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Genetic variation and population structure in the endangered greater horseshoe bat Rhinolophus ferrumequinum.

Following a dramatic decline last century, the British population of the endangered greater horseshoe bat Rhinolophus ferrumequinum is highly fragmented. To examine the consequences of fragmentation and limited dispersal on patterns of genetic structure and variation, we used microsatellite markers to screen bats from around 50% of the known maternity colonies in Britain, and two areas from continental Europe. Analyses revealed that Welsh and English colonies were genetically isolated. This, and lower variability in Britain than north France, may result from either genetic drift, or the species' colonization history. Gene flow among most neighbouring colonies was not generally restricted, with one exception. These findings have important implications for the ongoing conservation management of this species.

Animals↗

Genetic population structure and introgression in Anopheles dirus mosquitoes in South-east Asia.

Genetic structure and species relationships were studied in three closely related mosquito species, Anopheles dirus A, C and D in Thailand using 11 microsatellite loci and compared with previous mitochondrial DNA (mtDNA) data on the same populations. All three species were well differentiated from each other at the microsatellite loci. Given the almost complete absence of mtDNA differentiation between An. dirus A and D, this endorses the previous suggestion of mtDNA introgression between these species. The high degree of differentiation between the northern and southern population of An. dirus C (RST = 0.401), in agreement with mtDNA data, is suggestive of incipient species. The lack of genetic structure indicated by microsatellites in four populations of An. dirus A across northern Thailand also concurs with mtDNA data. However, in An. dirus D a limited but significant level of structure was detected by microsatellites over ~400 km in northern Thailand, whereas the mtDNA detected no population differentiation over a much larger area (>1200 km). There is prior evidence for population expansion in the mtDNA. If this is due to a selective sweep originating in An. dirus D, the microsatellite data may indicate greater barriers to gene flow within An. dirus D than in species A. Alternatively, there may have been historical introgression of mtDNA and subsequent demographic expansion which occurred first in An. dirus D so enabling it to accumulate some population differentiation. In the latter case the lack of migration-drift equilibrium precludes the inference of absolute or relative values of gene flow in An. dirus A and D.

Animals↗

[The population structure of the African swine fever virus based on the quantitative hemadsorption trait].

Subpopulation composition of 8 ASFV isolates and variants differing in virulence was evaluated comparatively by their haemadsorption capacity. The "quantitative haemadsorption marker" was shown to be useful for characterization of the strains, virus population phenotypic heterogeneity and structure. The marker expression was found to correlate with virulence: attenuated variants had low haemadsorption and more subpopulation components with that shift, and vice versa.

African Swine Fever Virus↗

Population structure of the malaria vector Anopheles funestus in Senegal based on microsatellite and cytogenetic data.

The study of chromosomal inversions distribution within natural Anopheles funestus populations from West Africa revealed high levels of genetic structuring. In Burkina Faso, this was interpreted as evidence for incipient speciation, and two chromosomal forms were described, namely 'Folonzo' and 'Kiribina'. Assignation of field collected specimens to one chromosomal form depends upon application of an algorithm based on chromosomal inversions. We assessed relevance and applicability of this algorithm on An. funestus populations from Senegal, where both forms occur. Furthermore, we estimated the level of genetic differentiation between populations using microsatellite loci spread over the whole genome. Significant genetic differentiation was revealed between geographical populations of An. funestus, and the pattern observed suggested isolation by distance. Chromosomal heterogeneity was not detected by microsatellite markers. Thus, although incipient speciation could not be ruled out by our data, our results suggest that differential environmental selection pressure acting on inversions should be considered a major factor in shaping their distribution in wild An. funestus populations.

Animals↗

Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

Agriculture↗

Digital and palmar dermatoglyphics and the population structure of the Upper Bologna Apennine.

Analysis of digital and palmar dermatoglyphics in an Italian mountain population was carried out. Dermatoglyphic variability was particularly investigated in samples from four different valleys. Microgeographical differences in qualitative and quantitative traits among valleys were found. The relationship between degree of endogamy and dermatoglyphic differences is discussed. The biological repercussion of isolation in the history of this Apennine population is also pointed out by means of comparisons with a nearby plains population characterized by low inbreeding.

Analysis of Variance↗

Population structure of Actinobacillus actinomycetemcomitans: a framework for studies of disease-associated properties.

The Actinobacillus actinomycetemcomitans population consists of a large number of clones among which the ubiquitous leukotoxin gene operon appears very homogeneous. Population genetic analyses performed by multilocus enzyme electrophoresis together with DNA fingerprinting and analyses of genomic DNA restriction fragment length polymorphisms (RFLP) on 97 strains isolated over a period of 45 years revealed that each of the serotypes a, b, c, d and e comprise genetically isolated subpopulations and that successful horizontal transfer of genomic DNA between strains of different serotypes appears to be extremely rare in vivo. In contrast, recombination between strains of the same serotype in general appears to take place in nature. The results provide evidence that non-serotypeable strains are serotype antigen-deficient variants originating from strains of the known serotypes. Serotype b and c strains may contain transmittable DNA sequences not found in strains of the other serotypes.

Actinobacillus Infections↗

Evaluating the performance of likelihood methods for detecting population structure and migration.

A plethora of statistical models have recently been developed to estimate components of population genetic history. Very few of these methods, however, have been adequately evaluated for their performance in accurately estimating population genetic parameters of interest. In this paper, we continue a research program of evaluation of population genetic methods through computer simulation. Specifically, we examine the software MIGRATEE-N 1.6.8 and test the accuracy of this software to estimate genetic diversity (Theta), migration rates, and confidence intervals. We simulated nucleotide sequence data under a neutral coalescent model with lengths of 500 bp and 1000 bp, and with three different per site Theta values of (0.00025, 0.0025, 0.025) crossed with four different migration rates (0.0000025, 0.025, 0.25, 2.5) to construct 1000 evolutionary trees per-combination per-sequence-length. We found that while MIGRATEE-N 1.6.8 performs reasonably well in estimating genetic diversity (Theta), it does poorly at estimating migration rates and the confidence intervals associated with them. We recommend researchers use this software with caution under conditions similar to those used in this evaluation.

Computer Simulation↗

Extreme population structuring in the threatened ghost bat, Macroderma gigas: evidence from mitochondrial DNA.

The ghost bat, Macroderma gigas, has undergone a major range contraction and is currently restricted around a few, highly disjunct maternity sites. The amount and distribution of mitochondrial DNA (mtDNA) variation within extant populations has been used to assess levels of current and historical maternal gene flow between these populations. An approximately 330 base pair fragment spanning a hypervariable area of the mtDNA control region was amplified and sequenced by using 22 individuals from four current ghost bat populations. The mean sequence diversity of 4.5% between populations was six times higher than that within populations (0.68%), and alleles within populations were monophyletic. Restriction enzyme analysis of amplified products from an additional 100 individuals revealed fixed allelic differences in the distribution of control region genotypes between the four populations. It is suggested that this extreme genetic subdivision is a consequence of long-term female philopatry. For the purposes of management each population should be treated as an independent entity. The depth of the genetic structuring suggests that the isolation of extant populations preceded the historical range contraction.

Alleles↗

Matriarchal genetic population structure of North American beluga whales Delphinapterus leucas (Cetacea: Monodontidae).

The North American beluga whale Delphinapterus leucas population has been divided into a number of putative geographical stocks based upon migration routes and areas of summer concentration. Nucleotide sequences of the mitochondrial DNA (mtDNA) control region were used to assess whether these geographical stocks are genetically distinct. Beluga whale samples from 25 sites were collected primarily from aboriginal subsistence hunts across North America from 1984 to 1994. Thirty-nine mtDNA haplotypes were identified in 628 beluga samples. No differences were found in the distribution of haplotypes between male and female beluga whales at any sampling site. These haplotypes segregated into two distinct assemblages in both a haplotype network and a neighbour-joining tree. The haplotype assemblages and a geographically disjunct distribution that suggests postglacial recolonization of the North American Arctic from two different refugia. An analysis of molecular variance based on haplotype relationships and frequency indicated genetic heterogeneity among beluga whale summering groups (P < or = 0.001). Sequence divergence estimates between sampling sites also indicated geographical differentiation, particularly between samples taken at east Hudson Bay or St Lawrence River and the western or central Arctic. The results of this study show a high degree of philopatry to specific summering areas by this highly mobile animal.

Animals↗

[Optimization model of spatial population structure: example of poplar moth laying eggs on leaves].

The authors analyze spatial distribution and survival of populations of poplar moth Litchcolletis populifoliella Tr. on its feeding plant--balsam poplar Populus balsamifera. Imago of the moth glue its eggs on the leaves thus determining the future location of their offspring on the host plant. Spatial distribution of eggs on leaf surface and distribution of leaves according egg numbers are not random. On the short distance from each egg the average number of eggs is less, than it should be in case of random distribution. While this distance increases up to some particular value the occurrence of eggs is higher than random. Thus, the eggs of moth are located by groups on the leaf surface. Within each group eggs are situated not very close to each other, this allowing larvae to lower competition for common resource. It is suggested that on the same feeding plant individuals have different interactions: competition, caused by limited quantity of resource and cooperation that is necessary to resist leaf defensive (antibiosis) reaction.

Animals↗

[Population structure of the forest Nentsi: demographic characteristics, marriage structure, migration and an analysis of mixing].

This report is a third one in a series of works devoted to the genetic structure (biodemographic studies) of the Forest Nentsy. The main parameters of the population studied were as follows: the total number in seven subpopulations amounting to 1734 persons, the sex ratio 0.93, percentage of children in the group of 0 to 15 years old--39,1%, reproductive and effective sizes--29,5% and 22,0%, respectively, the mean number and variance of offspring per mating, when reproduction is completed being 2,7 (5,2). It has been shown that kin and territorial subdivision of the population contributes to the formation of conjugal pairs and migration pattern. Within-kin matings make 0,041, whereas, according to the panmixia hypothesis, this value would be 0,243. The average index of isolation for particular subpopulation is 62,7%. An exchange of migrants occurs between adjacent groups. Migration stream to the different subpopulations varies in volume and ethnic composition. Analysis of the admixture based on the pedigree isoname method has shown that the proportion of the Forest Nentsy gene contribution to their own population is 74,4%. Data on subpopulation size, patterns of matings, migration and admixture may serve as a basis to account for intrapopulation heterogeneity.

Adolescent↗

Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans.

To understand how allopatric speciation proceeds, we need information on barriers to gene flow, their antiquity, and their efficacy. For marine organisms with planktonic larvae, much of this information can only be obtained through the determination of divergence between populations. We evaluated the importance of ocean barriers by studying the mitochondrial DNA phylogeography of Tripneustes, a pantropical genus of shallow water sea urchin. A region of cytochrome oxidase I (COI) was sequenced in 187 individuals from locations around the globe. The COI phylogeny agreed with a previously published phylogeny of bindin that barriers important to the evolution of Tripneustes are: (1) the cold water upwelling close to the tip of South Africa, (2) the Isthmus of Panama, (3) the long stretch of deep water separating the eastern from the western Atlantic, and (4) the freshwater plume of the Orinoco and the Amazon rivers between the Caribbean and the coast of Brazil. These barriers have previously been shown to be important in at least a subset of the shallow water marine organisms in which phylogeography has been studied. In contrast, the Eastern Pacific Barrier, 5000 km of deep water between the central and the eastern Pacific that has caused the deepest splits in other genera of sea urchins, is remarkably unimportant as a cause of genetic subdivision in Tripneustes. There is also no discernible subdivision between the Pacific and Indian Ocean populations of this genus. The most common COI haplotype is found in the eastern, central, and western Pacific as well as the Indian Ocean. Morphology, COI, and bindin data agree that T. depressus from the eastern Pacific and T. gratilla from the western Pacific are, in fact, the same species. The distribution of haplotype differences in the Indo-Pacific exhibits characteristics expected from a sea urchin genus with ephemeral local populations, but with high fecundity, dispersal, and growth: there is little phylogenetic structure, and mismatch distributions conform to models of recent population expansion on a nearly global scale. Yet, comparisons between local populations produce large and significant F(ST) values, indicating nonrandom haplotype distribution. This apparent local differentiation is only weakly reflected in regional divergence, and there is no evidence of isolation by distance in correlations between F(ST) values and either geographical or current distance. Thus, Tripneustes in the Indo-Pacific (but not in the Atlantic) seems to be one large metapopulation spanning two oceans and containing chaotic, nonequilibrium local variation, produced by the haphazard arrival of larvae or by unpredictable local extinction.

Animals↗

'Thus the Colliers and their wives...': migration, mate choice and population structure of some County Durham parishes in the mid-19th century.

AIM: Historical accounts of the mining population in County Durham, UK, offer two persistent representations of demographic behaviour--substantial mobility and occupational endogamy--which would influence the distribution of genes in the population. The aim of this paper is to test these predictions against 19th-century demographic data, comparing miners with other contemporary occupations. SUBJECTS AND METHODS: Four parishes in County Durham yielded data on 3653 birthplace-residence distances, calculated from locations recorded in the 1851 census enumerators' books, and on occupational endogamy and exogamy for 3784 marriages recorded in the Anglican registers, 1834-76. Endogamy was analysed by log-linear models and odds ratios. RESULTS: Median migration distances were similar in the miners and other occupations, though the proportion of migrants among the miners (99.7%) was higher than agricultural (87.0%) and general labourers (91%). Endogamy in the miners (76%) was higher than in other populations (maximum 39%), but further analysis showed that the miners' tendency to marry women from the same occupational background was less than among agricultural labourers or professional men. CONCLUSION: Predictions of high migration rate and endogamy among the mining populations were upheld, but there was little evidence that the behaviour of the miners differed from other occupational groups.

Coal Mining↗

Gene-history correlation and population structure.

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.

Genetic Variation↗