- Gene Expression
Current Biology has a special review issue out now on global genetic history of Homo sapiens. I guarantee you that your favorite geographic area is covered (Africa, Oceania, south Asia, east Asia, Europe, and the Americas), and your favorite sex chromosome (i.e. X and Y are discussed).
I've cut and pasted the abstracts for my reference and your convenience. Let me know if any of you actually read any of this stuff. If nothing else, click on the links and look at some of the rad-ass figures.
Open access - yay!
Archaeogenetics — Towards a ‘New Synthesis’?
It seems a timely moment to review human population history of the five continents as it emerges from recent archaeogenetic studies, as summarised in the reviews of this special issue of Current Biology. Has the ‘new synthesis’ — between genetics, archaeology and linguistics — arrived which I, perhaps incautiously, heralded a few years ago [1]? These highly informative reviews document, it seems to me, both achievement and uncertainty: the achievement relates to the remarkably consistent picture which has now emerged about the out-of-Africa emergence of our own species Homo sapiensand the initial peopling of the Earth. The uncertainty involves the application of archaeogenetics to the more recent, Holocene period, when most of the planet was already peopled — except much of Oceania — and sedentary, farming-based communities emerged. Here, it appears that much of our current understanding still depends on archaeological or, sometimes, linguistic evidence. And, with a few exceptions, the archaeogenetic evidence has not yet been assimilated into a genuine synthesis; but, let us begin with the good news.
The Evolution of Human Genetic and Phenotypic Variation in Africa
Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.
A new timescale has recently been established for human mitochondrial DNA (mtDNA) lineages, making mtDNA at present the most informative genetic marker system for studying European prehistory. Here, we review the new chronology and compare mtDNA with Y-chromosome patterns, in order to summarize what we have learnt from archaeogenetics concerning five episodes over the past 50,000 years which significantly contributed to the settlement history of Europe: the pioneer colonisation of the Upper Palaeolithic, the Late Glacial re-colonisation of the continent from southern refugia after the Last Glacial Maximum, the postglacial re-colonization of deserted areas after the Younger Dryas cold snap, the arrival of Near Easterners with an incipient Neolithic package, and the small-scale migrations along continent-wide economic exchange networks beginning with the Copper Age. The available data from uniparental genetic systems have already transformed our view of the prehistory of Europe, but our knowledge of these processes remains limited. Nevertheless, their legacy remains as sedimentary layers in the gene pool of modern Europeans, and our understanding of them will improve substantially when more mtDNAs are completely sequenced, the Y chromosome more thoroughly analysed, and haplotype blocks of the autosomal genome become amenable to phylogeographic studies.
South Asia — comprising India, Pakistan, countries in the sub-Himalayan region and Myanmar — was one of the first geographical regions to have been peopled by modern humans. This region has served as a major route of dispersal to other geographical regions, including southeast Asia. The Indian society comprises tribal, ranked caste, and other populations that are largely endogamous. As a result of evolutionary antiquity and endogamy, populations of India show high genetic differentiation and extensive structuring. Linguistic differences of populations provide the best explanation of genetic differences observed in this region of the world. Within India, consistent with social history, extant populations inhabiting northern regions show closer affinities with Indo-European speaking populations of central Asia that those inhabiting southern regions. Extant southern Indian populations may have been derived from early colonizers arriving from Africa along the southern exit route. The higher-ranked caste populations, who were the torch-bearers of Hindu rituals, show closer affinities with central Asian, Indo-European speaking, populations.
East Asia encompasses a wide variety of environments, peoples, cultures and languages. Although this review focuses on East Asia, no geographic region can be considered in isolation in terms of human population history, and migrations to and from East Asia have had a major impact. Here, we review the following topics: the initial colonization of East Asia, the direction of migrations between southeast Asia and northern Asia, the genetic relationships of East Asian hunter-gatherers and the genetic impact of various social practices on East Asian populations. By necessity we focus on insights derived from mitochondrial DNA and/or Y-chromosome data; ongoing and future studies of genome-wide SNP or multi-locus re-sequencing data, combined with the use of simulation, model-based methods to infer demographic parameters, will undoubtedly provide additional insights into the population history of East Asia.
The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci.
The Americas, the last continents to be entered by modern humans, were colonized during the late Pleistocene via a land bridge across what is now the Bering strait. However, the timing and nature of the initial colonization events remain contentious. The Asian origin of the earliest Americans has been amply established by numerous classical marker studies of the mid-twentieth century. More recently, mtDNA sequences, Y-chromosome and autosomal marker studies have provided a higher level of resolution in confirming the Asian origin of indigenous Americans and provided more precise time estimates for the emergence of Native Americans. But these data raise many additional questions regarding source populations, number and size of colonizing groups and the points of entry to the Americas. Rapidly accumulating molecular data from populations throughout the Americas, increased use of demographic models to test alternative colonization scenarios, and evaluation of the concordance of archaeological, paleoenvironmental and genetic data provide optimism for a fuller understanding of the initial colonization of the Americas.
There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the ‘hard sweep’ model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field.
