Ethnicity and biodemographic structure in the Arbëreshe of the province of Cosenza, southern Italy, in the XIX century

Cultural and environmental factors interact in determining the genetic structure of human populations. Bio-demographic investigations of ethnic minorities are able to disentangle the influences that these two components have on the evolution of the genetic structure of a population. The ethnic minority of the Arb?reshe of the province of Cosenza (Calabria, southern Italy) is analyzed in this paper and its bio-demographic structure in the early 1800s is compared with that of neighboring Italian populations. The data derive from surnames recorded in the birth registers of the 19 Arbdreshe municipalities of the province of Cosenza and in 5 non-Arb?reshe municipalities of the same province. Isonymy and repeated pairs of surnames are used to analyze the bio-demographic structure of these populations, while analysis of isonymic relationships is used to investigate the variability between populations. Higher values of marital isonymy and subdivision into subpopulations characterize the Arb?reshe populations with respect to their non-Arb?reshe neighbors. However, the high range of variability of these parameters suggests a strong influence of geographic location on the marriage pattern of each community. At the same time, cultural differences linked to group identity had a strong impact in limiting marriage exchanges between the different ethnic groups living in the province of Cosenza in the early 1800s. In fact, the analysis of isonymic relationships demonstrates that geographic location shaped kinship patterns among the Arbereshe communities, but it also shows that the non-Arb?reshe neighbors formed a clearly separate reproductive cluster.     

Genetic diversity of the chromosome X in aboriginal Siberian populations: The structure of linkage disequilibrium and haplotype phylogeography of the <Emphasis Type="Italic">ZFX</Emphasis> locus

The gene pool structure of aboriginal Siberian populations has been described based on the polymorphism of the ZFX gene located on the chromosome X. In the ten populations studied, 49 haplotypes were present, three of them with high frequencies. Comparison of the obtained results with the available data from the HapMap project revealed unique African haplotypes that occurred in the Yoruba with the frequency of 3–7% and were not found in other populations. The genetic differentiation coefficient of the Siberian ethnic groups studied was 0.0486. Correlation analysis using Mantel’s test did not detect significant correlations between the genetic distance matrix and the matrices of geographic, linguistic, and anthropological differences, although the correlation with the anthropological matrix was the highest. Phylogenetic analysis proved strong isolation of the African population from the other ethnic groups investigated. The Siberian populations were divided into two separate clusters: the first one included Yakuts, Buryats, and Kets, while the second cluster included Altaians, Tuvinians, and Khanty. Using the principal component analysis, the populations were combined into three groups clearly differing by manifestation of Caucasoid and Mongoloid components. The first group included residents of Europe and one of Khanty populations, the second group included populations of South Siberia and residents of China. Mongoloid populations of East Siberia, the Japanese, and Kets were combined into the third group. Barrier analysis revealed a similar structure of genetic differentiation of Siberian populations. Linkage disequilibrium structure was obtained for six ethnic groups of Siberia. In five of them (except for the Ket population), ten ZFX SNPs formed a single linkage block.     

On the evolution of heavy-metal tolerant populations in Armeria maritima: evidence from allozyme variation and reproductive barriers

The process of ecological differentiation leading to the evolution of heavy-metal tolerant populations in Armeria maritima was studied by comparing population genetic structure and pattern of gene flow between populations growing on heavy-metal contaminated against non-contaminated sites using allozyme markers. In addition the evolution of reproductive isolation among populations was studied by measuring pollen fertility in interpopulational hybrids. The allozyme data suggested that in A. maritima multiple independent evolutionary origins of heavy-metal tolerant populations have occurred in the absence of strong genetic bottlenecks. The pattern of gene flow among populations was consistent with the model of isolation by distance with considerable gene flow between neighbor populations, and no reduction of gene flow between tolerant and non-tolerant populations. Hence it appears that substantial gene flow has not hampered genetic differentiation, probably because of the high selection pressure for heavy-metal tolerance. The pattern of reproductive isolation among populations suggests that evolution of heavy-metal tolerant populations has not triggered the development of reproductive barriers against non-tolerant populations. However, partial reproductive isolation has occurred under geographic separation.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis

The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barriers. This review examines the genetic causes and consequences of inversions as recombination suppressors and the role that recombination suppression plays in establishing inversions in populations as they are involved in adaptation within heterogeneous environments. This often results in the formation of clines of gene arrangement frequencies among populations. Recombination suppression leads to the differentiation of the gene arrangements which may accelerate the accumulation of fixed genetic differences among populations. If these fixed mutations cause incompatibilities, then inversions pose important reproductive barriers between species. This review uses the evolution of inversions in Drosophila pseudoobscura and D. persimilis as a case study for how inversions originate, establish and contribute to the evolution of reproductive isolation.     

No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (<Emphasis Type="Italic">Ichthyosaura alpestris</Emphasis>) in densely settled landscapes

Linear landscape elements such as roads, railways and rivers have been shown to act as barriers to dispersal and gene flow, hence impeding functional connectivity and increasing genetic differentiation between individuals or populations on opposite sides of the barrier. Such putative barriers act through a confluence of mechanisms, including crossing mortality, barrier avoidance and modifications to organisms’ effective dispersal patterns. Small, terrestrial animals such as amphibians are predicted to be vulnerable to the effects of such barriers given their limited locomotive performance and their dependence on spatially distinct breeding habitats. Here, we examined the effects of highways and a wide river on Ichthyosaura alpestris in three regions of northern Switzerland by measuring the genetic differentiation between local populations and describing the spatial genetic structure. Moreover, we estimated effective population sizes as an indicator for the susceptibility of populations to random genetic drift. Based on genetic differentiation, we found evidence to suggest that the highways and river acted as barriers to gene flow for the newt in the study regions, but results were inconsistent when ignoring breeding ponds with low samples sizes. Admixture-based genetic clustering suggested the delineation of the genotypes to rough regional clusters, with only weak structure inferred within these clusters. Thus, results suggest that at present, highways and rivers do not substantially affect the genetic structure of I. alpestris within northern Switzerland in a negative manner. Alternatively, the lack of a distinct genetic structure in regional newt populations may be explained by, e.g., large effective population sizes.     

Pliocene–Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic–phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene–early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene.     

Patterns of reproductive isolation in a haplodiploid – strong post‐mating,prezygotic barriers among three forms of a social spider mite

In speciation research, much attention is paid to the evolution of reproductive barriers, preventing diverging groups from hybridizing back into one gene pool. The prevalent view is that reproductive barriers evolve gradually as a by‐product of genetic changes accumulated by natural selection and genetic drift in groups that are segregated spatially and/or temporally. Reproductive barriers, however, can also be reinforced by natural selection against maladaptive hybridization. These mutually compatible theories are both empirically supported by studies, analysing relationships between intensity of reproductive isolation and genetic distance in sympatric taxa and allopatric taxa. Here, we present the – to our knowledge – first comparative study in a haplodiploid organism, the social spider mite Stigmaeopsis miscanthi, by measuring premating and post‐mating, pre‐ and post‐zygotic components of reproductive isolation, using three recently diverged forms of the mite that partly overlap in home range. We carried out cross‐experiments and measured genetic distances (mitochondrial DNA and nuclear DNA) among parapatric and allopatric populations of the three forms. Our results show that the three forms are reproductively isolated, despite the absence of premating barriers, and that the post‐mating, prezygotic component contributes most to reproductive isolation. As expected, the strength of post‐mating reproductive barriers positively correlated with genetic distance. We did not find a clear pattern of prezygotic barriers evolving faster in parapatry than in allopatry, although one form did show a trend in line with the ecological and behavioural relationships between the forms. Our study advocates the versatility of haplodiploid animals for investigating the evolution of reproductive barriers.     

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad‐scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large‐scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.     

Population differentiation in perch Perca fluviatilis: environmental effects on gene flow?

Environmental parameters were used to investigate barriers to gene flow and genetic differentiation in the Eurasian perch (Perca fluviatilis L.) at a small geographical scale in an archipelago system. Significant genetic differentiation was found among locations. Distance per se did not play a major role in the reduction of gene flow. Instead, the largest genetic differences between populations correlated with major changes in environmental conditions, such as temperature at time of spawning. The results show that genetic divergence can arise between populations in habitats thought to be highly connected, and that environmental variables can influence the level of gene flow between populations, including those that are at small spatial scales (tens of kilometres). The importance of a landscape approach when investigating genetic differentiation and defining barriers to gene flow is highlighted.     

Genetic and morphological population differentiation in the rock-dwelling and specialized shrimp-feeding cichlid fish species <Emphasis Type="Italic">Altolamprologus compressiceps</Emphasis> from Lake Tanganyika,East Africa

With about 250 endemic species, Lake Tanganyika contains an extraordinarily diverse cichlid fish fauna, and thus represents an ideal model system for the study of pathways and processes of speciation. The Lamprologini form the most species-rich tribe in Lake Tanganyika comprising about 100 species in seven genera, most of which are endemic to the lake. They are territorial substrate-breeders and represent a monophyletic tribe. By combined analysis of population genetics and geometric morphometric markers, we assessed gene flow among three populations of the highly specialized shrimp-feeding rock-dweller Altolamprologus compressiceps, separated by geographic distance and ecological barriers. Five highly polymorphic microsatellite markers were analyzed in conjunction with 17 landmarks in order to compare genetic differences to body shape differences among populations. Both genetic and morphological analyses revealed significant differentiation among the three studied populations. A significant, but overall relatively low degree of genetic differentiation supports a very recent divergence. Phenotypic differentiation was primarily found in the head region of A. compressiceps. In agreement with findings in other cichlid species, similar adaptations to specialized feeding mechanisms can consequently lead to marginal shape changes in the trophic apparatus.     

Gene flow and genetic drift in urban environments

Evidence is growing that human modification of landscapes has dramatically altered evolutionary processes. In urban population genetic studies, urbanization is typically predicted to act as a barrier that isolates populations of species, leading to increased genetic drift within populations and reduced gene flow between populations. However, urbanization may also facilitate dispersal among populations, leading to higher genetic diversity within, and lower differentiation between, urban populations. We reviewed the literature on nonadaptive urban evolution to evaluate the support for each of these urban fragmentation and facilitation models. In a review of the literature with supporting quantitative analyses of 167 published urban population genetics studies, we found a weak signature of reduced within‐population genetic diversity and no evidence of consistently increased between‐population genetic differentiation associated with urbanization. In addition, we found that urban landscape features act as barriers or conduits to gene flow, depending on the species and city in question. Thus, we speculate that dispersal ability of species and environmental heterogeneity between cities contributes to the variation exhibited in our results. However, >90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on nonadaptive evolution. It is clear that species biology and city heterogeneity obscure patterns of genetic drift and gene flow in a quantitative analysis. Thus, we suggest that future research makes comparisons of multiple cities and nonurban habitats, and takes into consideration species' natural history, environmental variation, spatial modelling and marker selection.     

Extensive local‐scale gene flow and long‐term population stability in the intertidal mollusc Katharina tunicata (Mollusca: Polyplacophora)

The dispersal capabilities of intertidal organisms may represent a key factor to their survival in the face of global warming, as species that cannot adapt to the various effects of climate change will have to migrate to track suitable habitat. Although species with pelagic larval phases might be expected to have a greater capacity for dispersal than those with benthic larvae, interspecies comparisons have shown that this is not always the case. Consequently, population genetic approaches are being increasingly used to gain insights into dispersal through studying patterns of gene flow. In the present study, we used nuclear single‐nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) sequencing to elucidate fine‐scale patterns of genetic variation between populations of the Black Katy Chiton, Katharina tunicata, separated by 15–150 km in south‐west Vancouver Island. Both the nuclear and mitochondrial data sets revealed no genetic differentiation between the populations studied, and an isolation‐with‐migration analysis indicated extensive local‐scale gene flow, suggesting an absence of barriers to dispersal. Population demographic analysis also revealed long‐term population stability through previous periods of climate change associated with the Pleistocene glaciations. Together, the findings of the present study suggest that this high potential for dispersal may allow K. tunicata to respond to current global warming by tracking suitable habitat, consistent with its long‐term demographic stability through previous changes in the Earth's climate. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 589–597.     

Surprisingly little population genetic structure in a fungus‐associated beetle despite its exploitation of multiple hosts

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource‐associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well‐studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource‐associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource‐associated population genetic structure.     

Conservation of genetic diversity in slippery elm (<Emphasis Type="Italic">Ulmus rubra</Emphasis>) in Wisconsin despite the devastating impact of Dutch elm disease

Forest pest epidemics are responsible for many population declines reported in forest trees. While forest tree populations tend to be genetically diverse, in principle mortality resulting from disease could diminish that genetic diversity and alter the genetic structure of the remnant populations with consequences for the ability of a species to adapt to changing environments. Slippery elm (Ulmus rubra Muhl.) is a long-lived, wind-pollinated forest tree with a native range covering essentially all of eastern North America. Dutch elm disease (DED) caused by an introduced fungal pathogen (Ophiostoma ulmi) devastated North American elm populations, including slippery elm, beginning in the 1930s. Estimates of the numbers of elms lost to DED are unknown but range into the hundreds of millions of trees given their former abundance. In this study, the genotypes of 77 herbarium specimens collected between 1890 and 2004 in Wisconsin, and of 100 slippery elm trees from five wild Wisconsin populations, were characterized using 13 microsatellite loci. Levels of genetic diversity were compared between the herbarium specimens collected pre- and post-DED spread in Wisconsin. In addition, the levels of genetic diversity and degree of genetic differentiation were quantified in the five wild populations. The allelic diversity and expected levels of heterozygosity were similar between the pre- and post-DED herbarium specimens. The five wild populations were only slightly differentiated and no genetic bottleneck was detected for any population. At least in Wisconsin, slippery elm apparently has maintained levels of genetic diversity that could facilitate adaptation to future climatic and environmental changes.     

Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, <Emphasis Type="Italic">Miniopterus schreibersii</Emphasis>(Chiroptera: Vespertilionidae)

Background  

Various mechanisms such as geographic barriers and glacial episodes have been proposed as determinants of intra-specific and inter-specific differentiation of populations, and the distribution of their genetic diversity. More recently, habitat and climate differences, and corresponding adaptations have been shown to be forces influencing the phylogeographic evolution of some vertebrates. In this study, we examined the contribution of these various factors on the genetic differentiation of the bent-winged bat, Miniopterus schreibersii, in southeastern Europe and Anatolia.     

神农架山体对濒危植物连香树遗传结构影响的研究

山体屏障能阻断植物连续的生境,干扰居群的基因交流,从而影响植物居群的遗传结构.本研究应用AFLP标记探讨神农架地区南北坡4条河岸带分布的连香树4个居群的遗传多样性水平,以及山体隔离对居群遗传结构和基因流的影响.结果显示连香树居群水平的Nei's基因多样性(h)和Shannon信息指数(/)分别为0.116和0.173,遗传多样性水平相对较高.在遗传结构方面,邻接树(NJ)和主坐标分析的结果清晰地将南北坡分开,从居群和个体上都分成两组.并且STRUCTURE的结果显示基因流在同坡向的居群间比不同坡向的居群间要大.这些表明神农架山体可能对连香树居群的基因交流产生了一定的限制作用.神农架南北坡居群间的分化程度较低(FST为0.075),推测与连香树自身有较强的种子散布和花粉传播能力有关.本研究结果表明,神农架山体及相关的生态因子可能对连香树居群的基因交流产生了限制作用.     

Latitudinal Environmental Niches and Riverine Barriers Shaped the Phylogeography of the Central Chilean Endemic Dioscorea humilis (Dioscoreaceae)

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.     

Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis

Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis—a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in two dimensions over a 50 × 80-km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared with the surrounding food-crop plantation populations. Analysis of molecular variance indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.