X chromosome evidence for ancient human histories

Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China

Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.

Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders

In addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins. We discuss the possibility that segregation distortion during spermatogenesis accounts for a subset of ASD mutations. Finally, we detected modern-human-specific alleles in DYRK1A and TCF4. These variants are located within regions that display chromatin features typical of transcriptional enhancers in several brain areas, strongly suggesting a regulatory role. These SNPs thus represent candidates for association with neurodevelopmental disorders, and await experimental validation in future studies.

Signatures of human European Palaeolithic expansion shown by resequencing of non-recombining X-chromosome segments

Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs). Three such sequences on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 ×. These PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of X-chromosomal inheritance. This study demonstrates the potential of the use of X-chromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.

Within a sample from a population, the distribution of the number of descendants of a subsample's most recent common ancestor

Sample n individuals uniformly at random from a population, and then sample m individuals uniformly at random from the sample. Consider the most recent common ancestor (MRCA) of the subsample of m individuals. Let the subsample MRCA have j descendants in the sample (m ⩽ j ⩽ n). Under a Moran or coalescent model (and therefore under many other models), the probability that j = n is known. In this case, the subsample MRCA is an ancestor of every sampled individual, and the subsample and sample MRCAs are identical. The probability that j = m is also known. In this case, the subsample MRCA is an ancestor of no sampled individual outside the subsample. This article derives the complete distribution of j, enabling inferences from the corresponding p-value. The text presents hypothetical statistical applications pertinent to taxonomy (the gene flow between Neanderthals and anatomically modern humans) and medicine (the association of genetic markers with disease).

X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations

The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ∼500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

Local selection of human populations shapes complex evolution patterns of CXCL10 gene

CXC motif chemokine 10 (CXCL10) is a small cytokine belonging to the CXC chemokine family, and it is secreted by several cell types in response to IFN-γ and regulates immune responses through the recruitment and activation of lymphocytes. As CXCL10 is very important in T-cell immunity and infectious diseases, we studied the effect of natural selection on the CXCL10 locus. By sequencing 74 individuals from three human populations, we found a complex pattern of natural selection acting on the CXCL10 locus. We discovered a signature of balancing selection in the European population with a significant positive Tajima's D value (2.57, P=0.005) and an excess of intermediate frequency alleles. However, we observed an excess of high frequency-derived alleles and a significant Fay and Wu's test statistics (P=0.015) in the Chinese population, which suggests that recent selective sweeps under positive selection had occurred. Also, there are a lot of alleles showing great frequency difference among populations. These results demonstrate that local selection has shaped CXCL10 evolution and indicates that there exist different actions of natural selection on the CXCL10 locus in different populations. This study provides insights into the likely relative roles of natural selection and population history in shaping today's genetic variation at the CXCL10 locus, indicates the relationship between adaptation to past infection and predisposition to autoimmunity in modern populations, improves our understanding of CXCL10 evolution, and motivates further investigations of the role of CXCL10 in infectious diseases and autoimmune diseases.

Archaic human genomics

For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.

The date of interbreeding between Neandertals and modern humans

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

One of the key discoveries from the analysis of the Neandertal genome is that Neandertals share more genetic variants with non-Africans than with Africans. This observation is consistent with two hypotheses: interbreeding between Neandertals and modern humans after modern humans emerged out of Africa or population structure in the ancestors of Neandertals and modern humans. These hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans. We estimate this date by measuring the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

Development of multilocus putatively neutral DNA markers in the X-chromosome for population genetic studies in humans

BACKGROUND

It has now been well documented that the type (coding, non-coding) and location (nuclear, mitochondrial etc.) of genetic markers heavily influence evolutionary inferences; realistic assumptions can be drawn if multiple putatively neutral DNA fragments spread across the genome are used.

AIM

To infer human population history, Single Nucleotide Polymorphisms (SNPs), located in the non-coding regions of different genes in the X-chromosome have been developed as 'putatively neutral markers'.

SUBJECTS AND METHODS

A population sample consisting of 16 male individuals from the western part of India was utilized for sequencing eight DNA fragments located in introns of three genes (Duchenne muscular dystrophy, Factor IX and Pyruvate dehydrogenase E1 sub-unit) on the human X-chromosome. PCR amplification and DNA sequencing confirmed the polymorphic status of all the fragments.

RESULTS

Twenty nine SNPs were found to be segregating in the Western Indian population samples. Using these SNPs the nucleotide diversity and demographic parameters of the Western Indian population were estimated. Several tests of neutrality ascertained that all eight fragments evolve putatively neutrally. Further, linkage disequilibrium analyses confirmed this fact.

CONCLUSION

All eight DNA fragments seem to bear the characteristics to be considered as 'putatively neutral genetic markers' and thus, could be utilized for inference of human population and demographic histories.

Analytical framework for identifying and differentiating recent hitchhiking and severe bottleneck effects from multi-locus DNA sequence data

Hitchhiking and severe bottleneck effects have impact on the dynamics of genetic diversity of a population by inducing homogenization at a single locus and at the genome-wide scale, respectively. As a result, identification and differentiation of the signatures of such events from DNA sequence data at a single locus is challenging. This paper develops an analytical framework for identifying and differentiating recent homogenization events at multiple neutral loci in low recombination regions. The dynamics of genetic diversity at a locus after a recent homogenization event is modeled according to the infinite-sites mutation model and the Wright-Fisher model of reproduction with constant population size. In this setting, I derive analytical expressions for the distribution, mean, and variance of the number of polymorphic sites in a random sample of DNA sequences from a locus affected by a recent homogenization event. Based on this framework, three likelihood-ratio based tests are presented for identifying and differentiating recent homogenization events at multiple loci. Lastly, I apply the framework to two data sets. First, I consider human DNA sequences from four non-coding loci on different chromosomes for inferring evolutionary history of modern human populations. The results suggest, in particular, that recent homogenization events at the loci are identifiable when the effective human population size is 50,000 or greater in contrast to 10,000, and the estimates of the recent homogenization events are agree with the "Out of Africa" hypothesis. Second, I use HIV DNA sequences from HIV-1-infected patients to infer the times of HIV seroconversions. The estimates are contrasted with other estimates derived as the mid-time point between the last HIV-negative and first HIV-positive screening tests. The results show that significant discrepancies can exist between the estimates.

Loss and gain of function in SERPINB11: an example of a gene under selection on standing variation, with implications for host-pathogen interactions

Serine protease inhibitors (SERPINs) are crucial in the regulation of diverse biological processes including inflammation and immune response. SERPINB11, located in the 18q21 gene cluster, is a polymorphic gene/pseudogene coding for a non-inhibitory SERPIN. In a genome-wide scan for recent selection, SERPINB11 was identified as a potential candidate gene for adaptive evolution in Yoruba. The present study sought a better understanding of the evolutionary history of SERPINB11, with special focus on evaluating its selective signature. Through the resequencing of coding and noncoding regions of SERPINB11 in 20 Yorubans and analyzing primate orthologous sequences, we identified a full-length SERPINB11 variant encoding a non-inhibitory SERPIN as the putative candidate of selection – probably driven to higher frequencies by an adaptive response using preexisting variation. In addition, we detected contrasting evolutionary features of SERPINB11 in primates: While primate phylogeny as a whole is under purifying selection, the human lineage shows evidence of positive selection in a few codons, all associated with the active SERPINB11. Comparative modeling studies suggest that positively selected codons reduce SERPINB11's ability to undergo the conformational changes typical of inhibitory SERPINs – suggesting that it is evolving towards a new non-inhibitory function in humans. Significant correlations between SERPINB11 variants and the environmental variables, pastoralism and pathogen richness, have led us to propose a selective advantage through host-pathogen interactions, possibly linked to an adaptive response combating the emergence of infectious diseases in recent human evolution. This work represents the first description of a resurrected gene in humans, and may well exemplify selection on standing variation triggered by drastic ecological shifts.

Nonadaptive processes in primate and human evolution

Evolutionary biology has tended to focus on adaptive evolution by positive selection as the primum mobile of evolutionary trajectories in species while underestimating the importance of nonadaptive evolutionary processes. In this review, I describe evidence that suggests that primate and human evolution has been strongly influenced by nonadaptive processes, particularly random genetic drift and mutation. This is evidenced by three fundamental effects: a relative relaxation of selective constraints (i.e., purifying selection), a relative increase in the fixation of slightly deleterious mutations, and a general reduction in the efficacy of positive selection. These effects are observed in protein-coding, regulatory regions, and in gene expression data, as well as in an augmentation of fixation of large-scale mutations, including duplicated genes, mobile genetic elements, and nuclear mitochondrial DNA. The evidence suggests a general population-level explanation such as a reduction in effective population size (N(e)). This would have tipped the balance between the evolutionary forces of natural selection and random genetic drift toward genetic drift for variants having small selective effects. After describing these proximate effects, I describe the potential consequences of these effects for primate and human evolution. For example, an increase in the fixation of slightly deleterious mutations could potentially have led to an increase in the fixation rate of compensatory mutations that act to suppress the effects of slightly deleterious substitutions. The potential consequences of compensatory evolution for the evolution of novel gene functions and in potentially confounding the detection of positively selected genes are explored. The consequences of the passive accumulation of large-scale genomic mutations by genetic drift are unclear, though evidence suggests that new gene copies as well as insertions of transposable elements into genes can potentially lead to adaptive phenotypes. Finally, because a decrease in selective constraint at the genetic level is expected to have effects at the morphological level, I review studies that compare rates of morphological change in various mammalian and island populations where N(e) is reduced. Furthermore, I discuss evidence that suggests that craniofacial morphology in the Homo lineage has shifted from an evolutionary rate constrained by purifying selection toward a neutral evolutionary rate.

The microcephalin ancestral allele in a Neanderthal individual

Background

The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal.

Methodology/Principal Findings

Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination.

Conclusions/Significance

The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

Genetic structure in African populations: implications for human demographic history

The continent of Africa is the source of all anatomically modern humans that dispersed across the planet during the past 100,000 years. As such, African populations are characterized by high genetic diversity and low levels of linkage disequilibrium (LD) among loci, as compared to populations from other continents. African populations also possess a number of genetic adaptations that have evolved in response to the diverse climates, diets, geographic environments, and infectious agents that characterize the African continent. Recently, Tishkoff et al. (2009) performed a genome-wide analysis of substructure based on DNA from 2432 Africans from 121 geographically diverse populations. The authors analyzed patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers and identified 14 ancestral population clusters that correlate well with self-described ethnicity and shared cultural or linguistic properties. The results suggest that African populations may have maintained a large and subdivided population structure throughout much of their evolutionary history. In this chapter, we synthesize recent work documenting evidence of African population structure and discuss the implications for inferences about evolutionary history in both African populations and anatomically modern humans as a whole.

Origin and evolution of sulfadoxine resistant Plasmodium falciparum

The Thailand-Cambodia border is the epicenter for drug-resistant falciparum malaria. Previous studies have shown that chloroquine (CQ) and pyrimethamine resistance originated in this region and eventually spread to other Asian countries and Africa. However, there is a dearth in understanding the origin and evolution of dhps alleles associated with sulfadoxine resistance. The present study was designed to reveal the origin(s) of sulfadoxine resistance in Cambodia and its evolutionary relationship to African and South American dhps alleles. We sequenced 234 Cambodian Plasmodium falciparum isolates for the dhps codons S436A/F, A437G, K540E, A581G and A613S/T implicated in sulfadoxine resistance. We also genotyped 10 microsatellite loci around dhps to determine the genetic backgrounds of various alleles and compared them with the backgrounds of alleles prevalent in Africa and South America. In addition to previously known highly-resistant triple mutant dhps alleles SGEGA and AGEAA (codons 436, 437, 540, 581, 613 are sequentially indicated), a large proportion of the isolates (19.3%) contained a 540N mutation in association with 437G/581G yielding a previously unreported triple mutant allele, SGNGA. Microsatellite data strongly suggest the strength of selection was greater on triple mutant dhps alleles followed by the double and single mutants. We provide evidence for at least three independent origins for the double mutants, one each for the SGKGA, AGKAA and SGEAA alleles. Our data suggest that the triple mutant allele SGEGA and the novel allele SGNGA have common origin on the SGKGA background, whereas the AGEAA triple mutant was derived from AGKAA on multiple, albeit limited, genetic backgrounds. The SGEAA did not share haplotypes with any of the triple mutants. Comparative analysis of the microsatellite haplotypes flanking dhps alleles from Cambodia, Kenya, Cameroon and Venezuela revealed an independent origin of sulfadoxine resistant alleles in each of these regions.

Widespread resistance to chloroquine (CQ) and sulfadoxine-pyrimethamine (SP), the two least expensive and widely available antimalarial drugs, has become a major global public health challenge. It is known that point mutations in Plasmodium falciparum crt, dhfr and dhps genes contribute to resistance to CQ, pyrimethamine and sulfadoxine, respectively. CQ and pyrimethamine resistance spread to Africa and Asia from a few founding mutant lineages originating from the Thailand-Cambodia border. Here, we define the origins of dhps alleles in Cambodia and their relationships to African and South American counterparts. Three different triple mutant alleles including a novel allele comprised of 437G, 540N, and 581G mutations (S₄₃₆G₄₃₇N₅₄₀G₅₈₁A₆₁₃) were found in Cambodia as opposed to a single triple mutant allele in South America and two common double mutant alleles in Africa. Microsatellite data suggest strong selection operating on triple mutant alleles as compared to double and single mutants in Cambodia. We report three major independent origins for the double mutants and at least two independent origins for the highly resistant triple mutant dhps alleles in Cambodia. We also show that the resistant dhps alleles in Africa and South America have distinct origins from Cambodia. These results suggest that the evolution and spread of sulfadoxine resistance is different from CQ and pyrimethamine resistance.

Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history

It is well known that average levels of population structure are higher on the X chromosome compared to autosomes in humans. However, there have been surprisingly few analyses on the spatial distribution of population structure along the X chromosome. With publicly available data from the HapMap Project and Perlegen Sciences, we show a strikingly punctuated pattern of X chromosome population structure. Specifically, 87% of X-linked HapMap SNPs within the top 1% of F(ST) values cluster into five distinct loci. The largest of these regions spans 5.4 Mb and contains 66% of the most highly differentiated HapMap SNPs on the X chromosome. We demonstrate that the extreme clustering of highly differentiated SNPs on the X chromosome is not an artifact of ascertainment bias, nor is it specific to the populations genotyped in the HapMap Project. Rather, additional analyses and resequencing data suggest that these five regions have been substrates of recent and strong adaptive evolution. Finally, we discuss the implications that patterns of X-linked population structure have on the evolutionary history of African populations.

Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations

Background

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ∼6 kilobases, resequenced in ∼184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.

Conclusions/Significance

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (∼41 thousand years ago, ∼13-fold) than our food-producing populations (∼31 thousand years ago, ∼7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Culture, population structure, and low genetic diversity in Pleistocene hominins

Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.

Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

Background

Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions.

Results

Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM) model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000) than non-African populations (300–3,300). We estimate mean rates of bidirectional gene flow at 4.8 × 10^-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10^-3) than among African populations (2.7 × 10^-4). Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4).

Conclusion

We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

Populationsgenetik des humanen X-Chromosoms

Die mitochondriale DNA und das Y-Chromosom (ChrY) weisen einen sehr hohen Informationsgehalt hinsichtlich der Entwicklungsgeschichte des Menschen und der verwandtschaftlichen Nähe humaner Populationen auf. Das liegt daran, dass mit Ausnahme der pseudoautosomalen Regionen des ChrY beide genomischen Kompartimente nicht rekombinieren und dass die Typisierung haploider Marker automatisch die Identifizierung von Haplotypen erlaubt. Das X-Chromosom (ChrX) nimmt hinsichtlich seines Rekombinationsverhaltens eine intermediäre Stellung zwischen den Autosomen und dem ChrY ein. Auch seine populationsgenetische Bedeutung beruht z. T. auf der leichteren Identifizierbarkeit von Haplotypen. Während ChrY und mtDNA aber jeweils nur einen einzigen Locus mit einheitlicher Entwicklungsgeschichte repräsentieren, setzt sich das ChrX aus mehreren Abschnitten zusammen, die jeweils eine eigene Historie reflektieren können. Daher erscheinen ChrX-Studien immer dann besonders sinnvoll, wenn Subpopulationen voneinander unterschieden oder regionale ethnische Strukturen erforscht werden sollen. Aus populationsgenetischer Sicht spielt die Analyse von Kopplungsungleichgewichten zwischen ChrX-Markern eine besondere Rolle, da mit ihrer Hilfe genetische Isolate und die Abstammung einzelner Gruppierungen von kleinen Gründerpopulationen nachgewiesen werden können. Populationen mit häufigen und hohen Kopplungsungleichgewichten haben eine besondere Bedeutung für die Identifizierung der Gene, deren Variation zur Ätiologie multifaktorieller Erkrankungen beiträgt.

Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans

To understand the evolution of human mental activity, we performed population genetic analyses of nucleotide sequences ( approximately 11 kb) from a worldwide sample of 60 chromosomes of the N-acylsphingosine amidohydrolase (ASAH1) gene. ASAH1 hydrolyzes ceramides and regulates neuronal development, and its deficiency often results in mental retardation. In the region ( approximately 4.4 kb) encompassing exons 3 and 4 of this gene, two distinct lineages (V and M) have been segregating in the human population for 2.4 +/- 0.4 million years (MY). The persistence of these two lineages is attributed to ancient population structure of humans in Africa. However, all haplotypes belonging to the V lineage exhibit strong linkage disequilibrium, a high frequency (62%), and small nucleotide diversity (pi = 0.05%). These features indicate a signature of positive Darwinian selection for the V lineage. Compared with the orthologs in mammals and birds, it is only Val at amino acid site 72 that is found exclusively in the V lineage in humans, suggesting that this Val is a likely target of positive selection. Computer simulation confirms that demographic models of modern humans except for the ancient population structure cannot explain the presence of two distinct lineages, and neutrality is incompatible with the observed small genetic variation of the V lineage at ASAH1. On the basis of the above observations, it is argued that positive selection is possibly operating on ASAH1 in the modern human population.

Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas

Background

The X-linked SRPX2 gene encodes a Sushi Repeat-containing Protein of unknown function and is mutated in two disorders of the Rolandic/Sylvian speech areas. Since it is linked to defects in the functioning and the development of brain areas for speech production, SRPX2 may thus have participated in the adaptive organization of such brain regions. To address this issue, we have examined the recent molecular evolution of the SRPX2 gene.

Results

The complete coding region was sequenced in 24 human X chromosomes from worldwide populations and in six representative nonhuman primate species. One single, fixed amino acid change (R75K) has been specifically incorporated in human SRPX2 since the human-chimpanzee split. The R75K substitution occurred in the first sushi domain of SRPX2, only three amino acid residues away from a previously reported disease-causing mutation (Y72S). Three-dimensional structural modeling of the first sushi domain revealed that Y72 and K75 are both situated in the hypervariable loop that is usually implicated in protein-protein interactions. The side-chain of residue 75 is exposed, and is located within an unusual and SRPX-specific protruding extension to the hypervariable loop. The analysis of non-synonymous/synonymous substitution rate (Ka/Ks) ratio in primates was performed in order to test for positive selection during recent evolution. Using the branch models, the Ka/Ks ratio for the human branch was significantly different (p = 0.027) from that of the other branches. In contrast, the branch-site tests did not reach significance. Genetic analysis was also performed by sequencing 9,908 kilobases (kb) of intronic SRPX2 sequences. Despite low nucleotide diversity, neither the HKA (Hudson-Kreitman-Aguadé) test nor the Tajima's D test reached significance.

Conclusion

The R75K human-specific variation occurred in an important functional loop of the first sushi domain of SRPX2, indicating that this evolutionary mutation may have functional importance; however, positive selection for R75K could not be demonstrated. Nevertheless, our data contribute to the first understanding of molecular evolution of the human SPRX2 gene. Further experiments are now required in order to evaluate the possible consequences of R75K on SRPX2 interactions and functioning.

Tracing genetic history of modern humans using X-chromosome lineages

Genetic variability of the compound interrupted microsatellite DXS1238, in intron 44 of the dystrophin gene, provides evidence for a complex structure of the ancestral population that led to the emergence of modern humans. We sequenced DXS1238 in 600 X-chromosomes from all over the world. Forty four percent of African-specific chromosomes belong to the ancestral lineage that did not participate in the out-of-Africa expansion and subsequent colonization of other continents. Based on the coalescence analysis these lineages separated from those that contributed to the out-of-Africa expansion 366 +/- 136 thousands years ago (Kya). Independently, the analysis of the variance in the repeat length and of the decay of the ancestral alleles of the two DXS1238 repeats, GT and GA, dates this separation at more than 200 Kya. This suggests a complex demographic history and genetic structure of the African melting pot that led to the emergence of modern humans and their out-of-Africa migration. The subsequent subdivisions of human populations among different continents appear to be preceded by even more structured population history within Africa itself, which resulted from a restricted gene flow between lineages allowing for genetic differences to accumulate. If the transition to modern humans occurred during that time, it necessarily follows that genes associated with this transformation spread between subpopulations via gene flow. Otherwise, in spite of subsequent anatomical variation, Homo sapiens as a species could have emerged in Africa already between 300 and 200 Kya, i.e. before the mitochondrial DNA and well before the Y-chromosome most recent common ancestors.

Modern human origins in Australasia: Testing the predictions of competing models

The evolutionary background to the emergence of modern humans remains controversial. Four models have been proposed to explain this process and each has clearly definable and testable predictions about the geographical origins of early Australians and their possible biological interaction with other Pleistocene populations. The present study considers the phenetic affinities of early Australians from Kow Swamp (KS 1 and KS 5) and Keilor to Pleistocene Africans and Asians from calvarial dimensions. The study includes analyses employing log-transformed and size-corrected (Mosimann variables) data. The strongest signals to emerge are as follows: (1) a phenetic pattern in which Australians are most like each other, (2) all three crania possess a mosaic of archaic and modern features, (3) Kow Swamp crania also show strong affinities to archaic remains, (4) Keilor is more modern than KS 1 and KS 5 and (5) Keilor shows affinities to Pleistocene East Asian modern crania (Liujiang and Upper Cave 101) providing evidence for a broad regional morphology. The results refute the predictions of multi-species replacement models for early Australians but are consistent with single-species models. Combined with published evidence from DNA, the present study indicates that the Assimilation model presently offers the best explanation for the origins of Pleistocene Australians.

Molecular variability of the 16p13.3 region in Amerindians and its anthropological significance

A total of 1558 base pairs in the 16p13.3 region were investigated in 98 individuals of Mongolian, Northern Arctic and Amerindian affiliation, and the results compared with those obtained in a previous worldwide study of the same genomic region. Fifty-five polymorphic sites could be classified into thirty-five haplotypes from the total data. A median joining network based on the haplotypes revealed two distinct clusters: one with low diversity, with haplotypes found in all five geographic-ethnic categories; while the other, with the most divergent haplotypes, was composed mainly of Africans and a few Amerindians. Almost all neutrality parameters yielded significantly negative values. Demographic simulations with the exclusively Amerindian dataset rejected all scenarios, including a bottleneck beginning more than 12,000 years ago. The demographic scenarios tested considering population growth were similar among the Amerindian and worldwide or Eurasian data sets. The results suggest that Amerindians are a representative sample of Eurasian populations, preserving the signal of demographic growth from the out of Africa exodus and, together with data from uniparental markers, support a scenario of a bottleneck of moderate intensity during the peopling of the New World.

The X chromosome Alu insertions as a tool for human population genetics: data from European and African human groups

Alu elements are the most abundant mobile elements in the human genome (approximately 1,100,000 copies). Polymorphic Alu elements have been proved to be useful in studies of human origins and relationships owing to two important advantages: identity by descent and absence of the Alu element known to be the ancestral state. Alu variation in the X chromosome has been described previously in human populations but, as far as we know, these elements have not been used in population relationship studies. Here, we describe the allele frequencies of 13 'young' Alu elements of the X chromosome (Ya5DP62, Ya5DP57, Yb8DP49, Ya5a2DP1, Yb8DP2, Ya5DP3, Ya5NBC37, Yd3JX437, Ya5DP77, Ya5NBC491, Yb8NBC578, Ya5DP4 and Ya5DP13) in six human populations from sub-Saharan Africa (the Ivory Coast), North Africa (Moroccan High Atlas, Siwa oasis in Egypt, Tunisia), Greece (Crete Island) and Spain (Basque Country). Eight out of 13 Alu elements have shown remarkably high gene diversity values in all groups (average heterozygosities: 0.342 in the Ivory Coast, 0.250 in North Africa, 0.209 in Europe). Genetic relationships agree with a geographical pattern of differentiation among populations, with some peculiar features observed in North Africans. Crete Island and the Basque Country show the lowest genetic distance (0.0163) meanwhile Tunisia, in spite of its geographical location, lies far from the other two North African samples. The results of our work demonstrate that X chromosome Alu elements comprise a reliable set of genetic markers useful to describe human population relationships for fine-scale geographical studies.

Ascertainment Bias and the Pattern of Nucleotide Diversity at the Human ALDH2 Locus in a Japanese Population

Many East Asian human populations harbor a high-frequency deficiency allele for the aldehyde dehydrogenase 2 (ALDH2) enzyme, a critical protein involved in the metabolism of ethanol. Here we use resequencing and long-range SNP haplotype data from a Japanese sample to test whether patterns of nucleotide diversity and linkage disequilibrium at this locus are compatible with a standard neutral model of evolution. Examination of the pattern of polymorphism at a locus such as this, where the frequency of a common allele is known a priori, introduces an ascertainment bias that must be corrected for in analyses of the frequency spectrum of polymorphisms. We apply a flexible and generally applicable simulation approach to correct for this bias in our ALDH2 data and, also, to explore the effect of bias on the commonly used summary statistics Tajima's D, Fu and Li's D, and Fay and Wu's H. Our study finds no evidence that the pattern of genetic variation at ALDH2 differs from that expected under a standard neutral model. However, our general examination of ascertainment bias indicates that a priori knowledge of segregating alleles greatly affects the expected distributions of summary statistics. Under many parameter combinations we find that ascertainment bias introduces an elevated rate of false positives when summary statistics are used to test for deviations from a standard neutral model. However, we also show that over a wide range of conditions the power of all summary statistics can be greatly increased by incorporating prior knowledge of segregating alleles.

Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage

At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy approximately 37,000 years ago and swept to exceptionally high frequency (approximately 70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans approximately 1.1 million years ago and introgressed into humans by approximately 37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.

Archaic admixture in the human genome

One of the enduring questions in the evolution of our species surrounds the fate of 'archaic' forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25-40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

Reconstructing human origins in the genomic era

Analyses of recently acquired genomic sequence data are leading to important insights into the early evolution of anatomically modern humans, as well as into the more recent demographic processes that accompanied the global radiation of Homo sapiens. Some of the new results contradict early, but still influential, conclusions that were based on analyses of gene trees from mitochondrial DNA and Y-chromosome sequences. In this review, we discuss the different genetic and statistical methods that are available for studying human population history, and identify the most plausible models of human evolution that can accommodate the contrasting patterns observed at different loci throughout the genome.

Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations

Noncoding regions are usually less subject to natural selection than coding regions and so may be more useful for studying human evolution. The recent surveys of worldwide DNA variation in four 10-kb noncoding regions revealed many interesting but also some incongruent patterns. Here we studied another 10-kb noncoding region, which is in 6p22. Sixty-six single-nucleotide polymorphisms were found among the 122 worldwide human sequences, resulting in 46 genotypes, from which 48 haplotypes were inferred. The distribution patterns of DNA variation, genotypes, and haplotypes suggest rapid population expansion in relatively recent times. The levels of polymorphism within human populations and divergence between humans and chimpanzees at this locus were generally similar to those for the other four noncoding regions. Fu and Li's tests rejected the neutrality assumption in the total sample and in the African sample but Tajima's test did not reject neutrality. A detailed examination of the contributions of various types of mutations to the parameters used in the neutrality tests clarified the discrepancy between these test results. The age estimates suggest a relatively young history in this region. Combining three autosomal noncoding regions, we estimated the long-term effective population size of humans to be 11,000 +/- 2800 using Tajima's estimator and 17,600 +/- 4700 using Watterson's estimator and the age of the most recent common ancestor to be 860,000 +/- 258,000 years ago.

Genomics refutes an exclusively African origin of humans

Ten years ago, evidence from genetics gave strong support to the "recent African origin" view of the evolution of modern humans, which posits that Homo sapiens arose as a new species in Africa and subsequently spread, leading to the extinction of other archaic human species. Subsequent data from the nuclear genome not only fail to support this model, they do not support any simple model of human demographic history. In this paper, we study a process in which the modern human phenotype originates in Africa and then advances across the world by local demic diffusion, hybridization, and natural selection. While the multiregional model of human origins posits a number of independent single locus selective sweeps, and the "out of Africa" model posits a sweep of a new species, we study the intermediate case of a phenotypic sweep. Numerical simulations of this process replicate many of the seemingly contradictory features of the genetic data, and suggest that as much as 80% of nuclear loci have assimilated genetic material from non-African archaic humans.

Worldwide genetic variation at the 3'-UTR region of the LDLR gene: possible influence of natural selection

The low density lipoprotein receptor gene (LDLR) contains many Alu insertions, and is especially Alu-rich at its 3'-untranslated region (3'-UTR). Previous studies suggested that the LDLR 3'-UTR could regulate gene expression by the stabilization of its mRNA. Given the faster Alu evolutionary rate, and wondering about its consequences in a possibly regulatory locus, we have studied approximately 800 bp of 222 chromosomes from individuals of African, Asian, Caucasian and Amerind ancestry, to better understand the evolution of the worldwide genetic diversity at this locus. Twenty-one polymorphic sites, distributed in 15 haplotypes, were found. High genetic diversity was observed, concentrated in one Alu insertion (Alu U), which also shows a fast evolutionary rate. Genetic diversity is similar in all populations except Amerinds, suggesting a bottleneck during the peopling of the American continent. Three haplotype clusters (A, B, C) are distinguished, cluster A being the most recently formed (approximately 500,000 years ago). No clear geographic structure emerges from the haplotype network, the global F(st) (0.079) being lower than the average for the human genome. When ancestral population growth is taken into account, neutrality statistics are higher than expected, possibly suggesting the action of balancing selection worldwide.

Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes

The human N-acetyltransferase genes NAT1 and NAT2 encode two phase-II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called slow-acetylation phenotype reach high frequencies worldwide, which questions the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through the resequencing and genotyping of NAT1, NAT2, and the pseudogene NATP in a collection of 13 different populations with distinct ethnic backgrounds and demographic pasts. This combined study design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the long-range haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection, whereas NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in western/central Eurasians. This haplotype harbors the mutation 341T-->C and encodes the "slowest-acetylator" NAT2 enzyme, suggesting a general selective advantage for the slow-acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past approximately 6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse drug reactions. On the whole, the patterns observed for NAT2 well illustrate how geographically and temporally fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.

SNP selection at the NAT2 locus for an accurate prediction of the acetylation phenotype

PURPOSE

Genetic polymorphisms in the N-acetyltransferase 2 gene determine the individual acetylator status, which influences both the toxicity and efficacy profile of acetylated drugs. Determination of an individual's acetylation phenotype prior to initiation of therapy, through DNA-based tests, should permit to improve therapy response and reduce adverse events. However, due to extensive linkage disequilibrium between markers within NAT2, the genotyping of closely spaced markers yields highly redundant data: testing them all is expensive and often unnecessary. The objective of this study is to establish the optimal strategy to define, in the genetic context of a given ethnic group, the most informative set of single-nucleotide polymorphisms that best enables accurate prediction of acetylation phenotype.

METHODS

Three classification methods have been investigated (classification trees, artificial neural networks and multifactor dimensionality reduction method) in order to find the optimal set of single-nucleotide polymorphisms enabling the most efficient classification of individuals in rapid and slow acetylators.

RESULTS

Our results show that, in almost all population samples, only one or two single-nucleotide polymorphisms would be enough to obtain a good predictive capacity with no or only a modest reduction in power relative to direct assays of all common markers. In contrast, in Black African populations, where lower levels of linkage disequilibrium are observed at NAT2, a larger number of single-nucleotide polymorphisms are required to predict acetylation phenotype.

CONCLUSION

The results of this study will be helpful for the design of time- and cost-effective pharmacogenetic tests (adapted to specific populations) that could be used as routine tools in clinical practice.

The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L region

The innate immunity system constitutes the first line of host defense against pathogens. Two closely related innate immunity genes, CD209 and CD209L, are particularly interesting because they directly recognize a plethora of pathogens, including bacteria, viruses, and parasites. Both genes, which result from an ancient duplication, possess a neck region, made up of seven repeats of 23 amino acids each, known to play a major role in the pathogen-binding properties of these proteins. To explore the extent to which pathogens have exerted selective pressures on these innate immunity genes, we resequenced them in a group of samples from sub-Saharan Africa, Europe, and East Asia. Moreover, variation in the number of repeats of the neck region was defined in the entire Human Genome Diversity Panel for both genes. Our results, which are based on diversity levels, neutrality tests, population genetic distances, and neck-region length variation, provide genetic evidence that CD209 has been under a strong selective constraint that prevents accumulation of any amino acid changes, whereas CD209L variability has most likely been shaped by the action of balancing selection in non-African populations. In addition, our data point to the neck region as the functional target of such selective pressures: CD209 presents a constant size in the neck region populationwide, whereas CD209L presents an excess of length variation, particularly in non-African populations. An additional interesting observation came from the coalescent-based CD209 gene tree, whose binary topology and time depth (approximately 2.8 million years ago) are compatible with an ancestral population structure in Africa. Altogether, our study has revealed that even a short segment of the human genome can uncover an extraordinarily complex evolutionary history, including different pathogen pressures on host genes as well as traces of admixture among archaic hominid populations.

Species status and phylogeography of two closely related Coptolabrus species (Coleoptera: Carabidae) in South Korea inferred from mitochondrial and nuclear gene sequences

We investigated the species status and intraspecific phylogeography in South Korea of two ground beetle species, Coptolabrus jankowskii and Coptolabrus smaragdinus (Coleoptera: Carabidae), using statistical parsimony networks and nested clade analyses based on sequences from the mitochondrial cytochrome oxidase subunit I (COI) and nuclear phosphoenolpyruvate carboxykinase (PepCK) and wingless (Wg) genes. Although traditional parsimony tree construction generally failed to resolve interspecific relationships and construct biologically meaningful genealogies, analysis using statistical parsimony networks yielded statistically significant inter- and intraspecific genealogical structures. We found that although these two species represent a notable case of trans-species polymorphisms in both mitochondrial and nuclear gene sequences, their status as separate species was evidenced by the nonrandom association between species and nested clades at various nesting levels. The exceptional occurrence of shared identical or very similar COI sequences was considered to be the result of introgressive hybridization. In addition, range expansion and fragmentation events across the Korean Peninsula and adjacent islands were inferred from nested clade phylogeographical analyses. The COI gene revealed the geographical divergence of major eastern and western clades and historical biogeographical events within each major clade, whereas the nuclear PepCK gene, which did not reveal corresponding east-west clades, indicated past fragmentation and range expansion across wide areas that may have been the result of older biogeographical events. Thus, phylogeographical inferences drawn from analyses of mitochondrial and nuclear genes can reveal different and potentially complementary information about phylogeographical processes.

Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations

Uncertainty about the demographic history of populations can hamper genome-wide scans for selection based on population genetic models. To obtain a portrait of the effects of demographic history on genome variability patterns in Drosophila melanogaster populations, we surveyed noncoding DNA polymorphism at 10 X-linked loci in large samples from three African and two non-African populations. All five populations show significant departures from expectations under the standard neutral model. We detect weak but significant differentiation between East (Kenya and Zimbabwe) and West/Central sub-Saharan (Gabon) African populations. A skew toward high-frequency-derived polymorphisms, elevated levels of linkage disequilibrium (LD) and significant heterogeneity in levels of polymorphism and divergence in the Gabon sample suggest that this population is further from mutation-drift equilibrium than the two Eastern African populations. Both non-African populations harbor significantly higher levels of LD, a large excess of high-frequency-derived mutations and extreme heterogeneity among loci in levels of polymorphism and divergence. Rejections of the neutral model in D. melanogaster populations using these and similar features have been interpreted as evidence for an important role for natural selection in shaping genome variability patterns. Based on simulations, we conclude that simple bottleneck models are sufficient to account for most, if not all, polymorphism features of both African and non-African populations. In contrast, we show that a steady-state recurrent hitchhiking model fails to account for several aspects of the data. Demographic departures from equilibrium expectations in both ancestral and derived populations thus represent a serious challenge to detecting positive selection in genome-wide scans using current methodologies.

Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population

Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.

Conservation of theRB1gene in human and primates

Mutations in the RB1 gene are associated with retinoblastoma, which has served as an important model for understanding hereditary predisposition to cancer. Despite the great scrutiny that RB1 has enjoyed as the prototypical tumor suppressor gene, it has never been the object of a comprehensive survey of sequence variation in diverse human populations and primates. Therefore, we analyzed the coding (2,787 bp) and adjacent intronic and untranslated (7,313 bp) sequences of RB1 in 137 individuals from a wide range of ethnicities, including 19 Asian Indian hereditary retinoblastoma cases, and five primate species. Aside from nine apparently disease-associated mutations, 52 variants were identified. They included six singleton, coding variants that comprised five amino acid replacements and one silent site. Nucleotide diversity of the coding region (pi=0.0763+/-1.35 x 10(-4)) was 52 times lower than that of the noncoding regions (pi=3.93+/-5.26 x 10(-4)), indicative of significant sequence conservation. The occurrence of purifying selection was corroborated by phylogeny-based maximum likelihood analysis of the RB1 sequences of human and five primates, which yielded an estimated ratio of replacement to silent substitutions (omega) of 0.095 across all lineages. RB1 displayed extensive linkage disequilibrium over 174 kb, and only four unique recombination events, two in Africa and one each in Europe and Southwest Asia, were observed. Using a parsimony approach, 15 haplotypes could be inferred. Ten were found in Africa, though only 12.4% of the 274 chromosomes screened were of African origin. In non-Africans, a single haplotype accounted for from 63 to 84% of all chromosomes, most likely the consequence of natural selection and a significant bottleneck in effective population size during the colonization of the non-African continents.

Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes

To dissect the haplotype structure of candidate genes for disease association studies, it is important to understand the nature of genetic variation at these loci in different populations. We present a survey of haplotype structure and linkage disequilibrium of chemokine and chemokine receptor genes in 11 geographically-distinct population samples (n=728). Chemokine proteins are involved in intercellular signalling and the immune response. These molecules are important modulators of human immunodeficiency virus (HIV)-1 infection and the progression of the acquired immune deficiency syndrome, tumour development and the metastatic process of cancer. To study the extent of genetic variation in this gene family, single nucleotide polymorphisms (SNPs) from 13 chemokine and chemokine receptor genes were genotyped using the 5' nuclease assay (TaqMan). SNP haplotypes, estimated from unphased genotypes using the Expectation-Maximization-algorithm, are described in a cluster of four CC-chemokine receptor genes (CCR3, CCR2, CCR5 and CCRL2) on chromosome 3p21, and a cluster of three CC-chemokine genes [MPIF-1 (CCL23), PARC (CCL18) and MIP-1alpha (CCL3)] on chromosome 17q11-12. The 32 base pair (bp) deletion in exon 4 of CCR5 was also included in the haplotype analysis of 3p21. A total of 87.5 per cent of the variation of 14 biallelic loci scattered over 150 kilobases of 3p21 is explained by 11 haplotypes which have a frequency of at least 1 per cent in the total sample. An analysis of haplotype blocks in this region indicates recombination between CCR2 and CCR5, although long-range pairwise linkage disequilibrium across the region appears to remain intact on two common haplotypes. A reduced-median network demonstrates a clear relationship between 3p21 haplotypes, rooted by the putative ancestral haplotype determined by direct sequencing of four primate species. Analysis of six SNPs on 17q11-12 indicates that 97.5 per cent of the variation is explained by 15 haplotypes, representing at least 1 per cent of the total sample. Additionally, a possible signature of selection at a non-synonymous coding SNP (M106V) in the MPIF-1 (CCL23) gene warrants further study. We anticipate that the results of this study of chemokine and chemokine receptor variation will be applicable to more extensive surveys of long-range haplotype structure in these gene regions and to association studies of HIV-1 disease and cancer.

A structured ancestral population for the evolution of modern humans

The view that modern humans evolved through a bottleneck from a single founding group of archaic Homo is being challenged by new analyses of contemporary genetic variation. A wide range of middle to late Pleistocene ages for gene genealogies and evidence for early population structures point to a diverse and scattered ancestry associated with a metapopulation history of local extinctions, re-colonization and admixture. A different balance of the same processes has shaped chimpanzee diversity.