2015 – A Year in Human Evolution

2015 was a momentous year in findings on 100,000+ years of human evolution (see Pääbo 2015). It also marked the 30th anniversary of the seminal Higuchi et al. (1984) paper on sequencing ancient DNA from the quagga, an extinct equine (see Hagelberg et al 2015 for an excellent review). Thirty years on, large strides in sequencing technologies and statistical methods to reconstruct evolutionary processes (see Racimo et al. 2015 for a review of methods) have methodically tried to piece together a portrait of the past, not without its fair share of contentions. If there’s one thing to be said about studies of human genomic variation, it’s data, data, and more data (eg. 2500+ genomes reconstructed as part of the 1000 Genomes Project -, ~320 African genomes – Gurdasani et al. (2015), 100+ ancient genomes reconstructed by Allentoft et al. (2015)) Here I summarize some of these studies (geographically structured for no real reason) and wait with my RSS feeds open for what 2016 will bring!

The Out-of-Africa Bottleneck
While the Out-of-Africa bottleneck hypothesis has long been settled, its effect on modern, and archaic human genomes are hot topics as yet. Do et al. (2015) kicked off the year’s grand findings with their observation of a greater mutational load in Denisovans than in modern humans, or in Neanderthals. Whereas both simulations and empirical evidence from analysis of accumulations of deleterious mutations in modern humans outside of Africa indicate no apparent differences in the efficacy of natural selection due to the bottleneck’s founder events in European versus African humans as previously suggested (Lohmueller et al. 2008). Their study suggests a more complex relationship between standing genetic variation, in combination with founder effects, demography in driving mutational load in modern humans outside of Africa (see Henn et al. (2015) for a summary of recent findings on mutational load). Pagani et al. (2015) also reported the sequencing of 200+ genomes from Egyptian and Ethiopian peoples, and resolve evidence for the Northern route (via Egypt and Sinai) versus the Southern route (via Ethiopia and the Arabian peninsula), with more affinity in haplotypes from Egypt with non-African modern humans. An interesting study by Gallego Llorente et al. (2015) sequence an ancient (~3000 year old) Ethiopian male (“Mota”) genome to date the “back-to-Africa” colonization to at least 3000 ybp. Using the “Mota” as an unadmixed African reference, they also trace up to 7% of extant African ancestry to Eurasia, much greater than previously determined, with 0.2-0.7% of Neanderthal ancestry in the Yoruba and Mbuti. Recently, Alves et al. (2015) propose a complex model that supports long distance dispersal events to previously occupied demes during the Eurasian range expansion, and contraction during the last glacial maximum to explain subsequent genetic diversity distributions.

Admixture with other hominidae
Since last year’s findings of differential Neanderthal admixture in anatomically modern humans outside of Africa (particularly in Eastern Asians versus Europeans – Sankararaman et al. 2014, summarized in Pääbo 2015), numerous studies have attempted to address plausible scenarios of introgression and subsequent differential purging of Neanderthal alleles from humans. Kim and Lohmueller (2015), and Vernot and Akey (2015) study causalities in differential introgression of Neanderthals with modern East Asians versus Europeans, and reject models of a single wave of migration from Neanderthals into humans, bottlenecks, and differential selection, and support for secondary migrations from an unknown “ghost” population, or from Neanderthals to be consistent with the data. Two recent manuscripts (Harris and Nielsen 2015, Juric et al. 2015) use simulations to describe the overall depletion of Neanderthal ancestry across modern humans outside of Africa owing to differences in efficacy of selection in early generation hybrids, and the role of Hill-Robertson Interference (recombination and drift effects). Rogers (2015) also describes the potential role of chromosomal rearrangements in differential introgression between Neanderthals, Denisovans, and modern humans. With the availability of two more Denisovan genomes (Sawyer et al. 2015), and more archaic genomes in the pipeline, I daresay that fun projects about differential introgression between anatomically modern and archaic hominids have only just begun.

Dynamic history of Eurasia
Allentoft et al. (2015) described Bronze age population genomics in Eurasia using low-coverage genomes from 100+ ancient individuals, pointing to large scale migration events in the early Bronze age potentially leading to the spread of Indo-European languages. Among their interesting finds include the existence of high frequencies of skin pigmentation SNP’s in Bronze Age Eurasia, and low frequency of lactose tolerance, indicative of a much more recent onset of positive selection for lactose tolerance in Europe. In a similar study, Haak et al. (2015) also report the lactose tolerance finding, and join the language debate by documenting a similar massive migration event around 4500 ybp and its role in the evolution of Indo-European languages in Europe. Both studies are summarized by Novembre (2015). As Novembre puts it, “If genes were moving en masse, it is likely that words were too”, and also points to the importance of ancient DNA research in addressing age old social and political questions in “a more open and humane framework”, a statement that definitely rings true in the America studies that follow.

Meanwhile in the Americas
Skoglund et al. (2015) reported on the admixture history of Native Americans prior to their migration to the Americas via the Bering Strait, more than 15,000 ybp, pointing to a much more diverse ancestry of the first settlers than previously described. Rasmussen et al. (2015) also established the ancestry of the Kennewick Man to be predominantly Native American, with several modern Native American groups being derived from a population closely related to him, laying to rest the age-old controversy around his origins. As the Smithsonian reported (before, and after), sequencing more Native American genomes is key to bring forth a detailed picture of how America was peopled.

Elsewhere, and more data!
Numerous other studies –Schroeder et al. (2015), Sudmant et al. (2015), Bahcall (2015) and allied Icelandic genome papers, Ayub et al. (2015) also report genomic variation in current human populations – invaluable contributions to filling in the gaps in sampling, and unaddressed questions. It should be no surprise that all the papers I’ve referenced here (and the ones that I have missed) have laid the plans for a fun 2016!

In the famous words of Yoda,

Much to learn you still have, my old padawan…This is just the beginning!

Happy Holidays from the team at SEF!

References:

Allentoft, Morten E., et al. “Population genomics of Bronze Age Eurasia.” Nature 522.7555 (2015): 167-172.
Alves, Isabel, et al. “Long distance dispersal shaped patterns of human genetic diversity in Eurasia.” Molecular biology and evolution (2015): msv332.
Ayub, Qasim, et al. “The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection.” The American Journal of Human Genetics 96.5 (2015): 775-783.
Bahcall, Orli G. “Population genomics: Population-scale sequencing in Iceland.” Nature Reviews Genetics 16.5 (2015): 257-257.
Do, Ron, et al. “No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.” Nature genetics 47.2 (2015): 126-131.
Gurdasani, Deepti, et al. “The African Genome Variation Project shapes medical genetics in Africa.” Nature 517.7534 (2015): 327-332.
Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature (2015).
Hagelberg, Erika, Michael Hofreiter, and Christine Keyser. “Ancient DNA: the first three decades.” Philosophical Transactions of the Royal Society B: Biological Sciences 370.1660 (2015).
Harris K and Nielsen R. The genetic cost of Neanderthal introgression. bioRxiv doi: http://dx.doi.org/10.1101/030387
Henn, Brenna M., et al. “Estimating the mutation load in human genomes.” Nature Reviews Genetics (2015).
Higuchi, Russell, et al. “DNA sequences from the quagga, an extinct member of the horse family.” (1984): 282-284.
Juric I, Aeschbacher S, Coop G. The strength of selection againt Neanderthal introgression. bioRxiv doi: http://dx.doi.org/10.1101/030148
Kim, Bernard Y., and Kirk E. Lohmueller. “Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations.” The American Journal of Human Genetics (2015).
Llorente, M. Gallego, et al. “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent.” Science 350.6262 (2015): 820-822.
Lohmueller, Kirk E., et al. “Proportionally more deleterious genetic variation in European than in African populations.” Nature 451.7181 (2008): 994-997.
Novembre, John. “Human evolution: Ancient DNA steps into the language debate.” Nature 522.7555 (2015): 164-165.
Pääbo, Svante. “The diverse origins of the human gene pool.” Nature Reviews Genetics 16.6 (2015): 313-314.
Pääbo, Svante. “The contribution of ancient hominin genomes from Siberia to our understanding of human evolution.” Herald of the Russian Academy of Sciences 85.5 (2015): 392-396.
Pagani, Luca, et al. “Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians.” The American Journal of Human Genetics (2015).
Racimo, Fernando, et al. “Evidence for archaic adaptive introgression in humans.” Nature Reviews Genetics 16.6 (2015): 359-371.
Rasmussen, Morten, et al. “The ancestry and affiliations of Kennewick Man.” Nature (2015).
Rogers, Rebekah L. “Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans.” arXiv preprint arXiv:1505.07047 (2015).
Sankararaman, Sriram, et al. “The genomic landscape of Neanderthal ancestry in present-day humans.” Nature 507.7492 (2014): 354-357.
Sawyer, Susanna, et al. “Nuclear and mitochondrial DNA sequences from two Denisovan individuals.” Proceedings of the National Academy of Sciences (2015): 201519905.
Skoglund, Pontus, et al. “Genetic evidence for two founding populations of the Americas.” Nature 525.7567 (2015): 104-108.
Sudmant, Peter H., et al. “An integrated map of structural variation in 2,504 human genomes.” Nature 526.7571 (2015): 75-81.
Vernot, Benjamin, and Joshua M. Akey. “Complex history of admixture between modern humans and Neandertals.” The American Journal of Human Genetics 96.3 (2015): 448-453.
1000 Genomes Project Consortium. “A global reference for human genetic variation.” Nature 526.7571 (2015): 68-74.