Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long‐range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D‐loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.     

Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya

The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes.     

Analysis of mtDNA sequences shows Japanese native chickens have multiple origins

In this study, we analysed the mitochondrial DNA D-loop region of Japanese native chickens to clarify their phylogenetic relationships, possible maternal origin and routes of introduction into Japan. Seven haplogroups (Types A-G) were identified. Types A-C were observed in Jidori, Shokoku and related breeds. However, Type C was absent in Shokoku, which was introduced from China, while most Indonesian native chickens were included in the Type C haplogroup. Types D-G were observed in Shamo and related breeds. Type E had a close genetic relationship with Chinese native chickens. Our results indicate that some breeds were not introduced into Japan as suggested in conventional literature, based on low nucleotide diversity of certain chicken breeds. Sequences originating from China and Korea could be clearly distinguished from those originating from Southeast Asia. In each group, domestic chickens were divided into the Jidori-Shokoku and Shamo groups. These results indicate that Chinese and Korean chickens were derived from Southeast Asia. Following the domestication of red junglefowl, a non-game type chicken was developed, and it spread to China. A game type chicken was developed in each area. Both non-game and game chickens formed the foundation of Japanese native chickens.     

A cryptic mitochondrial DNA link between North European and West African dogs

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA(mt DNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups(matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf(Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1(but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.     

Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.     

Whole-mtDNA genome sequence analysis of ancient African lineages

Studies of human mitochondrial (mt) DNA genomes demonstrate that the root of the human phylogenetic tree occurs in Africa. Although 2 mtDNA lineages with an African origin (haplogroups M and N) were the progenitors of all non-African haplogroups, macrohaplogroup L (including haplogroups L0-L6) is limited to sub-Saharan Africa. Several L haplogroup lineages occur most frequently in eastern Africa (e.g., L0a, L0f, L5, and L3g), but some are specific to certain ethnic groups, such as haplogroup lineages L0d and L0k that previously have been found nearly exclusively among southern African "click" speakers. Few studies have included multiple mtDNA genome samples belonging to haplogroups that occur in eastern and southern Africa but are rare or absent elsewhere. This lack of sampling in eastern Africa makes it difficult to infer relationships among mtDNA haplogroups or to examine events that occurred early in human history. We sequenced 62 complete mtDNA genomes of ethnically diverse Tanzanians, southern African Khoisan speakers, and Bakola Pygmies and compared them with a global pool of 226 mtDNA genomes. From these, we infer phylogenetic relationships amongst mtDNA haplogroups and estimate the time to most recent common ancestor (TMRCA) for haplogroup lineages. These data suggest that Tanzanians have high genetic diversity and possess ancient mtDNA haplogroups, some of which are either rare (L0d and L5) or absent (L0f) in other regions of Africa. We propose that a large and diverse human population has persisted in eastern Africa and that eastern Africa may have been an ancient source of dispersion of modern humans both within and outside of Africa.     

Genetic diversity of donkey populations from the putative centers of domestication

Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mtDNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass (Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species.     

Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community

Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.     

古DNA的新发现支持现代人东亚起源说

1983年,科学家们根据线粒体DNA（mtDNA）系统发育树构建了首个现代人起源的分子模型,认为现代人起源于亚洲,但1987年非洲起源说的提出取代了这一亚洲起源说。非洲起源说所依赖的无限多位点假说以及分子钟假说后来被普遍认为是错误的且不切实际的。我们近几年提出了一个新的分子进化模式,即遗传多样性上限理论,重新构建了一个新的人类起源模型。这一模型与多地区起源说基本吻合, 重新把现代人类起源地定位在了东亚。非洲说与东亚说在线粒体进化树上的主要区别是单倍型N和R的关系,非洲起源说认为N是R的祖先,东亚说则反之。本研究引用了已发表的古代人群mtDNA数据,重点分析了线粒体单倍群N和R的关系。结果显示,三个最古老的人类（一个距今45000年,其他两个约40000年）都属于单倍群R;在距今39500到30000年前的人类样本中,绝大部分属于单倍群R下游的亚单倍群U,只有两例为单倍群N（Oase1距今39500年,Salkhit距今34425年）。这两例所属单倍型位于单倍群N下游最基本的未分化亚型,不属于今天存在的任何N下游单倍型,所以可能靠近单倍群N的根部。这些古DNA数据揭示单倍群R比单倍群N古老大约5000年,进一步证实了亚洲起源说的正确性,非洲说的依据不足。     

Chicken domestication: an updated perspective based on mitochondrial genomes

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A–I and W–Z. Common haplogroups A–G were shared by domestic chickens and red junglefowl. Rare haplogroups H–I and W–Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.     

Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa

Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the timing of the branching events within haplogroup T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East -25 kya. Our survey also points to a complex history of dispersal of this rare and informative haplogroup within the Near East and from the Near East to Europe and sub-Saharan Africa. The presence of T1a2 chromosomes in Near Eastern Jewish and non-Jewish populations may reflect early exiles between the ancient lands of Israel and Babylon. The presence of different subclades of T chromosomes in Europe may be explained by both the spread of Neolithic farmers and the later dispersal of Jews from the Near East. Finally, the moderately high frequency (-18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line.     

Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog-wolf hybridization

Studies of mitochondrial DNA (mtDNA) diversity indicate explicitly that dogs were domesticated, probably exclusively, in southern East Asia. However, Southwest Asia (SwAsia) has had poor representation and geographical coverage in these studies. Other studies based on archaeological and genome-wide SNP data have suggested an origin of dogs in SwAsia. Hence, it has been suspected that mtDNA evidence for this scenario may have remained undetected. In the first comprehensive investigation of genetic diversity among SwAsian dogs, we analyzed 582 bp of mtDNA for 345 indigenous dogs from across SwAsia, and compared with 1556 dogs across the Old World. We show that 97.4% of SwAsian dogs carry haplotypes belonging to a universal mtDNA gene pool, but that only a subset of this pool, five of the 10 principal haplogroups, is represented in SwAsia. A high frequency of haplogroup B, potentially signifying a local origin, was not paralleled with the high genetic diversity expected for a center of origin. Meanwhile, 2.6% of the SwAsian dogs carried the rare non-universal haplogroup d2. Thus, mtDNA data give no indication that dogs originated in SwAsia through independent domestication of wolf, but dog-wolf hybridization may have formed the local haplogroup d2 within this region. Southern East Asia remains the only region with virtually full extent of genetic variation, strongly indicating it to be the primary and probably sole center of wolf domestication. An origin of dogs in southern East Asia may have been overlooked by other studies due to a substantial lack of samples from this region.     

广东省地方鸡线粒体遗传多样性与母系起源

系统评估地方鸡的遗传变异水平并追溯其母系起源, 可为保护利用优质家禽种质资源库提供科学依据。本研究测定了广东省和邻省共12个地方鸡品种的线粒体DNA D-loop序列, 分析品种间的遗传距离与系统关系, 并构建单倍型系统发生树和中介网络图。360份样品共检测到60个突变位点, 均为转换。定义了85种单倍型, 归属于单倍型类群A、B、C和E, 在12个鸡品种中均有分布, 其中B是优势单倍型类群(187个, 51.94%), E次之(76个, 21.11%)。B02 和C01是优势单倍型(85个, 23.61%; 48个, 13.33%), 为12个鸡品种共有; E03位居第三(35个, 9.72%), 杏花鸡、黄郎鸡和宁都三黄鸡未见此单倍型。杏花鸡集中分布在单倍型类群B, 惠阳胡须鸡和中山沙栏鸡则主要分布在单倍型类群E; 怀乡鸡的单倍型数量最多, 中山沙栏鸡的最少。广东地方鸡品种间遗传距离为0.012-0.015, 单倍型多样性0.805 ± 0.047至0.949 ± 0.026, 核苷酸多样性0.0102 ± 0.0017至0.0138 ± 0.0009。邻接树和中介网络图将85种单倍型划分为进化枝A、B、C和E, 广东省与邻省地方鸡单倍型的地理分布模式相似。中性检验显示广东地方鸡未经历明显的群体历史扩张。结果表明广东地方鸡处于较好的保护状态, 遗传多样性水平较高, 品种的形成受到邻省和北方家鸡的影响, 东南亚红原鸡对广东地方鸡也有重要的遗传贡献。     

Excavating Y-chromosome haplotype strata in Anatolia

Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat (STR) loci. The major components (haplogroups E3b, G, J, I, L, N, K2, and R1; 94.1%) are shared with European and neighboring Near Eastern populations and contrast with only a minor share of haplogroups related to Central Asian (C, Q and O; 3.4%), Indian (H, R2; 1.5%) and African (A, E3*, E3a; 1%) affinity. The expansion times for 20 haplogroup assemblages was estimated from associated STR diversity. This comprehensive characterization of Y-chromosome heritage addresses many multifaceted aspects of Anatolian prehistory, including: (1) the most frequent haplogroup, J, splits into two sub-clades, one of which (J2) shows decreasing variances with increasing latitude, compatible with a northward expansion; (2) haplogroups G1 and L show affinities with south Caucasus populations in their geographic distribution as well as STR motifs; (3) frequency of haplogroup I, which originated in Europe, declines with increasing longitude, indicating gene flow arriving from Europe; (4) conversely, haplogroup G2 radiates towards Europe; (5) haplogroup E3b3 displays a latitudinal correlation with decreasing frequency northward; (6) haplogroup R1b3 emanates from Turkey towards Southeast Europe and Caucasia and; (7) high resolution SNP analysis provides evidence of a detectable yet weak signal (<9%) of recent paternal gene flow from Central Asia. The variety of Turkish haplotypes is witness to Turkey being both an important source and recipient of gene flow.     

Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes

Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape), with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.     

Paternal lineages in Libya inferred from Y‐chromosome haplogroups

Many studies based on genetic diversity of North African populations have contributed to elucidate the modelling of the genetic landscape in this region. North Africa is considered as a distinct spatial‐temporal entity on geographic, archaeological, and historical grounds, which has undergone the influence of different human migrations along its shaping. For instance, Libya, a North African country, was first inhabited by Berbers and then colonized by a variety of ethnic groups like Phoenicians, Greeks, Romans, Arabs and, in recent times, Italians. In this study, we contribute to clarify the genetic variation of Libya and consequently, of North African modern populations, by the study of Libyan male lineages. A total of 22 Y‐chromosome‐specific SNPs were genotyped in a sample of 175 Libyan males, allowing the characterization of 18 Y‐chromosomal haplogroups. The obtained data revealed a predominant Northwest African component represented by haplogroup E‐M81 (33.7%) followed by J(xJ1a,J2)‐M304 (27.4%), which is postulated to have a Middle Eastern origin. The comparative study with other populations (～5,400 individuals from North Africa, Middle East, Sub‐Saharan Africa, and Europe) revealed a general genetic homogeneity among North African populations (F_ST = 5.3 %; P‐value < 0.0001). Overall, the Y‐haplogroup diversity in Libya and in North Africa is characterized by two genetic components. The first signature is typical of Berber‐speaking people (E‐M81), the autochthonous inhabitants, whereas the second is (J(xJ1a,J2)‐M304), originating from Arabic populations. This is in agreement with the hypothesis of an Arabic expansion from the Middle East, shaping the North African genetic landscape. Am J Phys Anthropol 157:242–251, 2015. © 2015 Wiley Periodicals, Inc.     

Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin

The geographical distribution of single nucleotide polymorphism (SNP) in the mitochondrial genome of the human malaria parasite Plasmodium falciparum was investigated. We identified 88 SNPs in 516 isolates from seven parasite populations in Africa, Southeast Asia and Oceania. Analysis of the SNPs postulated a sub-Saharan African origin and recovered a strong negative correlation between within-population SNP diversity and geographic distance from the putative African origin over Southeast Asia and Oceania. These results are consistent with those previously obtained for nuclear genome-encoded housekeeping genes, indicating that the pattern of inheritance does not substantially affect the geographical distribution of SNPs.     

The local origin of the Tibetan pig and additional insights into the origin of Asian pigs

Background

The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig.

Methods and Findings

We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively.

Conclusions

We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.     

Genetic diversity patterns in the SR-BI/II locus can be explained by a recent selective sweep

The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of European, African, East Asian (including Southeast Asian), Middle-Eastern as well as Amerindian descent. Nine of the 14 polymorphisms observed are new. Four of the five variants causing amino acid replacements, G2S, S229G, R484W, and G499R, are likely to affect protein structure and function. SR-BI/BII diversity is partitioned among 19 haplotypes; all but one interconnected by single mutation or a recombination event. Such tight haplotype network and the unusual geographic partitioning of this diversity, high not only in Africa but in East Asia as well, suggests its recent origin and possible effect of selection. Coalescent analysis infers a relatively short time to the most recent common ancestor and points to population expansion in Africa and East Asia. These two continents differ significantly in pairwise F(ST) values, differing as well from a single cluster formed by Europe, Middle East and America. In the context of findings for similarly analyzed other loci, we propose that a selective sweep at the origin of modern human populations could explain the low level of ancestral SR-BI/II diversity. The unusually deep split between Africa and Asia, well beyond the Upper Paleolithic when inferred under neutrality, is consistent with subsequent geographical and demographic expansion favoring the accumulation of new variants, especially in groups characterized by large effective population sizes, such as Asians and Africans. The relevance of such partitioning of SR-BI/II diversity remains to be investigated in genetic epidemiological studies which can be guided by the present findings.     

Distribution of Asellia tridens (Chiroptera: Hipposideridae) lineages including representatives from Saudi Arabia

The genus Asellia was recently revised, giving an insight into the genetic and morphological characteristics of a group whose distribution spans from North Africa into Asia. We studied the genus further by considering additional mitochondrial markers and sampling localities. The deepest previously identified split in A. tridens is supported (Middle East/North Africa), along with the association of North and West African lineages. Central Saudi Arabia is found to represent the easternmost extent of a North African haplogroup when considering concatenated fragments of Cytochrome-b, NADH Dehydrogenase 2, and Cytochrome Oxidase 1 genes. New distribution data further emphasises the diversity found in the Middle East and suggests some mixing of haplotypes over long distances.