An African origin for the intimate association between humans and Helicobacter pylori

Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic differentiation, the age of an association between these bacteria with humans remains highly controversial. Here we show, using sequences from a large data set of bacterial strains that, as in humans, genetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale. Like humans, simulations indicate that H. pylori seems to have spread from east Africa around 58,000 yr ago. Even at more restricted geographic scales, where IBD tends to become blurred, principal component clines in H. pylori from Europe strongly resemble the classical clines for Europeans described by Cavalli-Sforza and colleagues. Taken together, our results establish that anatomically modern humans were already infected by H. pylori before their migrations from Africa and demonstrate that H. pylori has remained intimately associated with their human host populations ever since.     

Early human occupation of the Red Sea coast of Eritrea during the last interglacial

The geographical origin of modern humans is the subject of ongoing scientific debate. The 'multiregional evolution' hypothesis argues that modern humans evolved semi-independently in Europe, Asia and Africa between 100,000 and 40,000 years ago, whereas the 'out of Africa' hypothesis contends that modern humans evolved in Africa between 200 and 100 kyr ago, migrating to Eurasia at some later time. Direct palaeontological, archaeological and biological evidence is necessary to resolve this debate. Here we report the discovery of early Middle Stone Age artefacts in an emerged reef terrace on the Red Sea coast of Eritrea, which we date to the last interglacial (about 125 kyr ago) using U-Th mass spectrometry techniques on fossil corals. The geological setting of these artefacts shows that early humans occupied coastal areas and exploited near-shore marine food resources in East Africa by this time. Together with similar, tentatively dated discoveries from South Africa this is the earliest well-dated evidence for human adaptation to a coastal marine environment, heralding an expansion in the range and complexity of human behaviour from one end of Africa to the other. This new, wide-spread adaptive strategy may, in part, signal the onset of modern human behaviour, which supports an African origin for modern humans by 125 kyr ago.     

Y-chromosome evidence for no independent origin of modern human in China

East Asia is one of the few regions in the world where a large number of human fossils have been unearthed. The continuity of hominid fossils in East Asia, particularly in China has been presented as strong evidence supporting an independent origin of modern humans in this area. To search for such evidence of a possible independent origin of modern humans in China, a total of 9988 male individuals were sampled across China. Three Y-chromosome biallelic markers (M89, M130 and YAP), which were located at the non-recombinant region of Y-chromosome, were typed among the samples. Our result showed that all the individuals carry a mutation at one of the three loci. The three mutations (M89T, M130T, YAP⁺) coalesce to another mutation (M168T), which was originally derived from Africa about 31000 to 79000 years ago. In other words, all Y-chromosome samples from China, with no exception, were originally derived from a lineage of African origin. Hence, we conclude that even a very minor contribution ofin situ hominid origin in China cannot be supported by the Y-chromosome evidence.     

Huanglong Cave, a new late Pleistocene hominid site in Hubei Province, China

For the past two decades, the modern human origins debate has received significant interest from both the scientific community and the public. The two hypothe- ses “Out of Africa” and “Mutiregional evolution” are focuses of this debate[1-3]. In partic…     

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.     

Craniometric evidence for Palaeoamerican survival in Baja California

A current issue on the settlement of the Americas refers to the lack of morphological affinities between early Holocene human remains (Palaeoamericans) and modern Amerindian groups, as well as the degree of contribution of the former to the gene pool of the latter. A different origin for Palaeoamericans and Amerindians is invoked to explain such a phenomenon. Under this hypothesis, the origin of Palaeoamericans must be traced back to a common ancestor for Palaeoamericans and Australians, which departed from somewhere in southern Asia and arrived in the Australian continent and the Americas around 40,000 and 12,000 years before present, respectively. Most modern Amerindians are believed to be part of a second, morphologically differentiated migration. Here we present evidence of a modern Amerindian group from the Baja California Peninsula in Mexico, showing clearer affinities with Palaeoamerican remains than with modern Amerindians. Climatic changes during the Middle Holocene probably generated the conditions for isolation from the continent, restricting the gene flow of the original group with northern populations, which resulted in the temporal continuity of the Palaeoamerican morphological pattern to the present.     

Pleistocene Homo sapiens from Middle Awash,Ethiopia

The origin of anatomically modern Homo sapiens and the fate of Neanderthals have been fundamental questions in human evolutionary studies for over a century. A key barrier to the resolution of these questions has been the lack of substantial and accurately dated African hominid fossils from between 100,000 and 300,000 years ago. Here we describe fossilized hominid crania from Herto, Middle Awash, Ethiopia, that fill this gap and provide crucial evidence on the location, timing and contextual circumstances of the emergence of Homo sapiens. Radioisotopically dated to between 160,000 and 154,000 years ago, these new fossils predate classic Neanderthals and lack their derived features. The Herto hominids are morphologically and chronologically intermediate between archaic African fossils and later anatomically modern Late Pleistocene humans. They therefore represent the probable immediate ancestors of anatomically modern humans. Their anatomy and antiquity constitute strong evidence of modern-human emergence in Africa.     

Unexpectedly recent dates for human remains from Vogelherd

The human skeletal remains from the Vogelherd cave in the Swabian Jura of southwestern Germany are at present seen as the best evidence that modern humans produced the artefacts of the early Aurignacian. Radiocarbon measurements from all the key fossils from Vogelherd show that these human remains actually date to the late Neolithic, between 3,900 and 5,000 radiocarbon years before present (bp). Although many questions remain unresolved, these results weaken the arguments for the Danube Corridor hypothesis--that there was an early migration of modern humans into the Upper Danube drainage--and strengthen the view that Neanderthals may have contributed significantly to the development of Upper Palaeolithic cultural traits independent of the arrival of modern humans.     

Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans

Heritable variation is the raw material for evolutionary change, and understanding its genetic basis is one of the central problems in modern biology. We investigated the genetic basis of a classic phenotypic dimorphism in the nematode Caenorhabditis elegans. Males from many natural isolates deposit a copulatory plug after mating, whereas males from other natural isolates?including the standard wild-type strain (N2 Bristol) that is used in most research laboratories?do not deposit plugs. The copulatory plug is a gelatinous mass that covers the hermaphrodite vulva, and its deposition decreases the mating success of subsequent males. We show that the plugging polymorphism results from the insertion of a retrotransposon into an exon of a novel mucin-like gene, plg-1, whose product is a major structural component of the copulatory plug. The gene is expressed in a subset of secretory cells of the male somatic gonad, and its loss has no evident effects beyond the loss of male mate-guarding. Although C. elegans descends from an obligate-outcrossing, male?female ancestor, it occurs primarily as self-fertilizing hermaphrodites. The reduced selection on male?male competition associated with the origin of hermaphroditism may have permitted the global spread of a loss-of-function mutation with restricted pleiotropy.     

Patterns and rates of enamel growth in the molar teeth of early hominids

A recent study of the surface manifestation of incremental lines associated with enamel formation suggested that the crowns of early hominid incisor teeth were formed more rapidly than those of modern humans. In the absence of comparative data, the authors were forced to assume that enamel increments in fossil teeth were similar to those in modern humans. We have used evidence from the fractured surfaces of molar teeth to deduce estimates for both long- and short-period incremental growth markers within enamel in east African 'robust' australopithecine and early Homo teeth. We conclude that in these early hominids, crown formation times in posterior teeth, particularly in the large thick enamelled molar teeth of the east African 'robust' australopithecines, were shorter than those of modern humans. This evidence, considered together with data on crown and root formation times in modern apes, suggests that the posterior teeth in these hominids both formed and erupted more rapidly than those of modern man. These results have implications for attempts to assess dental and skeletal maturity in hominids.     

Mitochondrial genome variation and the origin of modern humans

The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.     

Genetic diversity of rice cultivars （Oryza sativa L.） in China and the temporal trends in recent fifty years

Public concern is often expressed at cultivars because the domestication and modern plant breeding have led to a reduction in the genetic diversity of crops and loss of genes, which could result in crops' genetic vulnerability to changes in the spectrum of pestssity of varieties in this zone is very important to the whole rice production in China. REZV, a important japonica rice production areas with more than 278 thousands ha rice which was about 71% of rice area in north China, accounted fo…     

An extant cichlid fish radiation emerged in an extinct Pleistocene lake

The haplochromine cichlid fish of the East African Great Lakes represent some of the fastest and most species-rich adaptive radiations known, but rivers in most of Africa accommodate only a few morphologically similar species of haplochromine cichlid fish. This has been explained by the wealth of ecological opportunity in large lakes compared with rivers. It is therefore surprising that the rivers of southern Africa harbour many, ecologically diverse haplochromines. Here we present genetic, morphological and biogeographical evidence suggesting that these riverine cichlids are products of a recent adaptive radiation in a large lake that dried up in the Holocene. Haplochromine species richness peaks steeply in an area for which geological data reveal the historical existence of Lake palaeo-Makgadikgadi. The centre of this extinct lake is now a saltpan north of the Kalahari Desert, but it once hosted a rapidly evolving fish species radiation, comparable in morphological diversity to that in the extant African Great Lakes. Importantly, this lake seeded all major river systems of southern Africa with ecologically diverse cichlids. This discovery reveals how local evolutionary processes operating during a short window of ecological opportunity can have a major and lasting effect on biodiversity on a continental scale.     

Genetic evidence for Near-Eastern origins of European cattle

The limited ranges of the wild progenitors of many of the primary European domestic species point to their origins further east in Anatolia or the fertile crescent. The wild ox (Bos primigenius), however, ranged widely and it is unknown whether it was domesticated within Europe as one feature of a local contribution to the farming economy. Here we examine mitochondrial DNA control-region sequence variation from 392 extant animals sampled from Europe, Africa and the Near East, and compare this with data from four extinct British wild oxen. The ancient sequences cluster tightly in a phylogenetic analysis and are clearly distinct from modern cattle. Network analysis of modern Bos taurus identifies four star-like clusters of haplotypes, with intra-cluster diversities that approximate to that expected from the time depth of domestic history. Notably, one of these clusters predominates in Europe and is one of three encountered at substantial frequency in the Near East. In contrast, African diversity is almost exclusively composed of a separate haplogroup, which is encountered only rarely elsewhere. These data provide strong support for a derived Near-Eastern origin for European cattle.     

High genetic diversity of Tibetan Mastiffs revealed by mtDNA sequences

Many studies have been reported the origin and evolution of domesticated animals, particularly dogs, however, few have system-atically examined the Tibetan Mastiff (TM), a dog that lives primarily in the Qing-Tibet Plateau. Here, we study the origin and evolution of TM based on the population comparison of mtDNA D-loop sequences from TM and other dogs across the world. Intriguingly, non-simultaneous arrivals of Tibetan Mastiffs ancestors to Tibet occurred, which may result from continuous Tibetans’ settlement on Qing-Tibet Plateau supported by archaeological and genetic evidence. High genetic and haplotype diversity and robust haplotypes sharing with other dogs unique to East Asia are observed in Tibetan Mastiff, supporting that it is a very archaic breed derived probably from East Asia.     

Archaeological study of ostrich eggshell beads collected from SDG site

Ostrich eggshell beads and fragments collected from SDG site reflect primordial art and a kind of symbolic behavior of modern humans. Based on stratigraphic data and OSL dating, these ostrich eggshell beads are probably in Early Holocene （〈 10 ka BP）o Two different prehistoric manufacturing pathways are usually used in the manufacture of ostrich eggshell beads in Upper Paleolithic. Accord- ing to statistic analysis of the characteristics of ostrich eggshell beads, Pathway 1 is identified from these collections. In pathway 1, blanks are drilled prior to being trimmed to rough discs. They exhibit great potential for the study of the origin of primordial art and the development of ancient cultures and provide important data for studying behavioral options adopted by hominids in SDG area. In addition, they bear important implications for the origin of modern humans in East Asia.     

Transcription regulation and animal diversity

Whole-genome sequence assemblies are now available for seven different animals, including nematode worms, mice and humans. Comparative genome analyses reveal a surprising constancy in genetic content: vertebrate genomes have only about twice the number of genes that invertebrate genomes have, and the increase is primarily due to the duplication of existing genes rather than the invention of new ones. How, then, has evolutionary diversity arisen? Emerging evidence suggests that organismal complexity arises from progressively more elaborate regulation of gene expression.     

Evolution of word-syllable structures and the diversity of world languages

A fundamental difference among modem lan- guages in the world are made by word-syllable structures （WSS）, not by distinctive phonemes. Language diversity is supposed to be an evolutionary result of the WSSs, which is decided by types of syllable constitution and the length of word by syllables. Here we use Swadesh lists of 179 modem languages to analyze their geographic distribution of WSS diversity index and try to discover their developing positions and depths in the evolutionary processes. We also set an ideal WSS offset model for languages, calculate the offset distance and offset direction of each language, and then divide languages into three groups according to the data result, each of which represents an evolutionary type. Our conclusion is that the WSS diversity and the WSS offset model represent the evolutionary trend of diversity and the evolutionary process of human languages in the world. In addition, every language nowadays keeps the most primary WSS features to some extent. Therefore, the WSS may be regarded as genetic factors of human languages.     

Evolution and molecular epidemiology of foot-and-mouth disease virus in China

Foot-and-mouth disease (FMD),caused by foot-and-mouth disease virus (FMDV),is considered one of the most important viral diseases of cloven-hoofed animals,causing severe economic losses in affected regions of the world.Three serotypes (A,O,and Asia 1) of FMDV have been identified in China since 1958.In addition,the occurrence of novel subtypes within these serotypes has made the epidemiology of FMDV more complicated over the last few years.In this review,we summarize the history and the current epidemiological situation in China,genetic diversity (e.g.,quasispecies dynamics,antigenic heterogeneity,and functional constraints),intertypic recombination,and the evidence for positive selection of different FMDV serotypes.We also assess these genetic data to understand the origin,evolution,and transmission of FMDV,the findings of which may be useful in developing control measures for future epidemics.     

Isotope assessment of Holocene human diets in the southwestern Cape, South Africa

Models of seasonal mobility to exploit seasonally abundant food sources have been proposed for prehistoric hunter-gatherers in many parts of the world. Some such hypotheses involve fundamental and insufficiently tested assumptions about the nature of both hunter-gatherer societies and the archaeological evidence that they leave. The present study is an independent test of such a hypothesis proposed for the southwestern Cape of South Africa. In this strongly ecologically differentiated area there are four distinct ecological zones that would have offered four different sets of resources to prehistoric people. Obvious modern seasonal fluctuations in these resources, plus a considerable amount of archaeological evidence, led to the suggestion that prehistoric hunter-gatherers moved in a regular seasonal cycle across the zones; this would have allowed them to make maximum use of temporarily plentiful plant and animal foods in some areas, while avoiding lean periods in others. However, as reported here, direct measurements of food intake, as reflected in the stable carbon isotope ratios of archaeological human skeletons, reveal that this was not the case. The implications of this study extend beyond the relevance to local archaeology to more general questioning of the ways in which archaeological data should be used to generate hypotheses.