African Origin of Modern Humans in East Asia: A Tale of 12,000 Y Chromosomes

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

Fine-Scale Population Admixture Landscape of Tai–Kadai-Speaking Maonan in Southwest China Inferred From Genome-Wide SNP Data

Guizhou Province harbors extensive ethnolinguistic and cultural diversity with Sino-Tibetan-, Hmong–Mien-, and Tai–Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups. The admixture history of Tai–Kadai-speaking populations in Guizhou needed to be characterized further. Thus, we genotyped genome-wide SNP data from 41 Tai–Kadai-speaking Maonan people and made a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the pattern of the sharing alleles and haplotypes. We found a genetic affinity among geographically different Tai–Kadai-speaking populations, especially for Guizhou Maonan people and reference Maonan from Guangxi. Furthermore, formal tests based on the f₃/f₄-statistics further identified an adjacent connection between Maonan and geographically adjacent Hmong–Mien and Sino-Tibetan people, which was consistent with their historically documented shared material culture (Zhang et al., iScience, 2020, 23, 101032). Fitted qpAdm-based two-way admixture models with ancestral sources from northern and southern East Asians demonstrated that Maonan people were an admixed population with primary ancestry related to Guangxi historical people and a minor proportion of ancestry from Northeast Asians, consistent with their linguistically supported southern China origin. Here, we presented the landscape of genetic structure and diversity of Maonan people and a simple demographic model for their evolutionary process. Further whole-genome-sequence–based projects can be presented with more detailed information about the population history and adaptative history of the Guizhou Maonan people.

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.

Role of culture in the emotional response towards komodo dragon in Komodo and Rinca Islands of Komodo National Park

Human emotions towards wildlife were seldom considered in wildlife conservation. This study seeks to identify, explore and understand the local communities perceptions and interactions with Komodo dragons. Data were collected from February to April 2018 in Komodo Village and Rinca Village of Komodo National Park, using close and semi-open questionnaires, three-scale Likert statements and interviews with 60 respondents. Although 98.5% considered Komodo as a dangerous species, in total, 60.6% of Komodo villagers had positive perceptions of their interactions with Komodo, while 47.6% of Rinca’s had moderate perceptions. Komodo attacks were less reported in Komodo Village despite the more frequent direct encounters. Komodo villagers have learnt how to adjust to the dangers, with 13% showed no actions during an encounter with the dragon, 77% pelt the dragon with rocks and 10% pulled it by the tail. On the contrary, 50% of Rinca Villagers, although showed no actions, but reported the sightings, 20% pelt it with rocks, 27% herd it with sticks and 3% hit it with wood. The different responses correlated with the different cultural beliefs and values towards Komodo. All Rinca villagers were migrants with no cultural attachments to the reptile, while for Komodo villagers, the dragons were perceived to be cousins, hence should not be harmed. Such perceptions have resulted in the approximately 83% of Komodo villagers believed they could co-exist with the dragons, and showed higher supports for its conservation (81.5%) than Rinca villagers (65.3%). This study confirms the importance of integrating local cultural values in building supports for conservation.

Human Attitude toward Reptiles: A Relationship between Fear, Disgust, and Aesthetic Preferences

Simple Summary

Although there are many articles about reptiles, no one has ever studied the human perception of reptiles as a whole, a group that would include representatives of different taxonomic clades. Thus, we designed a study of human perception of all reptiles focusing on the relationship between perceived fear, disgust, and aesthetic preferences. Respondents evaluated various reptile images and the results revealed that people tend to perceive them as two clearly distinct groups based on their similar morphotype—legless reptiles (incl. snakes) and other reptiles with legs. In the case of snakes, the most feared species also tend to be perceived as beautiful. Compared to the most feared reptiles with legs (lizards, turtle, crocodiles), the legless once tend to be perceived as more disgusting. In both groups, species perceived as the least beautiful were the same as those rated as the most disgusting. Thus, reptiles cannot be rated as both beautiful and disgusting at the same time.

Abstract

Focusing on one group of animals can bring interesting results regarding our attitudes toward them and show the key features that our evaluation of such animals is based on. Thus, we designed a study of human perception of all reptiles focusing on the relationship between perceived fear, disgust, and aesthetic preferences and differences between snakes and other reptiles. Two sets containing 127 standardized photos of reptiles were developed, with one species per each subfamily. Respondents were asked to rate the animals according to fear, disgust, and beauty on a seven-point Likert scale. Evaluation of reptile species shows that people tend to perceive them as two clearly distinct groups based on their similar morphotype. In a subset of lizards, there was a positive correlation between fear and disgust, while disgust and fear were both negatively correlated with beauty. Surprisingly, a positive correlation between fear and beauty of snakes was revealed, i.e., the most feared species also tend to be perceived as beautiful. Snakes represent a distinct group of animals that is also reflected in the theory of attentional prioritization of snakes as an evolutionary relevant threat.

Is Peking Man Still Our Ancestor?—Race and National Lineage

Since China participated in the Human Genome Project in the 1990s, implications of the debate surrounding the Homo erectus Peking Man’s ancestorship for nationalism wrapped in scientific jargon have been well comprehended by various segments of the society with ultranationalists and a liberal public opinion as the two extremes contesting each other. This divergence also cuts through the Chinese party-state. The discourse on a pure ancestry, an ancestral home, a natural bond between this ancestor and the environment, and most of all, a narrative that attributes remarkable lineal continuity to physical, mental, intellectual and even moral traits unique to this ancestor and its posterity, support fanatical racial nationalisms.

Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia

The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.

Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Background

From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia.

Results

The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.

Conclusions

The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.

Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

DNA methylation plays an important role for mammalian development. However, it is unclear whether the DNA methylation pattern is evolutionarily conserved. The Y chromosome serves as a powerful tool for the study of human evolution because it is transferred between males. In this study, based on deep-rooted pedigrees and the latest Y chromosome phylogenetic tree, we performed epigenetic pattern analysis of the Y chromosome from 72 donors. By comparing their respective DNA methylation level, we found that the DNA methylation pattern on the Y chromosome was stable among family members and haplogroups. Interestingly, two haplogroup-specific methylation sites were found, which were both genotype-dependent. Moreover, the African and Asian samples also had similar DNA methylation pattern with a remote divergence time. Our findings indicated that the DNA methylation pattern on the Y chromosome was conservative during human male history.

Population genetic studies in the genomic sequencing era

Recent advances in high-throughput sequencing technologies have revolutionized the field of population genetics. Data now routinely contain genomic level polymorphism information, and the low cost of DNA sequencing enables researchers to investigate tens of thousands of subjects at a time. This provides an unprecedented opportunity to address fundamental evolutionary questions, while posing challenges on traditional population genetic theories and methods. This review provides an overview of the recent methodological developments in the field of population genetics, specifically methods used to infer ancient population history and investigate natural selection using large-sample, large-scale genetic data. Several open questions are also discussed at the end of the review.

Arab gene geography: From population diversities to personalized medical genomics

Genetic disorders are not equally distributed over the geography of the Arab region. While a number of disorders have a wide geographical presence encompassing 10 or more Arab countries, almost half of these disorders occur in a single Arab country or population. Nearly, one-third of the genetic disorders in Arabs result from congenital malformations and chromosomal abnormalities, which are also responsible for a significant proportion of neonatal and perinatal deaths in Arab populations. Strikingly, about two-thirds of these diseases in Arab patients follow an autosomal recessive mode of inheritance. High fertility rates together with increased consanguineous marriages, generally noticed in Arab populations, tend to increase the rates of genetic and congenital abnormalities. Many of the nearly 500 genes studied in Arab people revealed striking spectra of heterogeneity with many novel and rare mutations causing large arrays of clinical outcomes. In this review we provided an overview of Arab gene geography, and various genetic abnormalities in Arab populations, including disorders of blood, metabolic, circulatory and neoplasm, and also discussed their associated molecules or genes responsible for the cause of these disorders. Although studying Arab-specific genetic disorders resulted in a high value knowledge base, approximately 35% of genetic diseases in Arabs do not have a defined molecular etiology. This is a clear indication that comprehensive research is required in this area to understand the molecular pathologies causing diseases in Arab populations.

Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers

Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region, discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using a molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ∼6 kya (thousand years ago) (assuming a constant substitution rate of 1×10(-9)/bp/year) indicates that ∼40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.

Early human speciation, brain expansion and dispersal influenced by African climate pulses

Early human evolution is characterised by pulsed speciation and dispersal events that cannot be explained fully by global or continental paleoclimate records. We propose that the collated record of ephemeral East African Rift System (EARS) lakes could be a proxy for the regional paleoclimate conditions experienced by early hominins. Here we show that the presence of these lakes is associated with low levels of dust deposition in both West African and Mediterranean records, but is not associated with long-term global cooling and aridification of East Africa. Hominin expansion and diversification seem to be associated with climate pulses characterized by the precession-forced appearance and disappearance of deep EARS lakes. The most profound period for hominin evolution occurs at about 1.9 Ma; with the highest recorded diversity of hominin species, the appearance of Homo (sensu stricto) and major dispersal events out of East Africa into Eurasia. During this period, ephemeral deep-freshwater lakes appeared along the whole length of the EARS, fundamentally changing the local environment. The relationship between the local environment and hominin brain expansion is less clear. The major step-wise expansion in brain size around 1.9 Ma when Homo appeared was coeval with the occurrence of ephemeral deep lakes. Subsequent incremental increases in brain size are associated with dry periods with few if any lakes. Plio-Pleistocene East African climate pulses as evinced by the paleo-lake records seem, therefore, fundamental to hominin speciation, encephalisation and migration.

Genetic polymorphism of human Y chromosome and risk factors for cardiovascular diseases: a study in WOBASZ cohort

Genetic variants of Y chromosome predispose to hypertension in rodents, whereas in humans the evidence is conflicting. Our purpose was to study the distribution of a panel of Y chromosome markers in a cohort from a cross-sectional population-based study on the prevalence of cardiovascular risk factors in Poland (WOBASZ study). The HindIII, YAP Y chromosome variants, previously shown to influence blood pressure, lipid traits or height, as well as SNPs defining main Y chromosome haplogroups, were typed in 3026, 2783 and 2652 samples, respectively. In addition, 4 subgroups (N∼100 each) representing extremes of LDL concentration or blood pressure (BP) were typed for a panel of 17 STRs. The HindIII and YAP polymorphism were not associated with any of the studied traits. Analysis of the haplogroup distribution showed an association between higher HDL level and hg I-M170 (P = 0.02), higher LDL level and hg F*(xI-M170, J2-M172, K-M9) (P = 0.03) and lower BMI and hg N3-Tat (P = 0.04). Analysis of STRs did not show statistically significant differences. Since all these associations lost statistical significance after Bonferroni correction, we conclude that a major role of Y chromosome genetic variation (defined by HindIII, YAP or main Y chromosome haplogroups) in determining cardiovascular risk in Poles is unlikely.

Inferring human history in East Asia from Y chromosomes

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.

The discovery of Artemisia annua L. in the Shengjindian cemetery, Xinjiang, China and its implications for early uses of traditional Chinese herbal medicine qinghao

ETHNOPHARMACOLOGICAL RELEVANCE

Artemisia annua L., with the ancient name of qinghao, is a traditional Chinese herbal medicine. It has appeared in many ancient Chinese medical manuscripts, which describe its uses to include treatment of wounds, alleviating intermittent fevers, as well as enhancing the brightness of eyes and even improving longevity.

MATERIALS AND METHODS

A sheaf of plant remains, including stalks and inflorescence intentionally placed in the corner of a tomb, have been recovered from the Shengjindian cemetery (about 2400-2000 BP on the basis of (14)C dating), Turpan, Xinjiang, China. The morphology of these materials was examined using a stereomicroscope and a scanning electron microscope. Ancient DNA was also extracted from these remains.

RESULTS

By comparing the morphological and DNA characteristics with modern specimens, these plant remains were identified to belong to Artemisia annua L. Owing to its strong fragrance, these plant remains are suggested as serving to disguise the odor of the deceased.

CONCLUSIONS

This is the first material archaeological evidence to date despite numerous records of A. annua in ancient Chinese texts as herbal medicine qinghao, though it seems to have been employed as odor suppressant, not for medical purpose.

Geographical distribution of MTHFR C677T, A1298C and MTRR A66G gene polymorphisms in China: findings from 15357 adults of Han nationality

Background

Methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C and methionine synthase reductase (MTRR) A66G polymorphisms are important genetic determinants for homocysteine (Hcy) levels, and are associated with several disorders. These polymorphisms are heterogeneously distributed worldwide. Our objective was to explore the geographical distributions of these polymorphisms in China.

Methodologies

15357 healthy adults were recruited from 10 regions. Buccal samples were collected and genomic DNA was isolated. Genotyping was performed using the fluorogenic 5′-nuclease assay.

Principal Findings

The prevalence of the three polymorphisms among different populations from China varied significantly and showed apparent geographical gradients. For MTHFR C677T, the frequencies of the 677T allele and the 677TT genotype were significantly higher among northern populations and ranged from the lowest values (24.0% and 6.4%, respectively) in Hainan (southern) to the highest values (63.1% and 40.8%, respectively) in Shandong (northern). For MTHFR A1298C, the 1298C allele and the 1298CC genotype frequencies were significantly higher among southern populations and increased from low values (13.1% and 1.4%, respectively) in Shandong to high values (25.7% and 6.7%, respectively) in Hainan. For A66G, the 66G allele and the 66GG genotype frequencies increased from lower values (23.7% and 5.4%, respectively) in Shandong to higher values (29.2% and 8.6%, respectively) in Hainan. The overall frequency of the 677T allele, 677TT genotype, 1298C allele, 1298CC genotype, 66G allele and 66GG genotype in the Chinese Han population was 45.2%, 23.2%, 18.6%, 3.9%, 25.7%, and 6.6%, respectively. No gender differences were found in the prevalence of both the MTHFR C677T and MTRR A66G polymorphisms.

Conclusions

This study indicates that there are marked geographical variations in the prevalence of the three polymorphisms among Chinese Han populations. Our baseline data may be useful for future researches in related fields.

Anatomically modern human in Southeast Asia (Laos) by 46 ka

Uncertainties surround the timing of modern human emergence and occupation in East and Southeast Asia. Although genetic and archeological data indicate a rapid migration out of Africa and into Southeast Asia by at least 60 ka, mainland Southeast Asia is notable for its absence of fossil evidence for early modern human occupation. Here we report on a modern human cranium from Tam Pa Ling, Laos, which was recovered from a secure stratigraphic context. Radiocarbon and luminescence dating of the surrounding sediments provide a minimum age of 51-46 ka, and direct U-dating of the bone indicates a maximum age of ~63 ka. The cranium has a derived modern human morphology in features of the frontal, occipital, maxillae, and dentition. It is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, and dental morphology. In the context of an increasingly documented archaic-modern morphological mosaic among the earliest modern humans in western Eurasia, Tam Pa Ling establishes a definitively modern population in Southeast Asia at ~50 ka cal BP. As such, it provides the earliest skeletal evidence for fully modern humans in mainland Southeast Asia.

Pollution trees: identifying similarities among complex pollutant mixtures in water and correlating them to mutagenicity

There are relatively few tools available for computing and visualizing similarities among complex mixtures and in correlating the chemical composition clusters with toxicological clusters of mixtures. Using the "intersection and union ratio (IUR)" and other traditional distance matrices on contaminant profiles of 33 specific water samples, we used "pollution trees" to compare these mixtures. The "pollution trees" constructed by neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) methods allowed comparison of similarities among these samples. The mutagenicity of each sample was then mapped to the "pollution tree". The IUR-distance-based measure proved effective in comparing chemical composition and compound level differences between mixtures. We found a robust "pollution tree" containing seven major lineages with certain broad characteristics: treated municipal water samples were different from raw water samples and untreated rural drinking water samples were similar with local water sources. The IUR-distance-based tree was more highly correlated to mutagenicity than were other distance matrices, i.e., MP/ML methods, sampling group, region, or water type. IUR-distance-based "pollution trees" may become important tools for identifying similarities among real mixtures and examining chemical composition clusters in a toxicological context.

Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes

Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.

Challenging views on the peopling history of East Asia: the story according to HLA markers

The peopling of East Asia by the first modern humans is strongly debated from a genetic point of view. A north-south genetic differentiation observed in this geographic area suggests different hypotheses on the origin of Northern East Asian (NEA) and Southern East Asian (SEA) populations. In this study, the highly polymorphic HLA markers were used to investigate East Asian genetic diversity. Our database covers a total of about 127,000 individuals belonging to 84 distinct Asian populations tested for HLA-A, -B, -C, -DPB1, and/or -DRB1 alleles. Many Chinese populations are represented, which have been sampled in the last 30 years but rarely taken into account in international research due to their data published in Chinese. By using different statistical methods, we found a significant correlation between genetics and geography and relevant genetic clines in East Asia. Additionally, HLA alleles appear to be unevenly distributed: some alleles observed in NEA populations are widespread at the global level, while some alleles observed in SEA populations are virtually unique in Asia. The HLA genetic variation in East Asia is also characterized by a decrease of diversity from north to south, although a reverse pattern appears when one only focuses on alleles restricted to Asia. These results reflect a more complex migration history than that illustrated by the "southern-origin" hypothesis, as genetic contribution of ancient human migrations through a northern route has probably been quite substantial. We thus suggest a new overlapping model where northward and southward opposite migrations occurring at different periods overlapped.

Molecular adaptation of modern human populations

Modern humans have gone through varied processes of genetic adaptations when their ancestors left Africa about 100,000 years ago. The environmental stresses and the social transitions (e.g., emergence of the Neolithic culture) have been acting as the major selective forces reshaping the genetic make-up of human populations. Genetic adaptations have occurred in many aspects of human life, including the adaptation to cold climate and high-altitude hypoxia, the improved ability of defending infectious diseases, and the polished strategy of utilizing new diet with the advent of agriculture. At the same time, the adaptations once developed during evolution may sometimes generate deleterious effects (e.g., susceptibility to diseases) when facing new environmental and social changes. The molecular (especially the genome-wide screening of genetic variations) studies in recent years have detected many genetic variants that show signals of Darwinian positive selection in modern human populations, which will not only provide a better understanding of human evolutionary history, but also help dissecting the genetic basis of human complex diseases.

Barrier requirements as the evolutionary "driver" of epidermal pigmentation in humans

Current explanations for the development of epidermal pigmentation during human evolution are not tenable as stand-alone hypotheses. Accordingly, we assessed instead whether xeric- and UV-B-induced stress to the epidermal permeability barrier, critical to survival in a terrestrial environment, could have "driven" the development of epidermal pigmentation. (1) Megadroughts prevailed in central Africa when hominids expanded into open savannahs [approximately 1.5-0.8 million years ago], resulting in sustained exposure to both extreme aridity and erythemogenic UV-B, correlating with genetic evidence that pigment developed approximately 1.2 million years ago. (2) Pigmented skin is endowed with enhanced permeability barrier function, stratum corneum integrity/cohesion, and a reduced susceptibility to infections. The enhanced function of pigmented skin can be attributed to the lower pH of the outer epidermis, likely due to the persistence of (more-acidic) melanosomes into the outer epidermis, as well as the conservation of genes associated with eumelanin synthesis and melanosome acidification (e.g., TYR, OCA2 [p protein], SLC24A5, SLC45A2, MATP) in pigmented populations. Five keratinocyte-derived signals (stem cell factor-->KIT; FOXn1-->FGF2; IL-1alpha, NGF, and p53) are potential candidates to have stimulated the sequential development of epidermal pigmentation in response to stress to the barrier. We summarize evidence here that epidermal interfollicular pigmentation in early hominids likely evolved in response to stress to the permeability barrier.

Large-scale mtDNA screening reveals a surprising matrilineal complexity in east Asia and its implications to the peopling of the region

In order to achieve a thorough coverage of the basal lineages in the Chinese matrilineal pool, we have sequenced the mitochondrial DNA (mtDNA) control region and partial coding region segments of 6,093 mtDNAs sampled from 84 populations across China. By comparing with the available complete mtDNA sequences, 194 of those mtDNAs could not be firmly assigned into the available haplogroups. Completely sequencing 51 representatives selected from these unclassified mtDNAs identified a number of novel lineages, including five novel basal haplogroups that directly emanate from the Eurasian founder nodes (M and N). No matrilineal contribution from the archaic hominid was observed. Subsequent analyses suggested that these newly identified basal lineages likely represent the genetic relics of modern humans initially peopling East Asia instead of being the results of gene flow from the neighboring regions. The observation that most of the newly recognized mtDNA lineages have already differentiated and show the highest genetic diversity in southern China provided additional evidence in support of the Southern Route peopling hypothesis of East Asians. Specifically, the enrichment of most of the basal lineages in southern China and their rather ancient ages in Late Pleistocene further suggested that this region was likely the genetic reservoir of modern humans after they entered East Asia.

The archaeogenetics of Europe

A new timescale has recently been established for human mitochondrial DNA (mtDNA) lineages, making mtDNA at present the most informative genetic marker system for studying European prehistory. Here, we review the new chronology and compare mtDNA with Y-chromosome patterns, in order to summarize what we have learnt from archaeogenetics concerning five episodes over the past 50,000 years which significantly contributed to the settlement history of Europe: the pioneer colonisation of the Upper Palaeolithic, the Late Glacial re-colonisation of the continent from southern refugia after the Last Glacial Maximum, the postglacial re-colonization of deserted areas after the Younger Dryas cold snap, the arrival of Near Easterners with an incipient Neolithic package, and the small-scale migrations along continent-wide economic exchange networks beginning with the Copper Age. The available data from uniparental genetic systems have already transformed our view of the prehistory of Europe, but our knowledge of these processes remains limited. Nevertheless, their legacy remains as sedimentary layers in the gene pool of modern Europeans, and our understanding of them will improve substantially when more mtDNAs are completely sequenced, the Y chromosome more thoroughly analysed, and haplotype blocks of the autosomal genome become amenable to phylogeographic studies.

Genetic perspectives on forager-farmer interaction in the Luangwa valley of Zambia

The transformation from a foraging way of life to a reliance on domesticated plants and animals often led to the expansion of agropastoralist populations at the expense of hunter-gatherers (HGs). In Africa, one of these expansions involved the Niger-Congo Bantu-speaking populations that started to spread southwards from Cameroon/Nigeria approximately 4,000 years ago, bringing agricultural technologies. Genetic studies have shown different degrees of gene flow (sometimes involving sex-biased migrations) between Bantu agriculturalists and HGs. Although these studies have covered many parts of sub-Saharan Africa, the central part (e.g. Zambia) was not yet studied, and the interactions between immigrating food-producers and local HGs are still unclear. Archeological evidence from the Luangwa Valley of Zambia suggests a long period of coexistence ( approximately 1,700 years) of early food-producers and HGs. To investigate if this apparent coexistence was accompanied by genetic admixture, we analyzed the mtDNA control region, Y chromosomal unique event polymorphisms, and 12 associated Y- short tandem repeats in two food-producing groups (Bisa and Kunda) that live today in the Luangwa Valley, and compared these data with available published data on African HGs. Our results suggest that both the Bisa and Kunda experienced at most low levels of admixture with HGs, and these levels do not differ between the maternal and paternal lineages. Coalescent simulations indicate that the genetic data best fit a demographic scenario with a long divergence (62,500 years) and little or no gene flow between the ancestors of the Bisa/Kunda and existing HGs. This scenario contrasts with the archaeological evidence for a long period of coexistence between the two different communities in the Luangwa Valley, and suggests a process of sociocultural boundary maintenance may have characterized their interaction.

Major east-west division underlies Y chromosome stratification across Indonesia

The early history of island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul approximately 45 ka ago and the much later Neolithic expansion of Austronesian-speaking farmers approximately 4 ka ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 single-nucleotide polymorphisms/indels and 12 short tandem repeats, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., Phi(ST) = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M, and S subclades) and likely reflect the initial wave of colonization of the region, whereas the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201 and P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122 and O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.

The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms

Tracing maternal and paternal lineages independently to explore breeding systems and dispersal strategies in natural populations has been high on the wish-list of evolutionary biologists. As males are the heterogametic sex in mammals, such sex-specific patterns can be indirectly observed when Y chromosome polymorphism is combined with mitochondrial sequence information. Over the past decade, Y-chromosomal markers applied to human populations have revealed remarkable differences in the demographic history and behaviour between the sexes. However, with a few exceptions, genetic data tracing the paternal line are lacking in most other mammalian species. This deficit can be attributed to the difficulty of developing Y-specific genetic markers in non-model organisms and the general low levels of polymorphisms observed on the Y chromosome. Here, we present an overview of the currently employed strategies for developing paternal markers in mammals. Moreover, we review the practical feasibility and requirements of various methodological strategies and highlight their future prospects when combined with new molecular techniques such as next generation sequencing.

Lekking displays in contemporary organizations: ethologically oriented, evolutionary and cross-species accounts of male dominance

PURPOSE

The purpose of this paper is to draw on scientific models in conceptualising the evolutionary bases of contemporary behaviours, and make cross-species comparisons, to account for male managerial activities in situ in health organizations.

DESIGN/METHODOLOGY/APPROACH

In the animal world, males of many species display in order to induce females to mate. Such lekking behaviour involves inter alia, strutting, puffing out, catching attention via the use of ornamental physical characteristics, exhibiting gaudily-coloured body parts, singing or splashing, and other courting and wooing strategies. The paper applies these behavioural repertoires as an explanatory device for male-dominant organizational lekking in a set of contemporary settings. It draws on six studies of managerial talk, appearance and behaviour in order to do so.

FINDINGS

Within the organizational lek male managers display mainly by power dressing, positioning, and exercising power and influence via verbal and behavioural means. Social and religious mores prohibit overt sexual coupling in organizations but lekking for other rewards is nevertheless pursued by male managers. The paper explores this managerial patterning, compares it to the lekking behaviour of other species, and discusses points of comparison and departure. It shows how male managers display within various sub-habitats, and discusses the central issues of appearance, tasks and work assignment, physical interaction structure, and talk and physiognomy.

PRACTICAL IMPLICATIONS

Understanding what makes people tick via deep explanations than are customarily rendered is a vital contribution of scholarship to the practical world of management.

ORIGINALITY/VALUE

The evolutionary bases of contemporary behaviours, and cross-species accounts, may prove useful paradigms for other theorists and empiricists in organizational studies, and could encourage the development of a new field that might be labeled evolutionary organizational behaviour.

Boundaries and clines in the West Eurasian Y-chromosome landscape: insights from the European part of Russia

Previous studies of Y chromosome variation have revealed that western Europe, the Volga-Ural region, and the Caucasus differ dramatically with respect to Y-SNP haplogroup composition. The European part of Russia is situated in between these three regions; to determine if these differences reflect clines or boundaries in the Y-chromosome landscape, we analyzed 12 Y-SNPs in 545 males from 12 populations from the European part of Russia. The majority of Russian Y chromosomes (from 74% to 94%) belong to three Y chromosomal lineages [I-M170, R1a1-M17, and N3-TAT] that are also frequent in the rest of east Europe, north Europe, and/or in the Volga-Ural region. We find significant but low correlations between haplogroup frequencies and the geographic location of populations, suggesting gradual change in the Y chromosome gene pool across western Eurasia. However, we also find some significant boundaries between populations, suggesting that both isolation and migration have influenced the Y chromosome landscape.

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Background

The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000–30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario.

Results

In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations.

Conclusion

We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

The biology of the colonizing ape

Hominin evolutionary history is characterized by regular dispersals, cycles of colonization, and entry into novel environments. This article considers the relationship between such colonizing capacity and hominin biology. In general, colonizing strategy favors rapid rates of reproduction and generalized rather than specialized biology. Physiological viability across diverse environments favors a high degree of phenotypic plasticity, which buffers the genome from selective pressures. Colonizing also favors the capacity to access and process information about environmental variability. We propose that early hominin adaptive radiations were based upon the development of such capacities as adaptations to unstable Pliocene environments. These components came together, along with fundamental changes in morphology, behavior, and cognition in the genus Homo, who exploited them in subsequent wider dispersals. Middle Pleistocene hominins and modern humans also show development of further traits, which correspond with successful probing of, and dispersals into, stressful environments. These traits have their precursors in primate or ape biology, but have become more pronounced during hominin evolution. First, short interbirth intervals and slow childhood growth allow human females to provision several offspring simultaneously, increasing the rate of reproduction in favorable conditions. This allows rapid recovery from population crashes, or rapid population growth in new habitats. Second, despite high geographical phenotypic variability, humans have high genetic unity. This is achieved by a variety of levels of plasticity, including physiology, behavior, and technology, which reduce the need to commit to genetic adaptation. Hominin behavior may increasingly have shaped both the ecological niches occupied and the selective pressures acting back on the genome. Such selective pressures may have been exacerbated by population dynamics, predicted to both derive from, and favor, the colonizing strategy. Exposure to ecological variability is likely to have generated particular selective pressures on female biology, favoring increasing steering of offspring ontogeny by maternal phenotype. We propose that the concept of hominins as "colonizing apes" offers a novel unified model for interpreting the suite of traits characteristic of our genus.

Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran

As part of a continuing investigation of the extent to which the genetic and linguistic relationships of populations are correlated, we analyzed mtDNA HV1 sequences, eleven Y chromosome bi-allelic markers, and 9 Y-STR loci in two neighboring groups from the southwest of Iran who speak languages belonging to different families: Indo-European-speaking Bakhtiari, and Semitic-speaking Arabs. Both mtDNA and the Y chromosome, showed a close relatedness of these groups with each other and with neighboring geographic groups, irrespective of the language spoken. Moreover, Semitic-speaking North African groups are more distant genetically from Semitic-speaking groups from the Near East and Iran. Thus, geographical proximity better explains genetic relatedness between populations than does linguistic relatedness in this part of the world.

Evolutionary, biologic, and social aspects of skin color

To understand the diversity of skin color now observed in people of the five continents, one has to go back in history. In fact, geology, archeological findings, biology and medical science, as well as anthropology, linguistics, and contemporary genetic techniques enable us to patch up a clear picture of the past up to the present - the evolution of the Homo sapiens. Owing to its undeniable visibility, skin color has always had a sociologic connotation, which has up to the present time caused division between people.

Life sciences and biotechnology in China

Life science and biotechnology have become a top priority in research and development in many countries as the world marches into the new century. China as a developing country with a 1.3 billion population and booming economy is actively meeting the challenge of a new era in this area of research. Owing to support from the government and the scientific community, and reform to improve the infrastructure, recent years have witnessed a rapid progress in some important fields of life science and biotechnology in China, such as genomics and protein sciences, neuroscience, systematics, super-hybrid rice research, stem cell and cloning technology, gene therapy and drug/vaccine development. The planned expansion and development of innovation in related sectors and the area of bioethics are described and discussed.