Guy got a lot of big names in paleoanthropology and archaeology to comment on his latest Smithsonian piece, “The Great Human Migration.” You may recognize Tim White and Ofer Bar-Yosef among the many he’s interviewed. Guy summarizes some major sites and recent finds, such as the artistic and symbolic nature of early Homo sapiens seen in the 164,000 years old artifacts from Pinnacle Point, South Africa and the 77,000 year old shell beads BlombosCave, also in South Africa. Guy also offers up a physical comparison of Homo sapiens to other hominids, such as Neandertals. He reviews both older and current genetic evidence on the evolution of humans.
You should read it if you don’t know much about paleoanthropology and other disciplines related to the evolution of modern humans and are interested in the subject. Guy synthesizes many different fields, from archaeology to paleontology to genetics, and offers up a pretty succint and clear review of what know about how modern humans got to where we are now.
PLoS Genetics has published a new population genetics paper. It summarizes the order by which the world was peopled through the use of a new statistical model. This has been a big question in anthropology, and has often relied on archaeology, linguistics, and ethnography to supplement the genetic and physical data. I don’t mean to imply that the question has been completely answered with this new paper — but it is a new approach to asking a very critical question.
The paper is titled, “Inferring Human Colonization History Using a Copying Model.” This study is based off of inheritance patterns of 2,000 SNPs from the Human Genome Diversity Project (HGDP) dataset from 2006. The dataset comes from 927 individuals from 53 different populations. Not all populations are included in this dataset, so there are gaps… But for any anthropologist out there who is interested with the tempo certain human populations radiated as well as their ancestry patterns, this open access paper is a must read.
The new “copy model” resolves much finer details because it compares the structure of chromosomes — i.e. how the haplotypes spread on a chromosome are inherited. This makes it possible to delve further back in time and identify smaller genetic contributions. You may know that other models have resorted to single loci, such as the Y-chromosome or mtDNA. It has been argued that these models oversimplify heredity. By analyzing shared parts of chromosomes across the entire human genome, the researchers believe their method can cope with much larger datasets, suggesting that over 500,000 genetic markers can be compared and contrasted in the future.
This paper has yielded both consistent and surprising results. For starters, the results are right inline with the Out of Africa model. In the video clips below, you can see that for yourself
Did you noticed that the San are the beginning population? That’s obviously because the San of Southern Africa are the first population in the ordering of chromosomes. According to Spencer Wells, the San are one of the oldest, if not the oldest, peoples in the world based upon the Y-chromosome. Exactly one month ago, a study of mitochondrial genetic diversity within Africa kinda challenged this claim. But because this study used the HGDP dataset from 2006, the results are restricted to the populations included in the sample. The San gave rise to the Biaka, Bantu, and Mbuti populations which are all below the Sahara.
The last lineage to arise in Africa are the Mozabites, and based upon the 2,000 SNPs they have less in common with other African populations than the others African populations have with themselves. The authors suggest that this observation is because there was a bottleneck in the Mozabites that is not shared by any other African population.
The Mozabites gave rise to all the Central Eurasian populations in the HGDP sample. The Mozabites also gave rise to the Central European populations. The first three populations to arise in Europe are the French, Tuscans, and Italians. Several Near Eastern and Central Asian populations also contributed to the peopling of Central Europe.
East Asians have an entirely distinct source of ancestry from European peoples. The Uygurs and Hazara gave rise to Cambodian, Mongolian, Oroquen, Xibo, Yi, Tu, Daur, and Naxi people of East Asia. The Han also received their ancestry from the Xibo and other populations. Just how distinct is this cut-off? Well, less than 10% of Europeans show ancestry from the Uygurs. Almost no Europeans show ancestry from the Hazara. The authors suggest that this observation is because the East Asian populations were established independently from Europeans and only relatively recent admixture has affected the 10% Uygur-ness in European populations.
Many populations in Europe have exhibited distinct genetic, cultural, and linguistic traits such as the Basque. This study has shown that the Sardianians, Russians, Orcadians, and the Basque show strong similarities to other Europeans — but have a lot more Near Eastern and Central Asian ancestry markers than other Europeans. For example, the Basque show some of their ancestry come from the Hezhen, a far Eastern population.
The Pacific Islanders receive ancestry from the Melanesians and Cambodians — not surprising. The first Native American populations (the Colombians) share ancestry to the Hazara, Han, and Xibo, also not surprising. But since modern people were screened, the Colombians show European ancestry — it is most likely because of the outstanding European occupation of the Americas in the last 500 or so years.
The somewhat surprising finding (at least surprising to the authors, editors of the paper, and apparently the bloggers at the Spittoon) is that there’s strong Mongolian ancestry signal in the Pima people. This is distinctly differently from the Colombians, who have a much different ancestry. The authors write that this suggest independent waves of migration in the Americas which contradicts ‘the current consensus.’
I believe that this statement should be revised because a more recent paper, published after this current paper was submitted, suggests that the Americas was peopled in multiple waves. I’m kinda surprised the editors didn’t catch this. I’m also surprised the the bloggers behind the Spittoon, the 23andMe blog, didn’t catch this. They are in the population genetics and personal genomics business, I expect them to keep current on their literature. Anyways, I was talking to Razib about this and he suggested if some sort of Na-Dene phenomenon could be happening. Definitely possibly… what do you think?
Inferred history of chromosomes for individual populations
Each frame shows the path that chromosomes took from their origin in Southern Africa in reaching the population labelled in each frame. The width of each line indicates the proportion of the chromosomes that travelled by that route, with the diameter of the circle indicating the total proportion of chromosomes that went via that location (diameter of San = 1.0). Values were estimated recursively, working backwards from the labelled population to the first by assuming that the amount of genetic material passed on by each population was proportional to the number of donor individuals it contributed. Click to see the original movie in high res.
This paper is not the first to work around the single loci comparison critique, but it is successful and provides a template for others to work on. I’m really interested to see this same model applied to more SNPs and more populations.
Hellenthal, G., Auton, A., Falush, D., Przeworski, M. (2008). Inferring Human Colonization History Using a Copying Model. PLoS Genetics, 4(5), e1000078. DOI: 10.1371/journal.pgen.1000078
Dienekes, Blaine, Razib, and Simon have all chimed in introducing us to a new paper from the American Journal of Human Genetics. It seems like a really interesting one, one that takes mtDNA to construct a phylogeny used to investigate what was happening to early Homo sapiens genetic diversity and populations within Africa. This study focuses on what was going on before the migrations out of Africa. The paper is titled, “The Dawn of Human Matrilineal Diversity,” and is open access. The research has already made it all the way onto some of my favorite news sources, such as Digg and Slashdot, but the big timers like CNN, BBC, the Economist, and the AFP are also carrying word.
The researchers constructed a mitochondrial phylogeny of 624 sub-Saharan individuals. They paid close attention to what’s going on with the phylogeny of the Khoisan, because previous research like Knight et al.‘s study on another loci, the Y-chromosome has shown that the Khoisan are carriers of oldest-diverging Y haplogroup, the Y-haplogroup A, indicating they may represent the deepest clade of modern humans. Recent research identified that the pygmy Khoisan populations share an ancestral and indigenous lineage of mtDNA with a neighboring population, the Bantu and this new study confirmed this.
The phylogenetic tree in this newer study is really informative. I’ve included it to the right. The researchers honed in on the mitochondrial haplogroup L, which is one of the oldest mtDNA haplogroups out there. The tree shows that early humans split into two small groups, demarcated by the L0 branch splitting from the L1’5 branch around 140,000 years ago. Based upon these two branches, the researchers were able to identify that one group was concentrated around eastern Africa (the L1’5 branch), while the other, the Khoisan’s L0 branch, in southern Africa. The sub-branches within the L1’5 clade represent all of the other L haplotypes in the entire remainder of humanity, including haplogroups of those that left Africa… further suggesting east Africa peoples were the main migrators out of Africa.
How could this happen? As populations of early humans migrated within Africa and reached southern Africa, they were cut off from the eastern African populations for a significant period of isolation to diverge into two separate clades. From ScienceDaily,
“Recent paleoclimatological data suggests that Eastern Africa went through a series of massive droughts between 135,000-90,000 years ago. It is possible that this climatological shift contributed to the population splits.”
The press is suggesting that this phenomenon indicated humans “started down the path of evolving into two separate species.” But that’s not true, they missed the part of the paper where populations came back together as a single, pan-African population about 40,000 years ago.
But, something is a little fishy, because as I already indicated, the coalescence calculations in this new paper indicate the Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool about 140,000 years ago. At that time, the five additional, currently extant maternal lineages (Haplogroups L1’5) existed in Eastern Africa, before the emergence of L0 branch. Looking at the phylogenetic tree, these haplogroups are more ancestral to the haplogroup L0 branch by at around 40,000 years, implying that the Khoisan may not be the deepest clade of living humans alive. This doesn’t match the Y-chromosome data, but we know already that mtDNA and Y-chromosome coalescent times aren’t the same… but this doesn’t match scores of other studies that indicate the Khoisan are a basal group of humans based off of their linguistic and cultural traits.
What this ultimately indicates is that eastern Africa may have truly been the cradle of humanity, at least the maternal cradle of modern humans. Which matches the fossil record, since some of the oldest remains of early human remains are also found in Eastern Africa, such as BOU-VP-16/1 and Omo 1 from Ethiopia.
BEHAR, D., VILLEMS, R., SOODYALL, H., BLUESMITH, J., PEREIRA, L., METSPALU, E., SCOZZARI, R., MAKKAN, H., TZUR, S., COMAS, D. (2008). The Dawn of Human Matrilineal Diversity. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2008.04.002
KNIGHT, A. (2003). African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages. Current Biology, 13(6), 464-473. DOI: 10.1016/S0960-9822(03)00130-1
Quintana-Murci, L., Quach, H., Harmant, C., Luca, F., Massonnet, B., Patin, E., Sica, L., Mouguiama-Daouda, P., Comas, D., Tzur, S., Balanovsky, O., Kidd, K.K., Kidd, J.R., van der Veen, L., Hombert, J., Gessain, A., Verdu, P., Froment, A., Bahuchet, S., Heyer, E., Dausset, J., Salas, A., Behar, D.M. (2008). Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proceedings of the National Academy of Sciences, 105(5), 1596-1601. DOI: 10.1073/pnas.0711467105
Now that I’m finally feeling a bit better, I feel really motivated to blog about these papers. I’ll be focusing on the copy number variation Nature paper as well as the variation and relationship of worldwide human populations Science paper, since they come to similar results but from different approaches. I’ll briefly touch on the deleterious genetic variation Nature paper, because it integrates a key concept into the fold.
Before I get into the thick of it, I wanna give a quick run down on a basic population genetic concept, linkage disequilibrium, because it is screened in all of these papers. It is crucial to understand this concept because it is what is fundamentally what is studied in nearly all population genetic studies. Okay, I’m sure you understand the importance… For any given gene, a sequence of DNA that is transcribed there could exist more than one variant or alleles. These alleles can differ from one another in many different ways, but for simplicity’s sake, we’ll consider only single nucleotide polymorphisms (SNPs) today. SNPs are differences in the same sequence of DNA between two or more alleles in only one base pair.
If SNPs exist in coding regions of a gene, they can be synonymous or nonsynonymous mutations. Mutations may have a bad connotation to you, and I’ll explain how synomymous mutations aren’t necessarily bad. The genetic code has a lot of redundancy; every three nucleotides that are in frame, may encode for an amino acid… but since there’s only 20 different amino acids but 64 different combinations of three nucleotides, some combinations encode for the same amino acid. Thus, if a SNP mutation exists in a coding region, but the two variants do not encode for different amino acids, the mutation is called a synonymous mutation. A nonsynonymous mutation can be more impactful, because in this situation, one of the SNPs alter the three base pair codon, and encode for a different amino acid that can change the structure and function of the resultant protein. Does this mean all nonsynonymous mutations are deleterious? No, often the amino acid difference isn’t that big and the protein’s function isn’t changed much… some other times the mutation can be dramatic and create a totally different protein, knocking down or out a cascade of functions the cell, tissue, organ, etc. maybe reliant upon.
SNPs can be inherited, if you didn’t know. Often they are inherited in long blocks, and that’s because of a unique phenomenon called homologous recombination. Homologous recombination occurs during DNA replication, when overlapping segments of DNA have two homologous regions which swap out with one another. I won’t get into the gory details, but it is really cool! If this occurs during meiosis, during gamete formation, the organism that develops from the recombined gametes inherits blocks of SNPs. The length of DNA that travels with a SNP during recombination varies dependent on how ‘new’ the SNP is. Newer SNPs fall in long areas of recombinant DNA, whereas older SNPs travel in shorter areas. People study the length of DNA associated with a SNP to determine ages of new alleles. The difference between lengths of DNA that travel with SNPs is ultimately what is linkage disequilibrium. I won’t get too into haplogroups, other than the situation when one or more SNPs travel together.
Okay that being said, I hope you have a general understanding of what’s happening at a molecular level to makes us vary in segments of DNA. These variations can be used to study our similarities and differences, figure out who came from whom, etc. The first of the papers that I wanna focus in on is Nature‘s “Genotype, haplotype and copy-number variation in worldwide human populations.” The authors of that study took about 526,000 SNPs and 400 copy number variations (the differences in the number of copies of a gene in the genomes of different people) found in 485 people from about 30 different populations. They observe that larger linkage disequilibrium is found in populations that are farther away from Africa? The indicates these “far from Africa” populations are newer compared to African populations, which suggest that African populations are ancestral to outside populations.
Next up to bat is the Science paper on the same topic. This paper one-ups the other in that it has more SNPs (650,000) from 938 people from 51 different populations. It is, as the authors quote, “the most comprehensive characterization to date of human genetic variation.” With more data, the authors were able to reconstruct a phylogenetic tree based upon genetic relationships. I consider the figure they were able to draw up a poster-board example for the Out of Africa hypothesis on human origins, even though I acknowledge John Hawks’ critique that this figure “assumes an Out of Africa” model of human migration, and tells us nothing on the mode and time when this migration occurs. What John Hawks points out is a problem with cladistics. In this study the authors establish an outgroup, the most ancestral group, which happens to be Africa. Thus, they force the phylogenetic tree to pattern as if Out of Africa happened. I don’t think their aim is to show us the timing of the out of Africa event, though, it is merely supposed to document a shared ancestry in Africa.
And here’s where I transition to the last paper, the Nature one on deleterious mutations are more prominent in a newer population, Europeans compared to Africans. This paper, “Proportionally more deleterious genetic variation in European than in African populations” kinda gives us a relative date that Hawks criticizes for. Once, newer populations, ones that are founded by comparatively smaller groups, occupy a niche and expand in populations size — mutations manifest bountifully. Mutations again, can be deleterious as well as advantageous, and in Europeans, a population that’s newer, negative selection has had less time compared to African populations to remove deleterious alleles from European populations.
I’m really happy these three papers came out when they did. Fresh on my mind, is still that one discussion on human genetic identity and human genetic variation. Ancestry and identity are two terms that often get muddled into easily digestible public relations burrito many anthropologists have been fed. There’s a real genetic basis for groups, we haven’t really known about it until now. Part of that has been because we’ve focused on identifying genetic ancestry in one or two loci, such as mtDNA and Y-chromosome, before. Now with more and more SNPs identified, we can point out unique ancestry markers with much greater resolution and begin to understand how our ancestry is structured genetically.
Jakobsson, M., Scholz, S.W., Scheet, P., Gibbs, J.R., VanLiere, J.M., Fung, H., Szpiech, Z.A., Degnan, J.H., Wang, K., Guerreiro, R., Bras, J.M., Schymick, J.C., Hernandez, D.G., Traynor, B.J., Simon-Sanchez, J., Matarin, M., Britton, A., van de Leemput, J., Rafferty, I., Bucan, M., Cann, H.M., Hardy, J.A., Rosenberg, N.A., Singleton, A.B. (2008). Genotype, haplotype and copy-number variation in worldwide human populations. Nature, 451(7181), 998-1003. DOI: 10.1038/nature06742
Li, J.Z., Absher, D.M., Tang, H., Southwick, A.M., Casto, A.M., Ramachandran, S., Cann, H.M., Barsh, G.S., Feldman, M., Cavalli-Sforza, L.L., Myers, R.M. (2008). Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Science, 319(5866), 1100-1104. DOI: 10.1126/science.1153717
Lohmueller, K.E., Indap, A.R., Schmidt, S., Boyko, A.R., Hernandez, R.D., Hubisz, M.J., Sninsky, J.J., White, T.J., Sunyaev, S.R., Nielsen, R., Clark, A.G., Bustamante, C.D. (2008). Proportionally more deleterious genetic variation in European than in African populations. Nature, 451(7181), 994-997. DOI: 10.1038/nature06611
If you didn’t catch this the first time I brought it up in September, the quick one sentence summary is these studies focused on evidence of ancient megadroughts from sediments cored from the bottom of Lake Malawi and comparing those findings with similar records from Lakes Tanganyika and Bosumtwi.
After a whole lot of logistical challenges, the team extracted a series of cores, some as much as 1247 feet (380 meters) long that spanned hundreds of thousands of years. Cores like these give a high level of resolution into the prehistoric ecology. Often oceanographers and climatologists use cores like these to study the diversity of plankton, aquatic invertebrates, etc. to reconstruct the flora and fauna at particular point in time. The authors found indicators of drought present in the cores from sampling species of invertebrates and plankton that only live in shallow, turbid, algae-rich waters — a situation very different from the deep, clearwater lake that Malawi is now.
This would have been a significant change to East Africa’s ecological make up… What was once tropical Africa was extraordinarily dry about 100,000 years ago, facilitating the migration of humans out of the Africa.