams of researchers have coalesced around a set of approache...
Chimpanzee communities are hundreds of years old
Kevin Langergraber and colleagues (2014) have undertaken a study of Y chromosome variation within chimpanzee communities of Uganda. Their goal was to estimat...
Naming archaic human populations
Ancient human populations like the Neandertals and Denisovans were not separate biological species.
The Altai Neandertal
It is notable that we now have evidence for interbreeding among every kind of hominin we have DNA from, and some we don’t.
Hunting the Denisovan belt
The other day I was having a long conversation about Denisovans and human origins. My friend suggested that “Denisovans” sound like some kind of Star Trek ci...
Population structure and chimpanzee malaria
A new paper examines the parasite load of a group of wild chimpanzees for Plasmodium, the parasite that causes malaria DeNys:2013. Several strains of Plasmod...
ARG is the word
Adam Siepel has written a very useful explainer about a new preprint he has posted with Matthew Rasmussen on the arXiv preprint server: “Our Paper: Genome-wi...
New Denisova and Neandertal DNA results reported
Elizabeth Pennisi reports from the Biology of Genomes conference at Cold Spring Harbor, New York: “More Genomes From Denisova Cave Show Mixing of Early Human...
Neandertal anti-defamation files, 17
Let no one say that I’m an uncritical voice about the many advantages of releasing preprints. They do have their downsides. Lack of editing is one.
Mailbag: North and South China
I read with interest your post on: http://johnhawks.net/weblog/reviews/neandertals/pigmentation/neandertal-introgression-1000-genomes-style-2011.html
ASHG notes on Gene Expression
Razib Khan has started writing up his notes on this week’s conference of the American Society of Human Genetics: “Reflections on the evolution at ASHG 2012”....
The North African Neandertal descendants
A new paper by Federico Snchez-Quinto and colleagues reports on comparisons of North African population samples with the Neandertal DNA project data Sanchez-...
Denisova at high coverage
Science today has released the new paper on the Denisova high-coverage genome by Mattias Meyer and colleagues from Svante Pääbo’s group Meyer:Denisova:2012. ...
Neandertal ancestry "Iced"
UPDATE (2015-10-21): This post has gotten some attention from social media recently, because Ötzi has been in the news. Later analyses have made clear that o...
Neandertal similarity in the HapMap samples
This post is from 2012 and the results here are no longer current. Readers can find more current information about Neandertal introgression in later posts.
The H preparation
Razib Khan comments on the current round of Henry Louis Gates ancestry programming: “Finding fake roots”, and “Reification is alright by me! Razib notes that...
Mailbag: Neandertal derived SNP alleles
Re: Neandertal introgression, 1000 Genomes style:
Understanding population differentiation
This lab has a take-home assignment, which is worth three points when you turn it in at next week’s lab section.
Measuring differences between populations
When individuals mate locally, different populations tend to diverge from each other in the frequencies of their alleles. Genetic differences between populat...
The risk gradient
Ann Gibbons reports Gibbons:diabetes:2011 from the International Congress of Human Genetics, on papers that examine GWAS risk alleles for type 2 diabetes: “D...
Mailbag: Spuds and mutts
Re: “How widespread is Denisovan ancestry today?” and “Potato sack race”:
Diversity doesn't point reliably to source populations
Worth amplifying from Dienekes’ Anthropology Blog, “Y chromosomes of the Bahamas”:
Braiding Denisovans into our ancestry
Dalton Luther reflects on the Denisovan admixture paper Skoglund:Jakobsson:2011 that I wrote about earlier this week (“How widespread is Denisovan ancestry t...
How widespread is Denisovan ancestry today?
Last month, David Reich and colleagues Reich:Denisova:2011 reported on estimates of Denisovan ancestry for island and mainland Asian populations. Their most ...
Y chronology awry
Dienekes links to and discusses a current paper by George Busby and colleagues Busby:peopling:2011 on the Y chromosome chronology for the settlement of Europ...
Floating on the data
Technology Review reports on a recent conference trying to spread data mining techniques. The point of departure is the growth of electronic sensor networks ...
Mailbag: Where did Neandertals come from?
Dr. Hawks, I greatly enjoyed your course on the rise of humans I purchased through the Teaching Company. I could not find the answer to this question: ...
A problem of fuzzy mammoths
Paleogenomics is changing the way we study evolution. In a number of cases, it now allows us to study extinct organisms with the same methods as we study liv...
Agriculture, population expansion and mtDNA variation
Earlier this spring, I wrote about a paper by Brenna Henn and colleagues that presented new data on SNP variation in recent African hunter-gatherer populatio...
Wolves in coyotes' clothing
Razib’s post on the genetics of canids (“A map of charismatic canid genomic variation”) does a nice summary of a recent paper in Genome Research, by vonHoldt...
Europe and China have different Neandertal genes
When last we saw the Vi 33.16 X chromosome, I was wresting out its secrets by looking for SNP haplotypes shared by this Neandertal with the European and Afri...
Hunter-gatherer kinship and band composition
Kim Hill and colleagues described in last week’s Science a study of kinship within bands of hunter-gatherers known from ethnographic research Hill:Co-residen...
Population structure within Africa: has "modern human origins" become a non sequitur?
When I wrote about the Denisova genome late last year, I claimed that “A large-scale reorganization of the science of human origins is upon us.”
Neandertal segments of X chromosomes
Last year, this Neandertal genome came out. No doubt you’ve heard about it. So maybe by now you’re wondering where the new science is that’s being done on th...
Mailbag: Y chromosome Adam
Hi John, I enjoy your blog very much. Ive been reading a lot recently on human origins and genetics (most recently, for example, Nicholas Wades book Before...
The Denisova genome FAQ
Today, a paper by David Reich and colleagues presents the nuclear genome of the Denisova pinky bone Reich:Denisova:2010. This is the second whole genome of a...
Open data genomics
Nature this week carries a story by Ewen Callaway titled, “The rise of the genome bloggers”. The main subject is Dienekes Pontikos, whose “Dodecad Ancestry P...
Copy number variation in 1000 Genomes
When I wrote earlier in the week about the 1000 Genomes Project results, I mentioned that a second paper was being published in Science. That paper, by Peter...
Now for anthropological genomics
The first of the papers describing results from the 1000 Genomes project has been released today in Nature 1000Genomes:Nature:2010.
Spatial dispersal, parallel adaptation, and the "Stooge effect"
Peter Ralph and Graham Coop have an interesting paper in the current Genetics, titled, “Parallel Adaptation: One or Many Waves of Advance of an Advantageous ...
French Neolithic discontinuities
Marie-France Deguilloux and colleagues Deguilloux:2010 present a short analysis of ancient mtDNA recovered from a Neolithic burial at Prissé-la-Charrière, be...
More on chimpanzee population structure
A reader reminded me of a second paper on chimpanzee population structure, using a different Bayesian framework, which came out shortly after the study by Jo...
Return of the Neanderchimps
Back in 2005, I reviewed the first description of fossil chimpanzee teeth, from the Middle Pleistocene of the Kapthurin Formation, Kenya, dating to around 50...
Using the Neandertal genome to uncover human evolutionary history
Before the Neandertal genome release last week, I was reading (thanks to a correspondent) an essay that James Noonan wrote for the current Genome Research. T...
African population structure and Neandertal population mixture
Green and colleagues, in their paper describing the Neandertal genome sequence, concluded that some genetic mixture between Neandertals and the contemporary ...
Multiregional evolution lives!
I’m going to point to Rex Dalton’s piece today with relatively little comment:
Selection's genome-wide effect on population differentiation
Alon Keinan and David Reich Keinan:Reich:2010 have tested an obvious prediction of the hypothesis that recent selection has had a major effect on variation a...
Climate reconstruction and human evolution, 2: Tracking climate change
I am examining the pathways that climate might have influenced human evolution, and as I wrote earlier, I’m focusing first on the issue of relatively short-t...
Neandertal races?
There’s a new paper in PLoS ONE by Virginie Fabre, Silvana Condemi and Anna Degioanni, titled “Genetic evidence of geographical groups among Neanderthals.” I...
Local adaptation in population sinks
Different populations of humans live at markedly different densities. Human populations historically have had very different growth rates. Although Pleistoce...
Surfing and recent selection
Genetic Future and Gene Expression have commented today on the relative roles of selection and demography in shaping the genetic differences between populati...
Were ancient Africans divided into small, isolated bands?
Last week when I wrote about the study of African mtDNA variation by Behar and colleagues, I focused on the issue of population size. To me, that must be th...
BROADLY CONSISTENT WATCH II
Looking back through the Chimpanzee Genome Consortium (2005) paper, I find this: