Craniometric variation,genetic theory,and modern human origins

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and, the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on withingroup variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevannt to issues of human origins. Our results are in agreement with mismatch distribution analysis of mtDNA, and they support a “weak Garden o Eden” model. In this model, modern-day variation can be explained by divergence from an initial source (perhaps Africa) into a number o small isolated populations, followed by later population expansion throughout our species. The major populationn expansions of Homo sapiens during and after the late Pleistocene have had the effect of “freezing” ancient patterns of population structure. While this is not the only possible scenario, we do note the close agreement with ecent analyses of mtDNA mismatch distibutions. © 1994 Wiley-Liss, Inc.     

Mitochondrial DNA and ancient population growth

In recent years, the study of mitochondrial DNA (mtDNA) variation has entered a new phase with an increasing emphasis on interpretations of demographic, rather than phylogenetic, history. Human mtDNA variation fits a “sudden expansion” model, where the human species expanded rapidly in size during the Late Pleistocene. This paper examines the sudden expansion model with the goal of partitioning total mtDNA diversity in contemporary populations into two components—diversity that existed prior to the population expansion and diversity that arose after the expansion. A method is developed for estimating these components. Analysis of mtDNA diversity within selected human populations shows that 64–80% of mtDNA diversity in contemporary populations arose after the expansion, a consequence of a high mutation rate relative to the number of generations since expansion. The basic model is extended to two components of excess diversity in sub-Saharan Africa—differences in population size before the expansion and differences in the timing of expansion. Results suggest that excess sub-Saharan African mtDNA diversity is due to the combined effects of the sub-Saharan African population being larger in size prior to the expansion and expanding earlier. Am J Phys Anthropol 105:1–7, 1998. © 1998 Wiley-Liss, Inc.     

Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions

The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.     

dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units

dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared with the CPU implementation, with minimal user burden. Motivated by this speed increase, I also extended dadi to four- and five-population models. This functionality is available in dadi version 2.1.0, https://bitbucket.org/gutenkunstlab/dadi/.     

Molecular evolution and modern human origins

While molecular evolutionists may be fascinated by the features and history of a particular gene or DNA segment, evolutionary anthropologists are often more interested in the activities and history of groups of people. We may want to know, for instance, when and where humans have migrated, how much exchange between groups has taken place, and how population sizes have changed. Population genetic theory provides the hope that through analyses of genetic data we will gain insight into the history of populations. Genetic data from extant human populations are now accruing at a remarkable rate. We might, therefore, expect to have answers in hand. There remains, however, a wide gap between the available theory and data; too often we fail to draw firm conclusions because our interpretation of analytic results requires that we make myriad assumptions about our data. In any one instance, these assumptions might include estimates of mutation rate, mutational mechanism, population sizes, the role that natural selection has played, and the rate of migration among groups. Often these assumptions are implicit, invisible to most. How, then, are we to make any progress? © 1998 Wiley-Liss, Inc.     

Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution

The recent extraction of mitochondrial DNA sequences from three European Neandertal fossils has led many to the conclusion that ancient DNA analysis supports the African replacement model of modern human origins and rejects models of multiregional evolution that propose some Neandertal ancestry in living humans. This conclusion is based, in part, on the lack of regional affinity of Neandertal DNA to that from living Europeans. Consideration of migration matrix models shows that this conclusion is premature, since under a model of interregional gene flow we expect to see similar levels of Neandertal ancestry in all contemporary regions, and living Europeans should not necessarily show closer affinity. The absence of regional affinity in Neandertal DNA does not distinguish between replacement and multiregional models.     

Ancient DNA analysis of human remains from the Upper Capital City of Kublai Khan

Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons.     

Neandertals,competition, and the origin of modern human behavior in the Levant

The East Mediterranean Levant is a small region, but its paleoanthropological record looms large in debates about the origin of modern humans and the fate of the Neandertals. For most of the twentieth century, the Levantine paleoanthropological record supported models of continuity and evolutionary transition between Neandertals and early modern humans. Recent advances in radiometric dating have challenged these models by reversing the chronological relationship between Levantine Neandertals and early modern humans. This revised chronostratigraphy for Levantine Middle Paleolithic human fossils raises interesting questions about the evolutionary relationship between Neandertals and early modern humans. A reconsideration of this relationship moves us closer to understanding the long delay between the origin of morphologically modern‐looking humans during the Middle Paleolithic (>130 Kyr) and the adaptive radiation of modern humans into Eurasia around the time of the transition from the Middle to Upper Paleolithic (50 to 30 Kyr).     

Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective

More than a third of the European pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroup (hg) H, the most frequent hg throughout western Eurasia. Although there has been considerable recent progress in studying mitochondrial genome variation in Europe at the complete sequence resolution, little data of comparable resolution is so far available for regions like the Caucasus and the Near and Middle East-areas where most of European genetic lineages, including hg H, have likely emerged. This gap in our knowledge causes a serious hindrance for progress in understanding the demographic prehistory of Europe and western Eurasia in general. Here we describe the phylogeography of hg H in the populations of the Near East and the Caucasus. We have analyzed 545 samples of hg H at high resolution, including 15 novel complete mtDNA sequences. As in Europe, most of the present-day Near Eastern-Caucasus area variants of hg H started to expand after the last glacial maximum (LGM) and presumably before the Holocene. Yet importantly, several hg H subclades in Near East and Southern Caucasus region coalesce to the pre-LGM period. Furthermore, irrespective of their common origin, significant differences between the distribution of hg H sub-hgs in Europe and in the Near East and South Caucasus imply limited post-LGM maternal gene flow between these regions. In a contrast, the North Caucasus mitochondrial gene pool has received an influx of hg H variants, arriving from the Ponto-Caspian/East European area.     

mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory

The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.     

Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros)

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. Taiwan formed around 5 million years ago from tectonic uplift, and has been connected to mainland Asia several times since its emergence. A central mountain range runs north to south, bisecting the island, and potentially impedes gene flow along an east-west axis. The Formosan lesser horseshoe bat (Rhinolophus monoceros) is endemic to Taiwan, where it is found mainly at low altitude. To determine the population structure and the demographic and colonization history of this species, we examined variation in the mitochondrial DNA control region in 203 bats sampled at 26 sites. We found very high haplotype and nucleotide diversity, which decreased from the centre to the south and north. Population differentiation followed a pattern of isolation by distance, though most regional genetic variance was attributable to differences between the relatively isolated southern population and those from other regions. A haplotype network was consistent with these findings and also suggested a southward colonization, followed by subsequent secondary contact between the south and other regions. Mismatch distributions were used to infer a past population expansion predating the last glacial maximum, and a neighbour-joining tree showed that R. monoceros formed a monophyletic grouping with respect to its sister taxa. Taken together, our results suggest that this taxon arose from a single period of colonization, and that demographic growth followed in the late Pleistocene. Current genetic structure reflects limited gene flow, probably coupled with stepwise colonization in the past. We consider explanations for the persistence of the species through multiple glacial maxima.     

Multiple dispersals and modern human origins

Despite a massive endeavour, the problem of modern human origins not only remains unresolved, but is usually reduced to “Out of Africa” versus multiregional evolution. Not all would agree, but evidence for a single recent origin is accumulating. Here, we want to go beyond this debate and explore within the “Out of Africa” framework an issue that has not been fully addressed: the mechanism by which modern human diversity has developed. We believe there is no clear rubicon of modern Homo sapiens, and that multiple dispersals occurred from a morphologically variable population in Africa. Pre-existing African diversity is thus crucial to the way human diversity developed outside Africa. The pattern of diversity—behavioural, linguistic, morphological and genetic—can be interpreted as the result of dispersals, colonisation, differentiation and subsequent dispersals overlaid on former population ranges. The first dispersals would have originated in Africa from where two different geographical routes were possible, one through Ethiopia/Arabia towards South Asia, and one through North Africa/Middle East towards Eurasia.     

基于DNA分子的现代人起源研究35年回顾与展望

1983年,有学者首次发表现代人线粒体DNA进化树,认为现代人可能起源自亚洲。1987年,又有学者按照分子钟假说得到线粒体在10-20万年前出自非洲的推论。随后,以分子钟为前提的Y染色体和常染色体DNA研究也支持了出非洲的结论,该结论逐渐成为分子进化领域的主流理论。2010年,对尼安德特人常染色体基因组的研究指出其对现代人有遗传贡献,这颠覆了人们先前关于现代人只来源自非洲,其他大洲的当地古人被完全取代的认知。目前,单地区起源说已经被修正为同化说。尽管学界对非洲人遗传多样性最高这一现象有共识,但是对该现象的不同解读却可以得出两种迥然不同的结果,现代人出亚洲说和出非洲说。大量研究证实基因组的大部分序列是有功能的,并处在遗传变异水平的饱和态,这质疑了中性理论以及由它推导的现代人出非洲说的合理性,而中性理论的提出恰恰是用来解释并非普遍存在的分子钟的。近年来已经有研究者从新理论的角度解读遗传多样性的饱和态和线性态,人们对现代人起源的认识将会进一步加深完善。     

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.