山顶洞人与现代华北人头骨非测量性特征比较及中国更新世晚期人类演化的一些问题

山顶洞人化石是迄今在东亚地区发现的数量最为丰富、保存状态最为完好的更新世晚期人类化石。多年来,山顶洞人作为东亚地区更新世晚期人类的代表,在研究东亚地区现代蒙古人种及美洲印第安人起源方面发挥着重要作用。随着对现代人起源与演化研究的深入,学术界对更新世晚期人类演化及现代人群形成过程的许多细节及演化机制予以了越来越多的注意,提出了现代人群出现时间及现代人群分化时间的概念。一些研究对山顶洞人的演化程度及其在东亚地区现代人群形成上的作用也提出了不同看法。为了深入探讨这些问题,本文对12项颅骨非测量特征在山顶洞人与现代中国人的表现情况进行了对比研究。发现有8项特征在山顶洞人与现代中国人之间具有不同的表现,作者认为山顶洞人在颅骨特征表现上较现代中国人具有更多的原始性。在此基础上,作者就更新世晚期人群内部变异、现代人群特征标准等问题进行了讨论。     

Global invasion history of the Mediterranean recluse spider: a concordance with human expansion

The dispersal of modern humans from their African origins to the rest of the occupied world is a topic of lively debate centering principally on single versus multiple dispersals. The Mediterranean recluse spider Loxosceles rufescens, a significant pest, has gained much of its current distribution through commensalism with humans. Therefore, the matrilineal history of this spider should reflect dispersal patterns of human females. Here, an assessment of genetic variation at mitochondrial markers in 347 colonies of L. rufescens from 104 geographic sites worldwide reveals a north African origin of the global populations of L. rufescens. This involves at least three separate events among which two involve coincidental dispersals, including one to north Africa, Europe, Asia, North America, and Australia and the other to north Africa, Europe, and Asia only. North African L. rufescens appear to have expanded initially into Israel and subsequently spread into Greece, where a subset of these populations went eastward into Iran and southeastern Asia. This corresponds to the modern human southern dispersal theory. Chinese populations appear to have expanded approximately 42 710–46 008 yr ago. The initial split between the Greek and Chinese populations dates to 41 412–44 444 yr ago, which coincides with the expansion of modern humans into Southeast and East Asia. Thus, the matrilineal history of Asian L. rufescens tracks the history of human dispersals over tens of thousands of years.     

Comparaison de l'expression de certains caractères crâniens sur les hominidés chinois du Pléistocène récent et de l'Holocène (grotte supérieure de Zhoukoudian, sites de Longxian et de Yanqing)

The human remains recovered from “Grotte supérieure de Zhoukoudian” are the best-preserved Late Pleistocene human fossils in East Asia. For decades, as the representative of the Late Pleistocene human in East Asia, the Upper Cave skulls have been playing important role in the research of origins of modern Mongoloids and American Indians. With the advance of the origin and evolution of modern humans, more attention has been paid to the details and the mechanisms for the late Pleistocene human evolution and the formation of modern human populations. Both the origin and diversification of modern humans have been stressed. Some studies further trigger the debaters on the Upper Cave Man concerning its evolutionary level and its role in the formation of modern human populations in East Asia. To further explore these problems, we examined and compared 12 non-metric features on the 3 Late Pleistocene Upper Cave skulls and 162 Holocene individuals earthed from two archaeological sites of North China (Longxian and Yanqing). Our results indicate that 8 on the 12 features have different expression patterns between Upper Cave Man and recent Chinese leading the authors to believe that more primitive expressions appeared on the Upper Cave Man than on recent Chinese populations. Based on these findings, some problems on the intragroup variation in Late Pleistocene and Holocene populations are discussed.     

Human genome diversity

Human genome diversity studies analyse genetic variation among individuals and between populations in order to understand the origins and evolution of anatomically modern humans (Homo sapiens sapiens). The availability of thousands of DNA polymorphisms (genetic markers) brings analytic power to these studies. Human genome diversity studies have clearly shown that the large part of genetic variability is due to differences among individuals within populations rather than to differences between populations, effectively discrediting a genetic basis of the concept of ‘race’. Evidence from paleontology, archaeology and genetic diversity studies is quite consistent with an African origin of modern humans more than 100 000 years ago. The evidence favors migrations out of African as the source of the original peopling of Asia, Australia, Europe and Oceania. An international program for the scientific analysis of human genome diversity and of human evolution has been developed. The Human Genome Diversity Project (HGDP) aims to collect and preserve biologic samples from hundreds of populations throughout the world, make DNA from these samples available to scientists and distribute to the scientific community the results of DNA typing with hundreds of genetic markers.     

Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

Background  

Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture.     

On the origin of cattle: How aurochs became cattle and colonized the world

Since their domestication in the Neolithic, cattle have belonged to our cultural heritage. The reconstruction of their history is an active field of research 1 that contributes to our understanding of human history. Archeological data are now supplemented by analyses of modern and ancient samples of cattle with DNA markers of maternal, paternal, or autosomal inheritance. The most recent genetic data suggest that maternal lineages of taurine cattle originated in the Fertile Crescent with a possible contribution of South‐European wild cattle populations, while zebu cattle originate from the Indus Valley. Subsequently, cattle accompanied human migrations, which led to the dispersal of domestic cattle of taurine, indicine, or mixed origin over Asia, Africa, Europe, and the New World. This has resulted in their adaptation to different environments and considerable variation in appearance and performance. More recently, rational management of breeding led to international movements of sires, which again changed the global patterns of genetic diversity.     

Recombination networks as genetic markers in a human variation study of the Old World

We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.     

Feral Cat Globetrotters: genetic traces of historical human‐mediated dispersal

Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA (ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human‐mediated global dispersal patterns of feral cats.     

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin

It is a matter of fact that the human gut microbiome also includes a non‐bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter‐gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre‐agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co‐occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome‐host co‐evolutionary process.     

Tales of the unexpected: Phylogeography of the arctic-alpine model plant Saxifraga oppositifolia (Saxifragaceae) revisited

Arctic-alpine biota occupy enormous areas in the Arctic and the northern hemisphere mountain ranges and have undergone major range shifts during their comparatively short history. The origins of individual arctic-alpine species remain largely unknown. In the case of the Purple saxifrage, Saxifraga oppositifolia, an important model for arctic-alpine plants, phylogeographic studies have remained inconclusive about early stages of the species' spatiotemporal diversification but have provided evidence for long-range colonization out of a presumed Beringian origin to cover today's circumpolar range. We re-evaluated the species' large-scale range dynamics based on a geographically extended sampling including crucial areas such as Central Asia and the (south-)eastern European mountain ranges and employing up-to-date phylogeographic analyses of a plastid sequence data set and a more restricted AFLP data set. In accordance with previous studies, we detected two major plastid DNA lineages also reflected in AFLP divergence, suggesting a long and independent vicariant history. Although we were unable to determine the species' area of origin, our results point to Europe (probably the Alps) and Central Asia, respectively, as the likely ancestral areas of the two main lineages. AFLP data suggested that contact areas between the two clades in the Carpathians, Northern Siberia and western Greenland were secondary. In marked contrast to high levels of diversity revealed in previous studies, populations from the major arctic refugium Beringia did not exhibit any plastid sequence polymorphism. Our study shows that adequate sampling of the southern, refugial populations is crucial for understanding the range dynamics of arctic-alpine species.     

Palatine torus in the pre-conquest inhabitants of the Canary Islands.

An unusually high frequency of palatine torus in prehistoric Canary Islands skeletal remains is investigated in terms of population origins, evolutionary forces (gene flow and genetic drift) and environmental effects. Palatine torus frequencies (percent presence) are compared between the Canary Islands sample and skeletal samples from proposed ancestral regions, including northwest Africa, northeast Africa, sub-Saharan Africa, southern Europe, northern Europe and western Asia. The frequency of palatine torus is much higher in the Canary Islands sample (23.8%) than in samples from Northern and sub-Saharan Africa (1.8-6.1%), southern Europe (7.5%) and western Asia (2.1%), but is much lower than in the sample from northern Europe (57.4%). Because biological and archaeological evidence provide strong support for a northwest African origin for indigenous Canary Islands populations, the relatively high occurrence of palatine torus in the Canary Islands populace cannot be explained by an alternative ancestry; rather, it may be best explained by either evolutionary forces such as genetic drift or gene flow, or by environmental forces, such as hard chewing or a heavy dependence on marine foods. Genetic drift and gene flow seem less likely, since frequencies of other dental traits known to be under strong genetic control do not differ greatly between the prehistoric Canary Islands and northwest African samples. Environmental factors such as diet seem the most likely explanation and may include heavy consumption of marine foods, which has been implicated in torus formation.     

Global Genetic Differentiation in a Cosmopolitan Pest of Stored Beans: Effects of Geography,Host-Plant Usage and Anthropogenic Factors

Genetic differentiation can be promoted allopatrically by geographic isolation of populations due to limited dispersal ability and diversification over time or sympatrically through, for example, host-race formation. In crop pests, the trading of crops across the world can lead to intermixing of genetically distinct pest populations. However, our understanding of the importance of allopatric and sympatric genetic differentiation in the face of anthropogenic genetic intermixing is limited. Here, we examined global sequence variation in two mitochondrial and one nuclear genes in the seed beetle Callosobruchus maculatus that uses different legumes as hosts. We analyzed 180 samples from 42 populations of this stored bean pest from tropical and subtropical continents and archipelagos: Africa, the Middle East, South and Southeast Asia, Oceania and South America. For the mitochondrial genes, there was weak but significant genetic differentiation across continents/archipelagos. Further, we found pronounced differentiation among subregions within continents/archipelagos both globally and within Africa but not within Asia. We suggest that multiple introductions into Asia and subsequent intermixing within Asia have generated this pattern. The isolation by distance hypothesis was supported globally (with or without continents controlled) but not when host species was restricted to cowpeas Vigna unguiculata, the ancestral host of C. maculatus. We also document significant among-host differentiation both globally and within Asia, but not within Africa. We failed to reject a scenario of a constant population size in the recent past combined with selective neutrality for the mitochondrial genes. We conclude that mitochondrial DNA differentiation is primarily due to geographic isolation within Africa and to multiple invasions by different alleles, followed by host shifts, within Asia. The weak inter-continental differentiation is most likely due to frequent inter-continental gene flow mediated by human crop trade.     

Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations

Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA^lys) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.     

Human population structure and its effects on sampling Y chromosome sequence variation

The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima's D (TD) and Fu and Li's D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.     

The Seroprevalence of Hepatitis C Antibodies in Immigrants and Refugees from Intermediate and High Endemic Countries: A Systematic Review and Meta-Analysis

MethodsFour electronic databases were searched from database inception until June 17, 2014 for studies reporting the prevalence of HCV antibodies among migrants. Seroprevalence estimates were pooled with a random-effect model and were stratified by age group, region of origin and migration status and a meta-regression was modeled to explore heterogeneity.ResultsData from 50 studies representing 38,635 migrants from all world regions were included. The overall anti-HCV prevalence (representing previous and current infections) was 1.9% (95% CI, 1.4–2.7%, I² 96.1). Older age and region of origin, particularly Sub-Saharan Africa, Asia, and Eastern Europe were the strongest predictors of HCV seroprevalence. The estimated HCV seroprevalence of migrants from these regions was >2% and is higher than that reported for most host populations.ConclusionAdult migrants originating from Asia, Sub-Saharan Africa and Eastern Europe are at increased risk for HCV and may benefit from targeted HCV screening.     

Essential biodiversity variables are not global

Recent initiatives have focused on biological diversity and the ecosystem services that it provides, and have proposed a series of “essential biodiversity variables,” as a means of describing and characterizing that diversity. Although such variables would shed considerable and interesting light on distribution of biodiversity-related dimensions, here, we examine the feasibility of assembling such data resources for terrestrial systems on worldwide extents, to evaluate whether they can be feasibly characterized globally. We found large-scale, consistent information gaps across five EBV-related dimensions (genetic composition, species populations, species traits, community composition, and primary biodiversity data), most markedly across Africa, the Middle East, Central Asia, and Eastern Europe; lesser gaps cover much of Asia and South America. Our results raise concerns that EBV-based initiatives, and the studies and policy decisions that they make, will be constrained from any global inference by these information gaps. Concrete progress towards making EBVs genuinely global will depend on adequate funding, training of high-level personnel, and creation of robust institutions in which to base these initiatives.     

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.     

Subspecies in the global human gut microbiome

Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large‐scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture‐independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single‐nucleotide variation clearly indicates the existence of sub‐populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies‐specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro‐inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.     

Multiple introductions and no loss of genetic diversity: invasion history of Japanese Rose, Rosa rugosa, in Europe

The shrub Rosa rugosa (Japanese Rose), native to East Asia, is considered one of the most troublesome invasive plant species in natural or semi-natural habitats of northern Europe and has proven very difficult to control. We aimed at disentangling the species’ invasion history in Europe, including determining the number of introductions and their geographic origin, and at investigating whether populations in the introduced and native ranges differ in genetic diversity, structure and degree of differentiation. We found that introduced (n = 16) and native (n = 16) populations had similar levels of genetic diversity at seven nuclear SSR (microsatellite) loci. European populations lack isolation by distance and are less genetically differentiated than are populations in East Asia. Multiple and at least three independent colonization events, one of which was particularly successful, gave rise to current R. rugosa populations in Europe. The geographic distribution patterns of these three genetic clusters could not be explained by natural dispersal alone, indicating that human mediated secondary dispersal is driving the expansion in Europe. One cluster representing three of the European populations was most likely derived from NW Japan, whereas the origin of the remaining thirteen populations could not clearly be resolved. The introduction and expansion in Europe occurred with no significant loss of genetic diversity. We conclude that high propagule pressure at the primary establishment phase is the most parsimonious explanation for this pattern. A potential for long distance seed dispersal, coastal habitat connectivity and an outcrossing breeding system are factors likely to have enabled populations of R. rugosa to avoid detrimental effects of genetic bottlenecks and will further increase the species’ range size and abundance in Europe. We recommend that human-mediated dispersal should be prevented in order to halt the continued expansion.