The role of the Vlax Roma in shaping the European Romani maternal genetic history

The Roma are comprised of many founder groups of common Indian origins but different socio-cultural characteristics. The Vlax Roma are one of the founder Roma populations characterized by a period of bondage in the historic Romanian principalities, and by the archaic Romanian language. Demographic history suggests different migration routes of Roma populations, especially after their arrival in Mesopotamia and the eastern boundary of the Byzantine Empire. Although various genetic studies of uniparental genetic markers showed a connection between Roma genetic legacy and their migration routes, precise sampling of Roma populations elucidates this relationship in more detail. In this study, we analyzed mitochondrial DNA of 384 Croatian Vlax Roma from two geographic locations in the context of 734 European Roma samples. Our results show that Roma migration routes are marked with two Near-Eastern haplogroups, X2 and U3, whose inverse proportional incidence clearly separates the Balkan and the Vlax Roma from other Roma populations that reached Europe as part of the first migration wave. Spatial and temporal characteristics of these haplogroups indicate a possibility of their admixture with Roma populations before arrival in Europe. Distribution of haplogroup M35 indicates that all Vlax Roma populations descend from one single founder population that might even reach back to the original ancestral Indian population. Founder effects followed by strict endogamy rules can be traced from India to contemporary small, local communities, as in the case of two Croatian Vlax Roma populations that show clear population differentiation despite similar origins and shared demographic history.     

Endemic origin and vast anthropogenic dispersal of the West Indian drywood termite

Cryptotermes brevis is a common pest of structural lumber and sheltered wood in much of the non-Asian tropics. Until now, no endemic locality, as confirmed by regenerating outdoor populations, was known. A termite survey of the northern coastal desert of Chile and the vicinity of Lima, Peru, yielded 61 outdoor populations of C. brevis taken from 23 different native and exotic species of host woods at 19 localities. We review the taxonomic and biogeographic history of C. brevis and suggest climatic and biological factors that favor or limit C. brevis distribution. We also propose a scenario implicating a post-Colombian release of C. brevis by shipboard infestations and the movement of infested wood during the early Spanish Empire to the present time.     

Reconstructing pedigrees: a stochastic perspective

A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data for present day individuals. This is motivated by the increasing availability of genomic sequences, but in this paper we take a more theoretical approach and consider what models of sequence evolution might allow pedigree reconstruction (given sufficiently long sequences). Our results complement recent work that showed that pedigree reconstruction may be fundamentally impossible if one uses just the degrees of relatedness between different extant individuals. We find that for certain stochastic processes, pedigrees can be recovered up to isomorphism from sufficiently long sequences.     

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.     

Reconstructing pedigrees: a combinatorial perspective

A pedigree is a directed graph that displays the relationship between individuals according to their parentage. We derive a combinatorial result that shows how any pedigree-up to individuals who have no extant (present-day) ancestors-can be reconstructed from (sex-labelled) pedigrees that describe the ancestry of single extant individuals and pairs of extant individuals. Furthermore, this reconstruction can be done in polynomial time. We also provide an example to show that the corresponding reconstruction result does not hold for pedigrees that are not sex-labelled. We then show how any pedigree can also be reconstructed from two functions that just describe certain circuits in the pedigree. Finally, we obtain an enumeration result for pedigrees that is relevant to the question of how many segregating sites are needed to reconstruct pedigrees.     

Complex genetic origin of Indian populations and its implications

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000?years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.     

Large-scale plant conservation in European semi-natural grasslands: a population genetic perspective

During the last century, unprecedented landscape fragmentation has severely affected many plant species occurring in once widespread semi-natural grasslands in Europe. Fragmentation reduces population size and increases isolation, which can jeopardize the persistence of populations. Recent large-scale ecological and genetic studies across several European countries indicate that fragmented populations of common plant species exhibit a strong genetic differentiation and local adaptation to their home sites, reducing their capacity to establish new populations elsewhere. We discuss the main genetic processes that determine the performance of plant populations in severely fragmented landscapes: namely inbreeding depression, genetic differentiation and genetic introgression. We stress the need for large-scale genetic studies to detect the geographical structure of genetic variation of fragmented plant populations, since nuclei of genetically independent groups of populations may become important targets of conservation. A thorough knowledge on the large-scale geographical structure of genetic variation for a sufficiently wide array of plant species can provide the basis to develop comprehensive conservation plans to preserve the ecological and evolutionary processes that generate and maintain biodiversity of fragmented semi-natural grasslands.     

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa.     

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。     

Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel - despite maternal inheritance and passive dispersal

ABSTRACT: BACKGROUND: When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. RESULTS: We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. CONCLUSIONS: This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation.     

Natal dispersal and genetic structure in a population of the European wild rabbit (Oryctolagus cuniculus)

A combination of behavioural observation, DNA fingerprinting, and allozyme analysis were used to examine natal dispersal in a wild rabbit population. Rabbits lived in territorial, warren based social groups. Over a 6-year period, significantly more male than female rabbits moved to a new social group before the start of their first breeding season. This pattern of female philopatry and male dispersal was reflected in the genetic structure of the population. DNA fingerprint band-sharing coefficients were significantly higher for females within the same group than for females between groups, while this was not the case for males. Wrighfs inbreeding coefficients were calculated from fingerprint band-sharing values and compared to those obtained from allozyme data. There was little correlation between the relative magnitudes of the F-statistics calculated using the two techniques for comparisons between different social groups. In contrast, two alternative methods for calculating F_ST from DNA fingerprints gave reasonably concordant values although those based on band-sharing were consistently lower than those calculated by an ‘allele’ frequency approach. A negative F_IS value was obtained from allozyme data. Such excess heterozygosity within social groups is expected even under random mating given the social structure and sex-biased dispersal but it is argued that the possibility of behavioural avoidance of inbreeding should not be discounted in this species. Estimates of genetic differentiation obtained from allozyme and DNA fingerprint data agreed closely with reported estimates for the yellow-bellied marmot, a species with a very similar social structure to the European rabbit.     

Long-distance dispersal vs vicariance: the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada

Here, we investigated the origin and genetic diversity of four alpine plant species co-occurring in the Spanish Sierra Nevada and other high mountains in south-western Europe by analysis of amplified fragment length polymorphisms (AFLPs). In Kernera saxatilis, Silene rupestris and Gentiana alpina we found intraspecific phylogroups corresponding to mountain regions as predicted by the vicariance hypothesis. Moreover, genetic distances between Sierra Nevada and Pyrenees populations were always higher than those between populations from the Pyrenees and the south-western Alps/Massif Central. This suggests successive disruption of gene exchange between mountain ranges as postglacial climatic warming proceeded from south to north. In Papaver alpinum, our data indicate that a central Pyrenean population arose via long-distance dispersal from the Sierra Nevada, and that vicariant separation events between the Sierra Nevada and the Pyrenees and between the Pyrenees and the south-western Alps occurred simultaneously. Overall, Sierra Nevada populations of all species investigated here preserve unexpectedly high (or not exceptionally reduced) genetic diversity. This testifies to the important influence of long-term isolation, i.e. vicariance, on genetic diversity through fostering the accumulation of new mutations and/or the fixation of ancestral ones.     

The effect of maternal care on child survival: a demographic, genetic, and evolutionary perspective

Models of population dynamics generally assume that child survival is independent of maternal survival. However, in humans, the death of a mother compromises her immature children's survival because children require postnatal care. A child's survival therefore depends on her mother's survival in years following her birth. Here, we provide a model incorporating this relationship and providing the number of children surviving until maturity achieved by females at each age. Using estimates of the effect that a mother's death has on her child's survival until maturity, we explore the effect of the model on population dynamics. Compared to a model that includes a uniform child survival probability, our model slightly raises the finite rate of increase lambda and modifies generation time and the stable age structure. We also provide estimates of selection on alleles that change the survival of females. Selection is higher at all adult ages in our model and remains significant after menopause (at ages for which the usual models predict neutrality of such alleles). Finally, the effect of secondary caregivers who compensate maternal care after the death of a mother is also emphasized. We show that allocare (as an alternative to maternal care) can have a major effect on population dynamics and is likely to have played an important role during human evolution.     

On the origin of mitochondria: a genomics perspective

The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.     

Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpina

Our data on the intercontinental population biology of Letharia vulpina show an unexpected shift from a recombining North American population with unique haplotypes to genetically depauperate Swedish and Italian populations, each with many representatives of a single repeated haplotype. Analysis of eight loci in 47 individuals supported recombination in North American populations and showed almost no variation among European populations. We infer that a genetic bottleneck caused by limited long-distance dispersal accounts for the lack of genetic variation found in marginal populations. This lack of variation in the European populations makes it impossible to use population genetic means to distinguish clonal reproduction from self-fertilization or even outcrossing, but phenotype indicates that reproduction in the marginal populations is by clonal spread, via soredia and isidioid soredia.     

Mitochondrial genetic variation in European, African and Indian cattle populations

Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575000 and 1150000 years ago; well outside the 10000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.     

Seed dispersal distance classes and dispersal modes for the European flora

Motivation

Although dispersal ability is one of the key features determining the spatial dynamics of plant populations and the structure of plant communities, it is also one of the traits for which we still lack data for most species. We compiled a comprehensive dataset of seed dispersal distance classes and predominant dispersal modes for most European vascular plants. Our seed dispersal dataset can be used in functional biogeography, dynamic vegetation modelling and ecological studies at local to continental scales.

Main Types of Variables Contained

Species were classified into seven ordered classes with similar dispersal distances estimated based on the predominant dispersal mode, the morphology of dispersal units (diaspores or propagules), life form, plant height, seed mass, habitat and known dispersal by humans. We evaluated our results by comparing them with dispersal distances calculated using the ‘dispeRsal’ function in R.

Spatial Location

Europe.

Time Period

Present.

Major Taxa and Level of Measurement

The seed dispersal dataset contains information on dispersal distance classes and the predominant dispersal mode for 10,327 most frequent and locally dominant European vascular plant species.

Software Format

Data are available in .csv format.     

Parkinson's disease: a genetic perspective

Parkinson's disease (PD) is a common neurodegenerative disorder in the aging population, affecting more than 1% over the age of 65 years. Certain rare forms of the disease are monogenic, representing 5-10% of PD patients, but there is increasing evidence that multiple genetic risk factors are important also for common forms of PD. To date, 13 genetic loci, PARK1-13, have been suggested for rare forms of PD such as autosomal dominant and autosomal recessive PD. At six of these loci, genes have been identified and reported by several groups to carry mutations that are linked to affected family members. Genes in which mutations have been linked to familial PD have also been shown to be candidate genes for idiopathic forms of PD, as those same genes may also carry other mutations that merely increase the risk. Four of the PARK genes, SNCA at PARK1, UCH-L1 at PARK5, PINK1 at PARK6 and LRRK2 at PARK8, have been implicated in sporadic PD. There are indeed multiple genetic risk factors that combine in different ways to increase or decrease risk, and several of these need to be identified in order to begin unwinding the causative pathways leading to the different forms of PD. In this review, we present the molecular genetics of PD that are understood today, to help explain the pathways leading to neurodegeneration.