Tag: Human Evolution

The sons of Adam: spirit, not blood

By Razib Khan | December 26, 2011 3:08 pm


Hominin increase in cranial capacity, courtesy of Luke Jostins


A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:

The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….

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The arc of primate social evolution

By Razib Khan | December 21, 2011 2:02 pm

A new paper in Nature, Stepwise evolution of stable sociality in primates, was written up in The New York Times with the provocative title, Genes Play Major Role in Primate Social Behavior, Study Finds. As noted in Joan Silk’s article on the paper it should really be phylogenetics play major role in primate social behavior. The model outlined in the paper indicates that phylogenetic relationships between major primate clades is a much better predictor of social organization and structure than simple adaptation to a specific environment, or a linear increase in social organization (group size) over time. Both of these latter dynamics would also be driven by genetic changes, and therefore tie “genes” to social behavior. In other words, genes always matter, it’s just how they matter that differs. Here’s the section of the abstract of the paper of major interest:

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Out of Africa to Out of Arabia

By Razib Khan | December 20, 2011 3:13 pm

Dienekes and Greg Cochran have been talking about this possibility for a few years. But a combination of archaeological finds and the current unsettled nature of the human evolutionary genomics literature means that “Out of Arabia” is a real possibility (not laugh-out-loud crazy and weird). So I took the liberty of cooking up a new design for the RichardDawkins.net website. Science is about updating our prior assumptions, so it shouldn’t be too much of an issue. What I wonder: how would the population of the Kingdom of Saudi Arabia feel about replacing Ethiopia and Kenya in human evolution documentaries? Addendum: To be clear, this isn’t to say I accept “Out of Arabia” for the origin of most modern humans, including within Africa. Rather, I think it’s not a crazy idea anymore, especially in light of the weird results which imply that West Africans may be genetically closer to non-Africans than to Pygmies and San (and it would make more sense of older uniparental results which imply back-migration from Eurasia into Africa).

CATEGORIZED UNDER: Evolution, Human Evolution

Culture evolves our bodies!

By Razib Khan | December 20, 2011 2:46 pm


Human cultural diversity


One of the most annoying aspects of talking about human evolution is the rather misguided idea that cultural evolutionary processes operate in a zero-sum environment in relation to biological evolutionary processes. The colloquial rendering of this idea is that because humans are a highly cultural plastic species, we are “beyond” biological evolution. Many researchers though suspect that on the contrary, because of cultural variation and plasticity we may be buffeted by even greater evolutionary pressures than is the norm for a relatively slow-breeding species with a small effective population size. Probably the best example of this is the ability of adults in several human populations to digest lactose sugar. This is, to not put too fine a point on it, a freak ability. Why would a mammal need to digest milk sugar as an adult after all? Well, you know why, the human mammal is wont to consume the milk of other mammals, which it has taken into bondage. Viewed from the outside the whole process is rather weird and Frankenstein-like, but we’ve been habituated to the normalcy of this sort of thing because of the diversity of cultural forms on evidence in H. sapiens (though in some societies the initial exposure to the fact that Europeans, for example, consume milk and milk products into adulthood was perceived to be highly strange).

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CATEGORIZED UNDER: Anthroplogy, Human Evolution

Modern humans in Arabia >100,000 years ago

By Razib Khan | November 30, 2011 5:49 pm

The genetic model of the “Out of Africa” scenario is getting more complex. There may be two waves, as well as the likelihood of admixture between the Neo-Africans and “archaic” hominins, such the Neandertals and Denisovans. From what I can gather the genetic evidence is now converging upon the sequence of events where African populations diverge >100,000 years ago (e.g., a deep separation between the ancestors of the Bushmen and the ancestors of West Africans), and a radiation of non-Africans at most ~75,000 years ago, and more likely ~50,000 years ago. There are still many holes to be plugged in. While we’re waiting on genetics, here’s an interesting paper using archaeological methods in PLoS ONE, The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia:

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Man is the environment of the rat

By Razib Khan | November 25, 2011 3:58 pm


The above is a figure from a new paper in PLoS ONE, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. Here’s the abstract:

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

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CATEGORIZED UNDER: Evolution, Human Evolution

Are most people "behaviorally modern"?

By Razib Khan | November 6, 2011 7:06 pm

Paintings at Lascaux, Prof saxx


Behavioral modernity:

Behavioral modernity is a term used in anthropology, archeology and sociology to refer to a set of traits that distinguish present day humans and their recent ancestors from both living primates and other extinct hominid lineages. It is the point at which Homo sapiens began to demonstrate a reliance on symbolic thought and to express cultural creativity. These developments are often thought to be associated with the origin of language.

First, I’d like to put into the record that I suspect that Neanderthals had language as we’d understand it. I suspect within the next few decades genomics may clarify the issue, because people with congenital linguistic defects will probably be sequenced to the point where we’ll get a sense of all the many regions of the genome necessary for language competency. We can then crosscheck that against the Neanderthal genome. So let’s take that off the table, even if it’s under dispute.

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MORE ABOUT: Human Evolution

How Archimedes' lever explains human evolution

By Razib Khan | November 5, 2011 6:38 pm

Last August I had a post up, The point mutation which made humanity, which suggested that it may be wrong to conceive of the difference between Neanderthals and the African humans which absorbed and replaced them ~35,000 years ago as a matter of extreme differences at specific genes. I was prompted to this line of thinking by Svante Pääbo‘s admission that he and his colleagues were searching for locations in the modern human genome which differed a great deal from Neanderthals as a way through which we might understand what makes us distinctively human. This sort of method has a long pedigree. Much of the past generation of chimpanzee genetics and now genomics has focused on finding the magic essence which differentiates us from our closest living relatives. Because of our perception of massive phenotypic differences between H. sapiens and Pan troglodytes the 95-99% sequence level identity is thought by some to be perplexing. Therefore models have emerged which appeal to gene regulation and expression, or perhaps other forms of variation such as copy number, to clear up how it can be that chimpanzees and humans differ so much. Setting aside that the perception of difference probably has some anthropocentric bias (i.e., would an alien think that chimpanzees and humans are actually surprisingly different in light of their phylogenetic similarities? I’m not so sure), it doesn’t seem to be unreasonable on the face of it to plumb the depths of the genomes of hominids so as to ascertain the source of their phenotypic differentiation.

But can this model work for differentiating different hominin lineages? Obviously there’s going to be a quantitative difference. The separation between chimpanzees and modern humans is on the order of 5 million years. The separation between Neanderthals and modern humans (or at least the African ancestors of modern humans ~50,000 years B.P.) is on the order of 500,000 years. An order of magnitude difference should make us reconsider, I think, the plausibility of fixed differences between two populations explaining phenotypic differences.

 

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The modern human coordination miracle

By Razib Khan | October 17, 2011 12:10 am

Thanks to Ed Yong several people on twitter have encountered my post, The point mutation which made humanity. My broader concern which I was attempting to highlight is that too often when we attempt to ascertain the origins of modern human success in relation to our archaic cousins/ancestors we presume that there must be a qualitative species-wide difference. So, for example, it used to be bandied about that a large effect mutation conferred upon the ancestors of modern humans the ability to speak with the fluency which we take for granted. For various reasons that seems less and less plausible.

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CATEGORIZED UNDER: Evolution, Human Evolution

The last 100,000 years in human history

By Razib Khan | September 25, 2011 8:02 pm

In light of the recent results in human evolutionary history some readers have appealed to me to create some sort of clearer infographic. There’s a lot to juggle in your head when it comes to the new models and the errors and uncertainties in estimates derived from statistical inference. Words are not always optimal, and there’s often something left out.

So I spent a few hours creating a series of maps which distill my own best guess as to what occurred over the past 100,000 years. I want to emphasize that this purely my own interpretation, based on what I know. This is naturally going to be biased (I don’t know as much about uniparental lineages as some of my readers, and have a weak grasp of a lot of morphological changes, etc.). But it is a place to start. I’ve put the maps into a slideshow. Please observe that in brackets I’ve put qualifies such as “high”, “medium” and “low” in regards to my assertions. That shows you how confident I am about a given assertion. I’m 100% sure that I’m wrong in a lot of the details here, but this is my best guess as to the shape of things over the past 100,000 years. Feel free to ask more in the comments. Also, take the dates with a little fudge room. If I used exact precise dates for everything there would be too many slides.

Note: You can’t see the slideshow in the RSS browser.

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Out of Africa onward to Wallacea

By Razib Khan | September 22, 2011 1:56 pm


There are two interesting and related papers out today which I want to review really quickly, in particular in relation to the results (as opposed to the guts of the methods). Taken together they do change our perception of how the world was settled by anatomically modern humans, and if the findings are found to be valid via replication (I think this is likely, in at least some parts) I was clearly wrong and misled others in assertions I made earlier on this weblog (more on that later). The first paper is somewhat easier to parse because it is in some ways a follow up on the paper from 2010 which documented admixture into Near Oceanian (Melanesian + Australian Aboriginal) populations from a distant hominin lineage, the Denisovans.

In this paper in The American Journal of Human Genetics they extend their geographic coverage. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania:

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

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The end of "archaic" H. sapiens

By Razib Khan | September 18, 2011 4:30 pm

The Pith: The Bushmen branch of the human family tree diverged ~130,000 years ago. The non-Africans branched off from the Africans ~50,000 years ago. The Europeans and East Asians diverged ~35,000 years ago.

One of the terms in paleoanthropology which can confuse is that of archaic Homo sapiens (AHS). This is in contrast to anatomically modern humans (AMH). A simple Out of Africa “recent-origin-with-replacement” model allowed to sidestep the semantic imprecision in tossing disparate populations into a generic category such as AHS (similarly, the term “animal” as opposed to “human” has some colloquial utility, but it’s not scientifically useful). But the possibility of admixture from archaic lineages in modern human populations forces us to grapple with the dichotomy between AHS and AMH, as modern humans may be a compound of these two categories (not to mention the idea of behaviorally modern humans, who are a subset of AMH).

I assume that fleshing out the details of a new paradigm which is both precise and accurate will be a project for the coming years. But before we move on we need to fix more sturdily our understanding of the genealogical relationships of contemporary human populations. Over the past few years there have been major strides in this domain, confirming the broad outline of a dominant African heritage for modern humans. Geneticists have moved from classical markers to SNP data, focusing on hundreds of thousands of genetic variants. But now they’re shifting to whole genome sequences, which with errors excepted encapsulate the totality of the lowest order aspect of human genetic variation.* Earlier this summer I reviewed a paper in Nature which was a foretaste, Inference of human population history from individual whole-genome sequences. Today Nature has published another, Bayesian inference of ancient human demography from individual genome sequences.

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Out of Africa's end?

By Razib Khan | September 17, 2011 12:54 pm

The BBC has a news report up gathering reactions to a new PLoS ONE paper, The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology. This paper reports on remains found in Nigeria which date to ~13,000 years B.P. that exhibit a very archaic morphology. In other words, they may not be anatomically modern humans. A few years ago this would have been laughed out of the room, but science moves. Here is Chris Stringer in the BBC piece:

“[The skull] has got a much more primitive appearance, even though it is only 13,000 years old,” said Chris Stringer, from London’s Natural History Museum, who was part of the team of researchers.

“This suggests that human evolution in Africa was more complex… the transition to modern humans was not a straight transition and then a cut off.”

Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.

They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought.

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When all probable things can not be right

By Razib Khan | September 14, 2011 8:35 pm

I’ve been chewing on the modern human range expansion into Neandertal territory paper for a few days now. But I haven’t been able to bring myself to say much. There are two reasons. First, it’s a simulation paper, and I don’t exactly know what I can say besides being skeptical of the plausibility of some of their results and their assumptions, unless I bother to replicate their simulations. There’s something of a “black-box” aspect from the outside operationally in the case of these sorts of research. Second, Ed Yong has boiled down the paper to its essence rather well, while John Hawks and Dienekes have offered their critiques. Dienekes and John get at one of my gnawing worries about all these sorts of models about deep history. Here’s John:

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Of beasts and men

By Razib Khan | September 5, 2011 9:23 pm

“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”

Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?

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Africans aren't pure humans either

By Razib Khan | September 5, 2011 3:38 pm

Last year when discussing the possible admixture of Neandertals with the ancestors of modern non-Africans I joked that Sub-Saharan Africans were “pure humans.” This was tongue-in-cheek in part because the results from the Neandertal genome shifted my assessment of the probability of archaic admixture within Africa as well. In other words, there may never have been a pure “human” type which expanded and assimilated archaic ancestry on the margins of its range. Species Platonism may be very misleading for our particular lineage. Rather, what it means to be human has always been in flux, a compromise between extremely different ancestral components.

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The divisibility of human ancestry

By Razib Khan | August 25, 2011 6:05 pm

The class human or H. sapiens refers to a set of individuals. On the grand scale it’s really not all that clear and distinct. When do “archaic” humans become “modern” humans? Taking into account human variation, what is a “human universal”? A set of organisms are given a name which denotes the reality that they may share common ancestry, and interact behaviorally, and are potential mates. But many of these phenomenon are fuzzy on the margins. Many of the same issues which emerge in the “species concept” debates are rather general up and down the scales of natural complexity. A similar problem crops up when we conflate the history of genes with the history of populations. Such a conflation has value and utility to a first approximation. The story of mitochondrial Eve was actually the history of one particular locus, the mitochondrial genome. But it did tell us quite a bit about the history of the human species, even if in hindsight it looks as if some scientists overinterpreted those findings. One of the major issues I’ve noticed over the past year, with the heightened likelihood of archaic admixture in the modern human genome, is that people regularly get confused by the difference between total genome ancestry, and the evolutionary history of one particular gene.

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Old Man's Culture

By Razib Khan | August 3, 2011 12:51 am

too

A few readers reminded me of the recent Rachel Caspari article in Scientific American, The Evolution of Grandparents. It’s actually based on her earlier research, published in PNAS in 2004, Older age becomes common late in human evolution. I was already pointed to this paper by Milford Wolpoff, who seems to be of the opinion this is a very underappreciated dynamic in our species’ history (note: he’s married to Caspari). And Wolpoff sent me a copy of the Scientific American article too, so it’s been in my “to read” folder for a bit.

Honestly it’s a lot more persuasive than the scientific paper because it’s so non-technical. It really makes me appreciate the power of science communication. I don’t know anything about the analysis of dental remains, so I really hummed along through a lot of the paper with minimal comprehension. With the article Caspari could present her results and interpretation more cleanly.

The major finding in the PNAS finding, which is reported in the Scientific American article, is the ratio of parents to grandparents in a total sample of ~750 remains separated by population class varies a great deal. Parents here means those who are 15-30 years old in age, and grandparents are those who are 30+ years in age. The major qualifier here is obviously potential, but that’s a side issue. What the authors found in their sample was quite striking: notice the huge qualitative shift when you move to a population set of Upper Paleolithic behaviorally modern humans (less than 50,000 years before the present). In contrast, the European Neandertals much more resemble the larger collection of archaic Homo (most of which would presumably have been termed “archaic H. sapiens” in the past because they span 50 to 150,000 years B.P.). This still leaves the question of whether this is nature or nurture is left hanging.

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CATEGORIZED UNDER: Anthroplogy, Culture, Human Evolution

Why the human X chromosome is less diverse

By Razib Khan | July 25, 2011 12:37 am

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 differences in the power of natural selection across those populations.

In the past few years there has been a finding that the human X chromosome exhibits less genetic diversity than the non-sex regions of the genome, the autosome. Why? On the face of it this might seem inexplicable, but a few basic structural factors derived from the architecture of the human genome present themselves.

First, in males the X chromosome is hemizygous, rendering it more exposed to selection. This is rather straightforward once you move beyond the jargon. Human males have only one copy of genes which express on the X chromosome, because they have only one X chromosome. In contrast, females have two X chromosomes. This is the reason why sex linked traits in humans are disproportionately male. For genes on the X chromosome women can be carriers of many diseases because they have two copies of a gene, and one copy may be functional. In contrast, a male has only a functional or nonfunctional version of the gene, because he has one copy on the X chromosome. This is different from the case on the autosome, where both males and females have two copies of every gene.

This structural divergence matters for the selective dynamics operative upon the X chromosome vs. the autosome. On the autosome recessive traits pay far less of a cost in terms of fitness than they do on the X chromosome, because in the case of the latter they’re much more often exposed to natural selection via males. In the rest of the genome recessive traits only pay the cost of their shortcomings when they’re present as two copies in an individual, homozygotes. A simple quasi-formal example illustrates the process.

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How did modern humans settle the world?

By Razib Khan | July 9, 2011 11:47 pm

In lieu of lots of text, above is a stylized representation of the routes which Neo-Africans took ~50 thousand years ago from their point of departure to parts unknown. The two colors represent two models. The red lines show two major streams issuing out of Africa, a northern route which pushed into the heart of Central Asia, and a southern oceanic one, which pushed all the way into Australia. The second differs, with eastern and western branches of non-African humanity. The models really start to break down within the last ~10,000 years. For example, by either model India has seen an admixture even between the two branches in the Holocene. Additionally, there may have been “false dawns” and admixtures.

In the early 2000s I accept the probable likelihood of the first model. But today I am more leaning toward the second. What’s your stance, and why? I’ll give my rationale below….

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