Genetic structure of the Aleuts and Circumpolar populations based on mitochondrial DNA sequences: a synthesis

The mtDNA variation of 198 Aleuts, as well as North American and Asian populations drawn from the literature, were analyzed to reconstruct the Aleuts' genetic prehistory and to investigate their role in the peopling of the Circumarctic region. From median-joining network analysis, three star-like clusters were identified in the Aleuts within the following subhaplogroups: A3, A7 (an Aleut-specific subclade of A3), and D2. Mismatch analyses, neutrality test scores, and coalescent time estimates for these three components provided evidence of two expansion events, one occurring at approximately 19,900 B.P. and the other at 5,400 B.P. Based on these findings and evidence from the archaeological data, four general models for the genetic prehistory of the Aleutian Island chain are proposed: 1) biological continuity involving a kin-structured peopling of the archipelago; 2) intrusion and expansion of a non-native biface-producing population dominated by subhaplogroup D2; 3) amalgamation of Arctic Small Tool tradition peoples characterized by D2 with an older Anangula substratum; and 4) biological continuity with significant gene flow from neighboring populations of the Alaskan mainland and Kodiak Island. The Aleut mtDNAs are consistent with the Circumarctic pattern by the fixation of A3 and D2, and the exhibition of depressed diversity levels relative to Amerind and Siberian groups. The results of this study indicate a broad postglacial reexpansion of Na-Dene and Esko-Aleuts from reduced populations within northern North America, with D2 representing a later infusion of Siberian mtDNAs into the Beringian gene pool.     

Genetic structure of kestrel populations and colonization of the Cape Verde archipelago

Genetic diversity and population structure were studied in eight populations of the kestrel Falco tinnunculus to identify the genetic consequences of spatial distribution and to infer the colonization patterns of the Cape Verde archipelago. We studied genetic differentiation and gene flow among seven island populations and one mainland population using nine microsatellite loci. Within the archipelago, differentiation was strong and genetic diversity and heterozygosity were low but variable among populations. Two subspecies F. tinnunculus neglectus on the northwestern islands and F. tinnunculus alexandri on all the other islands were identified as genetically distinct units. F. t. alexandri could be further separated into two groups on eastern and southern islands. Populations are probably founded by birds originating from the mainland. Immigration is more likely to the eastern and southern populations, whereas the northwestern islands with the lowest genetic diversity and highest differentiation are likely to exhibit fewer founding events by immigrants. The number of founding events on each island may depend not only on geographical distance to neighbouring populations, but also on directional immigration due to the northeastern trade winds. This may explain differences in genetic differentiation and diversity between populations and subspecies and may enable allopatric speciation.     

Hair snaring and molecular genetic identification for reconstructing the spatial structure of Eurasian lynx populations

Non-invasive genetic sampling (NGS) is being increasingly applied in wildlife monitoring and population genetic research. This study was designed to evaluate the use of NGS for reconstructing the spatial structure of populations of large felids. We developed a procedure for reliably genotyping individuals of Eurasian lynx (Lynx lynx) from samples obtained through a hair-trapping scheme based on a network of lynx scent-marking sites. The spatial locations of the identified genotypes were matched with the home ranges distribution of radio-tracked individuals, thus cross-checking the accuracy of the two methods. We analyzed DNA extracted from 170 hair samples and 11 blood samples from live-trapped lynx collected in 2004–2009 in the Bia?owie?a Primeval Forest, Poland. We obtained PCR products in 96 (67%) hair samples; 82 (85%) of them were reliably genotyped at 12 autosomal microsatellite loci following a multiple-tubes protocol and stringent quality-controls of the data set. The sample included 29 distinct genotypes; 18 were found only in hair samples, five were determined only in live-trapped animals, and six in both hair and blood samples. Based on linkage disequilibrium we estimated an effective population size N_e = 20.3 (90% CI = 15–28). The total population size estimated with Capwire was N_c = 32 (95% CI = 25–37) in close agreement with the observed number of genotypes. The genotypes obtained from hair samples were re-sampled on average 3.9 times and 50% of them were recorded for more than one year. The spatial distribution of six hair-genotypes was consistent with their home ranges obtained by radio-tracking in the same period. The distribution ranges of hair-trapped genotypes overlapped on average in 86.4% (mode 100%) with home ranges of the corresponding individuals. Hair-trapping and molecular identification is a reliable method for reconstructing the spatial organization of lynx population. It is likely to be also efficiently used in other rare and endangered species of felids in combination with data from other monitoring techniques, such as radio- and snow-tracking and photo-trapping.     

Isonymy and the genetic structure of Albanian populations

It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population.     

Herbivory modifies the genetic structure of birch populations

We studied the effects of selective herbivory on genetic diversity in seedling populations of silver birch ( Betula pendula ), a light-demanding pioneer tree species. The experimental populations consisted of 20 families competing with each other in dense stands. The seedling stands were randomly assigned to insect and vole exposure and fertilization treatments. The study covered the first two growing seasons, during which considerable thinning occurred within the experimental populations. We compared the observed mortality to a simulated control representing random mortality. Our results show that mortality resulted in decreased diversity compared to the simulated control. When insect and vole herbivory and nutrient enrichment treatments were compared to each other, taking into account differences in mortality due to the treatments, vole herbivory led to increased diversity among the tallest seedlings (i.e. canopy layer). This is noteworthy, since the canopy layer includes those with the best prospects of surviving in competition for light. When mortality was accounted for, 2-year natural exposure to insects had no effect on diversity; but cluster analysis showed that insect herbivory changed the genetic composition of the experimental populations. Our results demonstrate the importance of herbivores in shaping the genetic structure of plant populations during the thinning phase.     

Isozyme diversity and genetic structure of buckwheat populations

Genetic diversity of 35 Fagopyrum populations belonging to thirteen taxa was studied using isozyme variation at 16 loci for nine enzyme systems (ADH, α-AMY, EST, GDH, GOT, IDH, MDH, PGM, and POD). The mean number of alleles per locus (A_p) showed little variation, ranging from 1.38 to 1.71. The mean percentage of polymorphic (P) of the thirteen taxa was high, ranging from 68.75% to 93.75. The mean expected heterozygosity (H_e) ranged from 0.21 to 0.37. Obvious grouping of populations according to taxonomic species was found in the cluster analysis, confirmed that the thirteen taxa studied were independent, with a clear boundary. Based on the dendrogram, the phylogenic relationship of Fagopyrum species are in agreement with the achene size were found, and it was inferred that southwestern China should be the original center of cultivated buckwheat.     

On the neutrality of molecular genetic markers: pedigree analysis of genetic variation in fragmented populations

Many studies employ molecular markers to infer ecological and evolutionary processes, assuming that variation found at genetic loci offers a reliable representation of stochastic events in natural populations. Increasingly, evidence emerges that molecular markers might not always be selectively neutral. However, only a few studies have analysed how deviations from neutrality could affect estimates of genetic variation, using populations with known genealogy. We monitored changes in allozyme variation over eight generations in captive metapopulations of the butterfly Bicyclus anynana. Population demography was recorded by individually marking 35 000 butterflies and constructing pedigrees. We designed a computer program that simulated the inheritance of founder allozyme alleles in butterfly pedigrees. We thus tested whether the observed transmission of allozyme alleles could be explained by random genetic drift alone, or whether there was evidence for positive or negative selection. This analysis showed that in the smallest metapopulations the loss of allozyme variation exceeded the neutral rate. Possibly, linkage disequilibria between deleterious mutations and marker alleles resulted in background selection and a faster erosion of allozyme variation. In larger metapopulations, one locus (MDH) showed a significant heterozygote excess and smaller than expected loss in heterozygosity, observations consistent with (associative) overdominance. This study demonstrates that the neutrality of molecular markers cannot always be assumed, particularly in small populations with a high mutation load.     

The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago

Aim To test hypotheses that: (1) late Pleistocene low sea‐level shorelines (rather than current shorelines) define patterns of genetic variation among mammals on oceanic Philippine islands; (2) species‐specific ecological attributes, especially forest fidelity and vagility, determine the extent to which common genetic patterns are exhibited among a set of species; (3) populations show reduced within‐population variation on small, isolated oceanic islands; (4) populations tend to be most highly differentiated on small, isolated islands; and (5) to assess the extent to which patterns of genetic differentiation among multiple species are determined by interactions of ecological traits and geological/geographic conditions. Location The Philippine Islands, a large group of oceanic islands in Southeast (SE) Asia with unusually high levels of endemism among mammals. Methods Starch‐gel electrophoresis of protein allozymes of six species of small fruit bats (Chiroptera, Pteropodidae) and one rodent (Rodentia, Muridae). Results Genetic distances between populations within all species are not correlated with distances between present‐day shorelines, but are positively correlated with distances between shorelines during the last Pleistocene period of low sea level; relatively little intraspecific variation was found within these ‘Pleistocene islands’. Island area and isolation of oceanic populations have only slight effects on standing genetic variation within populations, but populations on some isolated islands have heightened levels of genetic differentiation, and reduced levels of gene flow, relative to other islands. Species associated with disturbed habitat (all of which fly readily across open habitats) show more genetic variation within populations than species associated with primary rain forest (all of which avoid flying out from beneath forest canopy). Species associated with disturbed habitats, which tend to be widely distributed in SE Asia, also show higher rates of gene flow and less differentiation between populations than species associated with rain forest, which tend to be Philippine endemic species. One rain forest bat has levels of gene flow and heterozygosity similar to the forest‐living rodent in our study. Main conclusions The maximum limits of Philippine islands that were reached during Pleistocene periods of low sea level define areas of relative genetic homogeneity, whereas even narrow sea channels between adjacent but permanently isolated oceanic islands are associated with most genetic variation within the species. Moreover, the distance between ‘Pleistocene islands’ is correlated with the extent of genetic distances within species. The structure of genetic variation is strongly influenced by the ecology of the species, predominantly as a result of their varying levels of vagility and ability to tolerate open (non‐forested) habitat. Readily available information on ecology (habitat association and vagility) and geological circumstances (presence or absence of Pleistocene land‐bridges between islands, and distance between oceanic islands during periods of low sea level) are combined to produce a simple predictive model of likely patterns of genetic differentiation (and hence speciation) among these mammals, and probably among other organisms, in oceanic archipelagos.     

The genetic structure of malaria parasite populations

The suggestion that a clonal population structure may typify Plasmodium populations has proved highly controversial. For the most part, existing population genetic data from wild populations contradict the idea and are consistent with randomly interbreeding populations. In this article, Andrew Read and Koren Day point out that these data could also be consistent with population subdivision and frequent nonrandom mating, which current sampling methods would be incapable of detecting.     

Multilocus estimation of genetic structure within populations

Spatial structure of genetic variation within populations is well measured by statistics based on the distribution of pairs of individual genotypes, and various such statistics have been widely used in experimental studies. However, the problem of uncharacterized correlations among statistics for different alleles has limited the applications of multiallelic, multilocus summary measures, since these had unknown sampling distributions. Usually multiple alleles and/or multiple loci are required in order to precisely measure spatial structures, and to provide precise indirect estimates of the amount of dispersal in samples of reasonable size. This article examines the correlations among pair-wise statistics, including Moran I-statistics and various measures of conditional kinship, for different alleles of a locus. First the correlations are mathematically derived for random spatial distributions, which allow averages over alleles and loci to be used as more powerful yet exact test statistics for the null hypothesis. Then extensive computer simulations are conducted to examine the correlations among values for different alleles under isolation by distance processes. For loci with more than three alleles, the results show that the correlations are remarkably and perhaps surprisingly small, establishing the principle that then alleles behave as nearly independent realizations of space-time stochastic processes. The results also show that the correlations are largely robust with respect to the degree of spatial structure, and they can be used in a straightforward manner to form confidence intervals for averages. The results allow a precise connection between observations in experimental studies and levels of dispersal in theoretical models.     

遗传学视角下东亚人群的起源和演化

东亚是研究解剖学意义上现代人迁徙和演化的重要地带之一,该地区现代人群的起源及形成问题一直都是人类学领域广泛关注的焦点。遗传学研究为重建东亚人群历史提供了新的视角和见解。越来越多的遗传学证据表明,现代人约20万年前起源于非洲的晚期智人,并于10万年前走出非洲,大约在5~6万年前沿海岸线快速到达东亚南部,进而扩散到整个东亚地区。早期智人可能对走出非洲的现代人有一定程度的遗传贡献。早期定居、文化同化、人群迁徙以及基因交流等,对东亚人群的起源和演化起着至关重要的作用。前期的研究对东亚人群的源流历史进行了细致的分析,很大程度上解决了考古学、历史学等领域长期以来存在的分歧,然而这还需通过全基因组学和古DNA研究的进一步验证。本文从遗传学视角梳理和总结了东亚人群起源、迁徙和演化的历史,完善了对东亚人群演变的系统认识,并对未来东亚人群源流历史研究的发展方向做了展望。     

Origins of Uralic-speaking populations: craniological evidence

Data on 55 modern cranial samples representing Uralic and other Eurasian populations were subjected to canonical variate (CV) and principal component (PC) analysis for 6 nonmetric and 14 metric traits, respectively. While PC1 and CV1 reveal strong east-to-west gradients among the Uralians, PC2 and CV2 separate most of them from the remaining groups, suggesting that they have descended from an ancestral proto-Uralian population. The biologically «Uralic» features survive in modern Uralic groups despite the fact that the initial split was followed by a long period of hybridization with widely dissimilar people. Our results confirm that the ancestors of many Turkish-speaking groups as well as the Yukaghirs belonged to the proto-Uralic community.     

The founding mothers: the genetic structure of newly established Daphnia populations

Colonization dynamics may strongly influence within and among population genetic variation and evolutionary potential of populations. We here analyze the genetic structure during the first three years of 12 cyclical parthenogenetic Daphnia populations in newly created pond habitats. One to three genotypes were observed to colonize the populations, indicating a limited number of founders. Pronounced changes in genetic structure were associated with hatching of sexual dormant eggs after a period of absence of the newly founded populations from the active community. Despite rapid colonization, genetic differentiation among populations was fairly high with limited decay over time, suggesting long-lasting founder effects. After initial colonization, no new alleles were observed in any of the populations, and our analyses suggests that this reflects reduced establishment success of later arrivals. Rare alleles increased in frequency, which likely is the result of inbreeding depression in selfed offspring of initially abundant clones, providing a fitness advantage to the sexual offspring of initially rare clones.     

Social organization and genetic structure: insights from codistributed bat populations

The impact of ecology and social organization on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organization, all of which are codistributed in an ancient forest habitat that has been exceptionally buffered from radical habitat shifts. Over one thousand individuals were captured at foraging sites and genotyped at polymorphic microsatellite loci. Analyses of spatially explicit genotype data revealed interspecies differences in the extent of movement and gene flow and genetic structure across continuous intact forest. Highest positive genetic structure was observed in tree-roosting taxa that roost either alone or in small groups. By comparison, a complete absence of genetic autocorrelation was noted in the cave-roosting colonial species across the study area. Our results thus reveal measurable interspecies differences in the natural limits of gene flow in an unmodified habitat, which we attribute to contrasting roosting ecology and social organization. The consequences of ecology and behaviour for gene flow have important implications for conservation. In particular, tree-roosting species characterized by lower vagility and thus gene flow will be disproportionally impacted by landscape-scale forest clearance and habitat fragmentation, which are prevalent in the study region. Our method also highlights the usefulness of rapid sampling of foraging bats for assaying genetic structure, particularly where roosting sites are not always known.     

蚜虫种群遗传多样性的影响因素及分子基础

蚜虫是一个复杂的类群 ,不同种群之间常常表现遗传多样性 ,特别是同种蚜虫的不同种群 ,这种多样性与环境因素 (寄主植物、地理气候条件等 )的影响密切相关 ,而且蚜虫种群多样性无论在细胞学水平 ,还是分子生物学水平均表现明显的遗传分化。该文在分析了蚜虫种群遗传多样性影响因素的基础上 ,从蚜虫核型变化、核DNA和线粒体DNA遗传分化和多样性方面总结了导致蚜虫种群遗传多样性的内在分子基础 ,并讨论了研究蚜虫种群遗传多样性的重要意义和前景     

Trypanosoma cruzi: genetic structure of populations and relevance of genetic variability to the pathogenesis of chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or, occasionally, overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but it is likely that the genetic variability of both the host and the parasite are of importance. In this work we review the the genetic structure of T. cruzi populations and analyze the importance of genetic variation of the parasite in the pathogenesis of the disease under the light of the histotropic-clonal model.