The Unz Review: An Alternative Media Selection
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Human Evolution

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Eurogenes points me to this interesting conference with a book of abstracts, Human Dispersals in the Late Pleistocene - Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens. Below are those of interest to me.... Philipp Gunz Max Planck Institute for Evolutionary Anthropology Leipzig, Germany Evolution and development of the modern human face and... Read More
A new paper in PNAS, Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne, weighs in the question of whether the Châtelperronian culture were Neandertals, with an answer in the affirmative in this case: The details about stratigraphy are beyond me. But the protein and mtDNA
Update Ignore stuff on mutation rate. Confused mutation rate per year with per generation. Moral of story: read more closely! End update The genetic data from the Sima de los Huesos (SH) hominins has finally been published in Nature. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins: A unique assemblage of... Read More
According to a new paper in Nature, Ancient gene flow from early modern humans into Eastern Neanderthals, a basal population of anatomically modern humans mixed with eastern Neanderthal populations on the order of ~100,000 years ago. The figure above is from the paper, and shows (on the left) the proportions and direction of gene flow... Read More
Over at Nature Ewan Callaway has a piece up, Neanderthals had outsize effect on human biology. The upshot is that the few percent of archaic admixture in modern humans, who descend from a Neo-African group ~50,000 years ago, may have significance functionally, and been driven by adaptation. This is not surprising. Greg Cochran and Henry... Read More
Sometimes it is useful to enter into the record what you think, even if it is not fully formed, or even not strongly held. After reading a review on mutational load in human populations, which lingered long over demographic inferences of our species' fluctuations in population size, as well as conversations with Gregory Cochran and... Read More
A quick follow up to my previous post. To recap, a new paper in Science reports high (20-40%) derived frequencies for an allele which seems correlated with higher rates of aneuploidy. Anueploidy is bad, because often it results in nonviable offspring (individuals with Down syndrome have a viable anueploidy). The strange thing about this region... Read More
The above figure is from Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. The author has presented this work at meetings, so I knew it was pending. One of major angles here is that you now have an actionable genotype whereby one can make calculations of likelihood of aneuploidy.. If you... Read More
God knows I would sleep more if it weren't for bioRxiv. A new single author preprint debuts a new method, 3P-CLR, which extends XP-CLR, as a method to detect natural selection. The key is that it uses an explicit three-population tree to pick up selection events after the most recent, and second most recent, divergence... Read More
Humans are a pretty big deal. I'm human, you're human. We're a very successful large mammal. A substantial proportion of the earth's biomass is us, or, is due to us. So the field of human paleoanthropology gets a lot of attention in comparison to something like materials science, even though materials science is far more... Read More
The above is a figure from The genetic legacy of the Mongols, and illustrates the concept of a "star-shaped phylogeny." This is basically a phenomenon where a massively rapid demographic expansion of one particular lineage results in a host of nearly simultaneously mutational events which derive from the ancestral state. It is illustrated by the... Read More
Citation: Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences
Sebastian Lippold, Hongyang Xu, Albert Ko, Mingkun Li, Gabriel Renaud, Anne Butthof, Roland Schroeder, Mark Stoneking
bioRxivdoi: 10.1101/001792
A new paper posted on bioArxiv surveys Y chromosomal and mtDNA diversity using over 600 males from the HGDP data set. Their goal is to compare differences in variation and long term demography between the two sexes. This is not an unimportant topic, sex specific demographics are relevant to mating patterns, and effective population size... Read More
screenshot-from-2013-12-18-184017
A new paper in Nature fleshes out some details about the relationships between Denisovans, Neanderthals, and modern humans, as well as possible others. I believe the figure above gives the flavor of the general findings in terms of phylogenetics, though if you want more I recommend Carl Zimmer in The New York Times. It has... Read More
Pigmentation is one of the few complex traits in the post-genomic era which has been amenable to nearly total characterization. The reason for this is clear in hindsight. As far back as the 1950s (see The Genetics of Human Populations) there were inferences made using human pedigrees which suggested that normal human variation on this... Read More
There is the fact of evolution. And then there is the long-standing debate of how it proceeds. The former is a settled question with little intellectual juice left. The latter is the focus of evolutionary genetics, and evolutionary biology more broadly. The debate is an old one, and goes as far back as the 19th... Read More
Like many people I've been following the tales of the Hobbits of Flores, H. floresiensis, with some interest since 2004. And, like most people I have no personal expertise or skill which is relevant to evaluating whether this putative hominin species actually is a new species (as opposed to a pathological modern human). So how... Read More
As recently as 10 years ago one could plausibly talk about mtDNA Eve and Y chromosomal Adam. The "Human Story" might then be stylized into a rapid expansion from a small core East African population which flourished ~100,000 years ago, and engaged in a jailbreak sweep out of Africa and across the rest of the... Read More
There's an excellent paper up at Cell right now, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. It synthesizes genomics, computational modeling, as well as the effective execution of mouse models to explore non-pathological phenotypic variation in humans. It was likely due the last element that this paper, which pushes... Read More
I have mentioned the PLoS Genetics paper, The Date of Interbreeding between Neandertals and Modern Humans, before because a version of it was put up on arXiv. The final paper has a few additions. For example, it mentions the generally panned (at least in the circles I run in) PNAS paper which suggested that ancient... Read More
If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It's a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the... Read More
Who to trust? That is the question when you don't know very much (all of us). Trust is precious, and to some extent sacred. That's why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was... Read More
Well, not really...but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends: The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It's outlined by Richard Klein... Read More
The always informative Ann Gibbons has a piece in Slate, The Neanderthal in My Family Tree. There is almost nothing new for regular readers of this weblog, but it's rather awesome that Slate is now publishing stuff like this. Many people are simply unaware of the new paleogenomics. Case in point, a good friend who... Read More
New Scientist has a piece up, Europeans did not inherit pale skins from Neanderthals, based on a paper I blogged last month. One thing that I hadn't though about in detail...how did anatomically modern humans of various shades perceive Neandertals of various shades? For example, it seems highly likely that there were swarthy Neandertals and... Read More
John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past... Read More
Over at Haldane's Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up. But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is... Read More
Dienekes Pontikos has a long post up on how reticulation within phylogenetic trees may distort our perception of human natural history when we force the data into a more conventional tree (i.e., bifurcation after bifurcation). The concrete reason for this rethinking is the high probability of "archaic admixture" into the dominant genetic signal of anatomically... Read More
The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It's for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence... Read More
The Pith: the evolution of lighter skin is complex, and seems to have occurred in stages. The current European phenotype may date to the end of the last Ice Age. A new paper in Molecular Biology and Evolution, The timing of pigmentation lightening in Europeans, is rather interesting. It's important because skin pigmentation has been... Read More
There have been several recent studies reemphasizing diet over exercise (timely because Americans are kind of fat, on average). A new piece in The New York Times looking at the Hadza of Tanzania, who are hunter-gatherers, seems to reiterate this point, Debunking the Hunter-Gatherer Workout: We found that despite all this physical activity, the number... Read More
ADMIXTURE and STRUCTURE tests aren’t formal mixture tests. Yes! In fact, in the "open science" community this issue is repeated over and over and over, because people routinely get confused (our audience does not consist of population geneticists and phylogeneticists by and large). So sometimes it is necessary to lay it out in detail as... Read More
Matt Ridley has a column up, Did Your Ancestor Date a Neanderthal? In it he juxtaposes the two recent papers which got some attention on the relationship of modern humans to Neandertals. To be frank I think it took too much of the "two sides/opposing views/views differ" tack. From what I can gather the scientific... Read More
Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here's what Reich said: Here's what Nick Patterson, Reich's colleague told me via email: Ancient structure in Africa was... Read More
Dienekes tips me off to the fact that the long-awaited Reich lab paper on Neandertal admixture dating has finally been put on arXiv! The date of interbreeding between Neandertals and modern humans: This isn't the only group working on the Neandertal genomic admixture story. From reading his blog you probably know that John Hawks is... Read More
Dienekes reflects on the seemingly simultaneous appearance of behavioral modernityin South Africa and Europe and Australia, pending the acceptance of the most recent finds. This part is very important in my opinion: I see no reason to think that these were the ancestors of the San. Over 45,000 years I think the most likely option... Read More
If you are interested in genomics and human evolution, a new review paper in PLoS Genetics is a must read, Genomic Data Reveal a Complex Making of Humans. A must read not because you need to agree with the thrust of the authors' arguments, but because it provides a thorough bibliography for the last 2... Read More
Forgot to highlight one of the coolest abstracts from SMBE 2012, A genomewide map of Neandertal ancestry in modern humans: One of the predictions of assimilation of a large intrusive population with a small but long endemic population is that there will be biased representation of adaptive alleles from the latter into the former. In... Read More
Over the years one issue that crops up repeatedly in human evolutionary genetics and paleoanthropology (or more precisely, the popular exposition of the topics in the media) is the idea that is that "population X are the most ancient Y." X will always refer to a population within a larger set, Y, which is defined... Read More
The new article in The American Journal of Human Genetics, A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root, is open access, so you should check it out. The discussion gets to the heart of the matter: Supported by a consensus of many colleagues and after a few years of hesitation, we... Read More
The face is an important aspect of our phenotype. So important that facial recognition is one of many innate reflexive cognitive competencies. By this, I mean that you can recognize a face in a gestalt manner, just like you can recognize a set of three marbles. You don't have to think about it in a... Read More
There's a report in Science about a new short paper about Neandertal pigmentation genetics. The context is this. First, in 2007 an ingenuous paper was published which inferred that it may be that Neandertals had red hair, at least based on an N = 2 from two divergent locations. The new study looks at three... Read More
The title is tongue in cheek. But I have been noting with interest Dienekes' trial runs with TreeMix. With it he has discovered a very peculiar admixture event, at least as determined by the software. The results are below, with my clarifying labels: Basically the software seems to be implying that there has been gene... Read More
Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there's a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow... Read More
Several people have emailed me about the Solutrean hypothesis. The trigger is the publication of Across Atlantic Ice: The Origin of America's Clovis Culture. To my surprise this has received a lot of media attention. The Washington Post, io9, and The New Scientist. Granted, the coverage has been appropriately skeptical. But it still gets to... Read More
After my post on the 'race question' I thought it would be useful to point to Jerry Coyne's 'Are there human races'?. The utility is that Coyne's book Speciation strongly shaped my own perceptions. I knew the empirical reality of clustering before I read that book, but the analogy with "species concept" debates was only... Read More
Well, the paper is finally out, New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. In case you don't know, Ötzi the Iceman died 5,300 years ago in the alpine region bordering Austria and Italy. His seems to have been killed. And due to various coincidences his body was also... Read More
There's a new paper out, Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. The primary results are above. Basically, using 13 mtDNA samples the authors conclude that it looks as if there was a founder effect for Neanderthals in Western Europe ~50 K years ago, generating a very... Read More
There has been a lot of talk in the media about a new paper which reports that the Y chromosome is not deteriorating, as had been previously inferred from the data. In the 2004 Bryan Sykes wrote Adam's Curse: A Future Without Men which used this model as a framing device (and naturally elicited great... Read More
In The New York Times, DNA Turning Human Story Into a Tell-All: First, for reasons of novelty we are emphasizing the exotic tendrils of the human family tree. Even Chris Stringer, the modern paleontological father of "Out of Africa," is claiming we're hybrids! But let's not forget that non-Africans are the product of a very... Read More
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"