Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities

The establishment of Jewish communities in the territory of contemporary Portugal is archaeologically documented since the 3rd century CE, but their settlement in Trás‐os‐Montes (NE Portugal) has not been proved before the 12th century. The Decree of Expulsion followed by the establishment of the Inquisition, both around the beginning of the 16th century, accounted for a significant exodus, as well as the establishment of crypto‐Jewish communities. Previous Y chromosome studies have shown that different Jewish communities share a common origin in the Near East, although they can be quite heterogeneous as a consequence of genetic drift and different levels of admixture with their respective host populations. To characterize the genetic composition of the Portuguese Jewish communities from Trás‐os‐Montes, we have examined 57 unrelated Jewish males, with a high‐resolution Y‐chromosome typing strategy, comprising 16 STRs and 23 SNPs. A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of either strong drift or founder effects. A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non‐Jewish populations (R1b1b2‐M269, ～28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a‐M267), ～12%; J2‐M172, ～25%; T‐M70, ～16%] and in consequence Trás‐os‐Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non‐Jewish population. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Male lineages in South American native groups: evidence of M19 traveling south

With this study, we aimed to determine the different male ancestral components of two Native American communities from Argentina, namely Toba and Colla. The analysis of 27 Y-chromosome SNPs allowed us to identify seven different haplogroups in both samples. Chromosomes carrying the M3 mutation, which typically defines the Native American haplogroup Q1a3a, were seen most frequently in the Toba community (90%). Conversely, Q1a3a was represented in 34% of the Colla Y-chromosomes, whereas haplogroup R1b1, the main representative of western European populations, exhibited the highest frequency in this population (41%). Different M3 sublineages in the Toba community could be identified by observing point mutations at both DYS385 and M19 loci. A microvariant at DYS385, named 16.1, has been characterized, which helps to further subdivide Q1a3a. It is the first time the M19 mutated allele is described in a population from Argentina. This finding supports the old age of the lineages carrying the M19 mutation, but it contradicts the previous hypothesis that the M19 mutated allele is confined to only two Equatorial-Tucano population groups from the north region of South America. The detection of M19 further south than previously thought allows questioning of the hypothesis that this lineage serves as an example of isolation after colonization. This observation also affirms the strong genetic drift to which Native Americans have been subjected. Moreover, our study illustrates a heterogeneous contribution of Europeans to these populations and supports previous studies showing that most Native American groups were subjected to European admixture that primarily involved immigrant men.     

Deep into the roots of the Libyan Tuareg: a genetic survey of their paternal heritage

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.     

Genetic structure of the paternal lineage of the Roma people

According to written sources, Roma (Romanies, Gypsies) arrived in the Balkans around 1,000 years ago from India and have subsequently spread through several parts of Europe. Genetic data, particularly from the Y chromosome, have supported this model, and can potentially refine it. We now provide an analysis of Y-chromosomal markers from five Roma and two non-Roma populations (N = 787) in order to investigate the genetic relatedness of the Roma population groups to one another, and to gain further understanding of their likely Indian origins, the genetic contribution of non-Roma males to the Roma populations, and the early history of their splits and migrations in Europe. The two main sources of the Roma paternal gene pool were identified as South Asian and European. The reduced diversity and expansion of H1a-M82 lineages in all Roma groups imply shared descent from a single paternal ancestor in the Indian subcontinent. The Roma paternal gene pool also contains a specific subset of E1b1b1a-M78 and J2a2-M67 lineages, implying admixture during early settlement in the Balkans and the subsequent influx into the Carpathian Basin. Additional admixture, evident in the low and moderate frequencies of typical European haplogroups I1-M253, I2a-P37.2, I2b-M223, R1b1-P25, and R1a1-M198, has occurred in a more population-specific manner.     

Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.     

Y chromosome haplotype distribution of brown bears (Ursus arctos) in Northern Europe provides insight into population history and recovery

High‐resolution, male‐inherited Y‐chromosomal markers are a useful tool for population genetic analyses of wildlife species, but to date have only been applied in this context to relatively few species besides humans. Using nine Y‐chromosomal STRs and three Y‐chromosomal single nucleotide polymorphism markers (Y‐SNPs), we studied whether male gene flow was important for the recent recovery of the brown bear (Ursus arctos) in Northern Europe, where the species declined dramatically in numbers and geographical distribution during the last centuries but is expanding now. We found 36 haplotypes in 443 male extant brown bears from Sweden, Norway, Finland and northwestern Russia. In 14 individuals from southern Norway from 1780 to 1920, we found two Y chromosome haplotypes present in the extant population as well as four Y chromosome haplotypes not present among the modern samples. Our results suggested major differences in genetic connectivity, diversity and structure between the eastern and the western populations in Northern Europe. In the west, our results indicated that the recovered population originated from only four male lineages, displaying pronounced spatial structuring suggestive of large‐scale population size increase under limited male gene flow within the western subpopulation. In the east, we found a contrasting pattern, with high haplotype diversity and admixture. This first population genetic analysis of male brown bears shows conclusively that male gene flow was not the main force of population recovery.     

Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.     

Peopling of three Mediterranean islands (Corsica,Sardinia, and Sicily) inferred by Y-chromosome biallelic variability

An informative set of biallelic polymorphisms was used to study the structure of Y-chromosome variability in a sample from the Mediterranean islands of Corsica and Sicily, and compared with data on Sardinia to gain insights into the ethnogenesis of these island populations. The results were interpreted in a broader Mediterranean context by including in the analysis neighboring populations previously studied with the same methodology. All samples studied were enclosed in the comparable spectrum of European Y-chromosome variability. Pronounced differences were observed between the islands as well as in the percentages of haplotypes previously shown to have distinctive patterns of continental phylogeography. Approximately 60% of the Sicilian haplotypes are also prevalent in Southern Italy and Greece. Conversely, the Corsican sample had elevated levels of alternative haplotypes common in Northern Italy. Sardinia showed a haplotype ratio similar to that observed in Corsica, but with a remarkable difference in the presence of a lineage defined by marker M26, which approaches 35% in Sardinia but seems absent in Corsica. Although geographically adjacent, the data suggest different colonization histories and a minimal amount of recent gene flow between them. Our results identify possible ancestral continental sources of the various island populations and underscore the influence of founder effect and genetic drift. The Y-chromosome data are consistent with comparable mtDNA data at the RFLP haplogroup level of resolution, as well as linguistic and historic knowledge.     

The impact of group fissions on genetic structure in Native South America and implications for human evolution

In a series of publications beginning in the 1960s, Neel and colleagues suggested that genetically nonrandom, or "lineal", population fissions contributed to genetic structure in ancient human groups. The authors reached this conclusion by studying the genetic consequences of village fissions among the Yanomamo, a Native South American group thought to have been relatively unaffected by European contact and, therefore, representative of the human past. On the basis of ethnographic accounts and pedigree data, they further concluded that patrilineal relationships were particularly important in shaping the genetic structure of villages following fissions. This study reexamines the genetic consequences of village fissions using autosomal STRs, Y-chromosome STRs, and mitochondrial DNA sequences collected from large samples of individuals from multiple Yanomamo villages. Our analyses of the autosomal STRs replicate the previous finding that village fissions have produced substantial genetic structure among the Yanomamo. However, our analyses of Y-chromosome STRs and mtDNA d-loop polymorphisms suggest that other population processes, including village movements, inter-village migration, and polygynous marriage, affect genetic structure in ways not predicted by a simple model of patrilineal fissions. We discuss the broader implications of population fissions for human evolution and the suitability of using the Yanomamo as a model for the human past.     

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next‐generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern‐Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human‐mediated land‐use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.     

Genetic diversity,population structure and rickettsias in Amblyomma ovale in areas of epidemiological interest for spotted fever in Brazil

Amblyomma ovale (Ixodida: Ixodidae) Koch, 1844 is widely‐reported in the neotropical region and is the main vector in the epidemic cycle of Rickettsia parkeri strain Atlantic rainforest, a bioagent of a milder variety of spotted fever (SF). Because species with wide geographical distributions are known to exhibit variations that influence their vectorial capacity, the present study aimed to analyze genetic diversity and rickettsia infection of A. ovale collected during the investigation and surveillance of SF cases in the Cerrado and Atlantic rainforest (ARF) Brazilian biomes. Samples had their DNA extracted, amplified and sequenced for 16S rDNA, 12S rDNA, cytochrome oxidase subunit II and D‐loop markers for tick analyses, as well as the gltA, htrA, ompA and ompB genes for rickettsia detection. Between 11 and 33 A. ovale haplotypes were identified, all of them exclusive to areas within individual analyzed biome areas. The A. ovale populations appeared to be structured, with Cluster I restricted to Cerrado + ARF isolated in Caatinga and Cluster II to ARF continuous area. Rickettsia bellii, R. parkeri strain Atlantic rainforest (first report for Goiás state, Cerrado), Rickettsia asemboensis (first record in A. ovale for Brazil) and Rickettsia felis (first detection in this ixodid) were identified. A. ovale clusters were not associated with rickettsia types.     

Genetic structure of Arabian Peninsula dromedary camels revealed three geographic groups

Dromedary camels (Camelus dromedarius) are widespread in the desert and semi-desert areas of Africa, the Arabian Peninsula, some parts of southwest Asia and Australia. In the Arabian Peninsula, these well-adapted species have been classified based on their ecology into Desert camels, found mainly in the north and center of the Peninsula, Mountain camels, distributed along the west and south of the Peninsula, and Beach camels, populating the west to southwest of the Peninsula. Here, we aimed to investigate the genetic relationship between 386 camels corresponding to 12 dromedary populations from different geographical locations and ecology in the Arabian Peninsula with the genotyping of 17 microsatellite loci. No significant deviation was observed in heterozygosity, allelic richness, Fis (inbreeding coefficient) among the studied populations had a mean value of 0.5849, 4.808 and 0.04, respectively. A mean Fst (fixation index) value of 0.0304 was calculated for the various populations with the highest value obtained between racing Omani and Awarik camel populations (0.079). Both the neighbor-joining phylogenetic tree and the STRUCTURE analysis divided the populations into three different groups corresponding to their Arabian Peninsula geographic location (North, Central and West, South-West, and South-East of the Arabian Peninsula), rather than their ecological classification, with a high level of genetic admixture and gene flow among them. Investigating the genetic relationship of dromedary populations in the Arabian Peninsula can be considered as the first milestone to conserve this well-adapted species. The results obtained here need to be further validated using whole genome sequencing data.     

土家族源流的遗传学初探

通过分析湖北恩施、湖南吉首地区土家族两个人群样本,利用14个Y染色体非重组区(NRY)单倍群分型技术对土家族的遗传结构进行了研究。分型结果结合其他地区土家族两个人群和相关民族群体进行主成分分析,并将分析结果根据不同人群的地理分布展示在地图上。然后对各主成分和单倍群进行偏相关分析来探讨它们之间的相关性。结果显示土家族主体与汉族在父系结构上比较接近,但依然有一定的区别。同时还发现龙山地区唯一保留土家语的土家族与氐羌族群有很明显的相关性,这说明土家族最早的起源可能正是氐羌民族。实验结果表明,恩施和吉首地区的大部分土家族与周边民族群体间的血缘交流频繁;而龙山和永顺的土家族更能代表土家先民的遗传结构,他们与西部氐羌族群密切相关。     

Genetic investigation of the patrilineal kinship structure of early medieval Ireland

A previous study of Irish Y-chromosomes uncovered a likely patrilineal kinship basis to the most prominent early Irish tribal entity/kingdom, the Uí Néill, who dominated the North of the Island during the early medieval period (600-1,000 AD). However, it is unknown to what extent this was a general feature of the multitude of Irish kingdoms that existed over the same period. Irish surnames are patrilineally inherited in a similar manner to the Y-chromosome and their origin can often be traced to pre-existing tribal units. We genotyped 17 microsatellites in 247 Y-chromosomes from men with surnames that are purported to be derived from two different tribes (Eóganacht and Dál Cais) from the Southern province of Munster, as well as a third cohort of random names from the same geographic area. Although there is some sharing of Y-chromosomes between surnames of the same putative origin, there was no clear distinction between either grouping and the control, suggesting that the level of Uí Néill patrilineal kinship was not a universal feature of Irish tribal units. In turn this argues that an extensive extended clan or biological legacy of an eponymous founding ancestor was not necessarily a crucial factor in their establishment.     

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.     

Genetic structure of Korean populations of bumblebees Bombus ignitus (Hymenoptera: Apidae) as revealed by microsatellite markers

Bumblebee Bombus ignitus, which is indigenous to Korea, Japan, and China, has been recognized as a valuable pollinator for both crops and wild plants. Bombus ignitus has now become commercially important as a pollinator because of its use in the agricultural industry, particularly for greenhouse pollination. For long‐term management and effective conservation of B. ignitus, an understanding of the genetic structure of its naturally occurring populations is practically important. In this study, the genetic structure among the five populations of B. ignitus in South Korea was assessed using nine microsatellite loci. These markers showed high levels of genetic variability, with the number of alleles ranging from 6 to 22 (mean = 13.4) and the frequency of the most common allele ranging from 0.11 to 0.66. Only the Sabuk (SB) population showed a genetic signature of a recent bottleneck, which was further supported by the lowest level of allelic richness (AR) (mean AR = 3.944). Genetic differentiation was highly significant among all pairs of populations (P < 0.001) across the nine microsatellite markers, suggesting a lack of gene flow among those populations. Interestingly, F_ST (and R_ST and D_est) values were always greater for the Taebaek population than for the four remaining populations. The phylogenetic analysis showed evidence supporting our hypothesis that the Taebaek population is genetically more divergent than the other populations. Overall, our results suggest that the Korean populations of B. ignitus might have undergone geographic isolation and have become highly separated spatially from one another, thereby having a limited range of migration among their local habitats.     

Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi‐aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range‐wide sampling. We documented a global demographic and spatial expansion approximately 0.1–0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent‐wide gene flow among hippopotamus populations, and hence, no clear continental‐scale genetic structuring remains. Nevertheless, present‐day hippopotamus populations are genetically disconnected, probably as a result of the mid‐Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah‐adapted ungulate mammals and should be further investigated in other water‐associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long‐term decline.     

Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation

The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel (672 individuals from 52 populations). The geographic distribution of patterns of variation was roughly consistent with previous studies, with the major exception that 1 highly divergent haplotype (haplotype X, hX) was observed at low frequency in widely scattered non-African populations and not at all observed in sub-Saharan African populations. Microsatellite (short tandem repeat) variation within the sequenced region was low among copies of hX, even though the estimated time of ancestry of hX and other sequences was 1.44 Myr. The estimated age of the common ancestor of all hX copies was 5,230 years (95% consistency index: 2,000-75,480 years). To further address the presence of hX in Africa, additional samples from Chad and Tanzania were screened. Five additional copies of hX were observed, consistent with a history in which hX was present in Africa prior to the migration of modern humans out of Africa and with eastern Africa being the source of non-African modern human populations. Taken together, these features of hX-that it is much older than other haplotypes and uncommon and patchily distributed throughout Africa, Europe, and Asia-present a cautionary tale for interpretations of human history.