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Demographic History (demographic + history)
Kinds of Demographic History Selected AbstractsGENETIC EVIDENCE ON THE DEMOGRAPHY OF SPECIATION IN ALLOPATRIC DOLPHIN SPECIESEVOLUTION, Issue 4 2002Matthew P. Hare Abstract Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 × 104 to 10.9 × 104) during 0.74,1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations. [source] Defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholis squamata (Ophiuroidea)MOLECULAR ECOLOGY, Issue 7 2008E. BOISSIN Abstract At a time when biodiversity is threatened, we are still discovering new species, and particularly in the marine realm. Delimiting species boundaries is the first step to get a precise idea of diversity. For sympatric species which are morphologically undistinguishable, using a combination of independent molecular markers is a necessary step to define separate species. Amphipholis squamata, a cosmopolitan brittle star, includes several very divergent mitochondrial lineages. These lineages appear totally intermixed in the field and studies on morphology and colour polymorphism failed to find any diagnostic character. Therefore, these mitochondrial lineages may be totally interbreeding presently. To test this hypothesis, we characterized the genetic structure of the complex in the French Mediterranean coast using sequences of mitochondrial DNA (16S) and for the first time, several nuclear DNA markers (introns and microsatellites). The data revealed six phylogenetic lineages corresponding to at least four biological species. These sibling species seem to live in syntopy. However, they seem to display contrasted levels of genetic diversity, suggesting they have distinct demographic histories and/or life-history traits. Genetic differentiation and isolation-by-distance within the French Mediterranean coasts are revealed in three lineages, as expected for a species without a free larval phase. Finally, although recombinant nuclear genotypes are common within mitochondrial lineages, the data set displays a total lack of heterozygotes, suggesting a very high selfing rate, a feature likely to have favoured the formation of the species complex. [source] Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropodsMOLECULAR ECOLOGY, Issue 2 2008ERIC D. CRANDALL Abstract Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographical patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea-level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographical patterns in two species of highly dispersive neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from > 1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata, respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographical discordance. N. albicilla has maintained reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Nem > 75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea-level stands. Results indicate that ecologically similar, codistributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographical structure. [source] The genetic structure of populations from Haiti and Jamaica reflect divergent demographic historiesAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Tanya M. Simms Abstract The West Indies represent an amalgamation of African, European and in some cases, East Asian sources, but the contributions from each ethnic group remain relatively unexplored from a genetic perspective. In the present study, we report, for the first time, allelic frequency data across the complete set of 15 autosomal STR loci for general collections from Haiti and Jamaica, which were subsequently used to examine the genetic diversity present in each island population. Our results indicate that although both Haiti and Jamaica display genetic affinities with the continental African collections, a stronger African signal is detected in Haiti than in Jamaica. Although only minimal contributions from non-African sources were observed in Haiti, Jamaica displays genetic input from both European and East Asian sources, an admixture profile similar to other New World collections of African descent analyzed in this report. The divergent genetic signatures present in these populations allude to the different migratory events of Africans, Europeans, and East Asians into the New World. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source] Linkage disequilibrium patterns and genetic structure of Amerindian and non-Amerindian Brazilian populations revealed by long-range X-STR markersAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Fabio P.N. Leite Abstract The extent of X-chromosome linkage disequilibrium (LD) was studied in a southern Brazilian population, and in a pool of samples from Amerindian populations. For this purpose, 11 microsatellites, located mostly in a Xq region comprising ,86 Mb was investigated. The lower Amerindian gene diversity associated with significant differences between the populations studied indicated population structure as the main cause for the higher LD values in the Amerindian pool. On the other hand, the LD levels of the non-Amerindian Brazilian sample, although less extensive than that of the Amerindians, were probably determined by admixture events. Our results indicated that different demographic histories have significant effects on LD levels of human populations, and provide a first approach to the X-chromosome ancestry of Amerindian and non-Amerindian Brazilian populations, being valuable for future studies involving mapping and population genetic studies. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Shipwrecks and founder effects: Divergent demographic histories reflected in Caribbean mtDNAAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2005Antonio Salas Abstract During the period of the Atlantic slave trade (15th,19th centuries), millions of people were forced to move from Africa to many American destinations, changing dramatically the human landscape of the Americas. Here, we analyze mitochondrial DNA from two different American populations with African ancestry, with hitherto unknown European and Native American components. On the basis of historical records, African-Americans from Chocó (Colombia) and the Garífunas (or "Black Carib") of Honduras are likely to have had very different demographic histories, with a significant founder effect in the formation of the latter. Both the common features and differences are reflected in their mtDNA composition. Both show a minor component (,16%) from Native Central/South Americans and a larger component (,84%) from sub-Saharan Africans. The latter component is very diverse in the African-Americans from Chocó, similar to that of sub-Saharan Africans, but much less so in the Garífunas, with several mtDNA types elevated to high frequency, suggesting the action of genetic drift. Am J Phys Anthropol, 2005. © 2005 Wiley-Liss, Inc. [source] The population genetic effects of ancestry and admixture in a subdivided cattle breedANIMAL GENETICS, Issue 4 2009T. C. Bray Summary The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability (HE = 0.63,0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations (HE = 0.52,0.55) and higher differentiation (FST > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method-based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data. [source] Monastic mortality: Durham Priory, 1395,15291ECONOMIC HISTORY REVIEW, Issue 4 2006JOHN HATCHER This article presents reliable data on the life expectancy of the monks of Durham Priory between 1395 and 1529. The number of years that monks survived in this northern monastery plunged precipitously in the second half of the fifteenth century before staging a partial recovery in the early sixteenth. The experience of Durham monks mirrors the scale, direction, and timing of the data already produced for the monks of Canterbury and Westminster. While the precise relationship between monastic mortality and that of the population at large remains difficult to determine, there can be no doubt that the symmetry that has been established between mortality in three monasteries located in different parts of the country has important implications for our understanding of the demographic history of late medieval England. [source] RAPID SPECIATION FOLLOWING RECENT HOST SHIFTS IN THE PLANT PATHOGENIC FUNGUS RHYNCHOSPORIUMEVOLUTION, Issue 6 2008Pascal L. Zaffarano Agriculture played a significant role in increasing the number of pathogen species and in expanding their geographic range during the last 10,000 years. We tested the hypothesis that a fungal pathogen of cereals and grasses emerged at the time of domestication of cereals in the Fertile Crescent and subsequently speciated after adaptation to its hosts. Rhynchosporium secalis, originally described from rye, causes an important disease on barley called scald, although it also infects other species of Hordeum and Agropyron. Phylogenetic analyses based on four DNA sequence loci identified three host-associated lineages that were confirmed by cross-pathogenicity tests. Bayesian analyses of divergence time suggested that the three lineages emerged between ,1200 to 3600 years before present (B.P.) with a 95% highest posterior density ranging from 100 to 12,000 years B.P. depending on the implemented clock models. The coalescent inference of demographic history revealed a very recent population expansion for all three pathogens. We propose that Rhynchosporium on barley, rye, and Agropyron host species represent three cryptic pathogen species that underwent independent evolution and ecological divergence by host-specialization. We postulate that the recent emergence of these pathogens followed host shifts. The subsequent population expansions followed the expansion of the cultivated host populations and accompanying expansion of the weedy Agropyron spp. found in fields of cultivated cereals. Hence, agriculture played a major role in the emergence of the scald diseases, the adaptation of the pathogens to new hosts and their worldwide dissemination. [source] Population structure in the South American tern Sterna hirundinacea in the South Atlantic: two populations with distinct breeding phenologiesJOURNAL OF AVIAN BIOLOGY, Issue 4 2010Patrícia J. Faria The South American tern Sterna hirundinacea is a migratory species for which dispersal, site fidelity and migratory routes are largely unknown. Here, we used five microsatellite loci and 799,bp partial mitochondrial DNA sequences (Cytochrome b and ND2) to investigate the genetic structure of South American terns from the South Atlantic Ocean (Brazilian and Patagonian colonies). Brazilian and Patagonian colonies have two distinct breeding phenologies (austral winter and austral summer, respectively) and are under the influence of different oceanographic features (e.g. Brazil and Falklands/Malvinas ocean currents, respectively), that may promote genetic isolation between populations. Results show that the Atlantic populations are not completely panmictic, nevertheless, contrary to our expectations, low levels of genetic structure were detected between Brazilian and Patagonian colonies. Such low differentiation (despite temporal isolation of the colonies) could be explained by demographic history of these populations coupled with ongoing levels of gene flow. Interestingly, estimations of gene flow through Maximum likelihood and Bayesian approaches has indicated asymmetrical long term and contemporary gene flow from Brazilian to Patagonian colonies, approaching a source,sink metapopulation dynamic. Genetic analysis of other South American tern populations (especially those from the Pacific coast and Falklands,Malvinas Islands) and other seabird species showing similar geographical distribution (e.g. royal tern Thalasseus maximus), are fundamental in gaining a better understanding of the main processes involved in the diversification of seabirds in the southern hemisphere. [source] A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelopeJOURNAL OF BIOGEOGRAPHY, Issue 3 2010Eline D. Lorenzen Abstract Aim, Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long-standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location, The sub-Saharan savanna biome of East and southern Africa. Methods, Mitochondrial DNA control-region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent-based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results, Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr,1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07,0.37) than for the southern lineage (0.35 Ma; 0.10,0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation-by-distance among populations. Main conclusions, The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer-standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa. [source] Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in TaiwanJOURNAL OF BIOGEOGRAPHY, Issue 5 2006Su-Hwa Wu Abstract Aim, The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location, The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods, The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs. Nested clade analysis was conducted with the computer program ceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programs arlequin and hapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results, Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions, This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [source] The divergence of two independent lineages of an endemic Chinese gecko, Gekko swinhonis, launched by the Qinling orogenic beltMOLECULAR ECOLOGY, Issue 12 2010JIE YAN Abstract The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual-based phylogenetic analyses of nucDNA and Bayesian-clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male-biased dispersal in this species. High genetic divergence, long-term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species. [source] High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear lociMOLECULAR ECOLOGY, Issue 10 2008K. KAMIYA Abstract Differences in demographic history, life-history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade-intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides, a shade-intolerant pioneer tree species that occupies forest gaps in warm-temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci (FST = 0.32,0.64), as expected from the insect-pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind-pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium. This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides. [source] Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropodsMOLECULAR ECOLOGY, Issue 2 2008ERIC D. CRANDALL Abstract Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographical patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea-level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographical patterns in two species of highly dispersive neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from > 1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata, respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographical discordance. N. albicilla has maintained reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Nem > 75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea-level stands. Results indicate that ecologically similar, codistributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographical structure. [source] Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickensMOLECULAR ECOLOGY, Issue 11 2007JEFF A. JOHNSON Abstract Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and mdiv). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (,), population divergence time (t), and time to the most recent common ancestor (TMRCA) from mdiv were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history. [source] Phylogeography of the montane caddisfly Drusus discolor: evidence for multiple refugia and periglacial survivalMOLECULAR ECOLOGY, Issue 8 2006STEFFEN U. PAULS Abstract We studied the genetic population structure and phylogeography of the montane caddisfly Drusus discolor across its entire range in central and southern Europe. The species is restricted to mountain regions and exhibits an insular distribution across the major mountain ranges. Mitochondrial sequence data (COI) of 254 individuals from the entire species range is analysed to reveal population genetic structure. The data show little molecular variation within populations and regions, but distinct genetic differentiation between mountain ranges. Most populations are significantly differentiated based on FST and exact tests of population differentiation and most haplotypes are unique to a single mountain range. Phylogenetic analyses reveal deep divergence between geographically isolated lineages. Combined, these results suggest that past fragmentation is the prominent process structuring the populations across Europe. We use tests of selective neutrality and mismatch distributions, to study the demographic population history of regions with haplotype overlap. The high level of genetic differentiation between mountain ranges and estimates of demographic history provide evidence for the existence of multiple glacial refugia, including several in central Europe. The study shows that these aquatic organisms reacted differently to Pleistocene cooling than many terrestrial species. They persisted in numerous refugia over multiple glacial cycles, allowing many local endemic clades to form. [source] Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf populationMOLECULAR ECOLOGY, Issue 6 2006J. ASPI Abstract The Finnish wolf population (Canis lupus) was sampled during three different periods (1996,1998, 1999,2001 and 2002,2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period. [source] Phylogeography and systematics of zebra mussels and related speciesMOLECULAR ECOLOGY, Issue 4 2006GREGORY W. GELEMBIUK Abstract The genus Dreissena includes two widespread and aggressive aquatic invaders, the zebra mussel, Dreissena polymorpha, and the quagga mussel, Dreissena bugensis. This genus evolved in the Ponto-Caspian Sea basin, characterized by dynamic instability over multiple timescales and a unique evolutionary environment that may predispose to invasiveness. The objectives of this study were to gain insights into the demographic history of Dreissena species in their endemic range, to reconstruct intraspecific phylogeographic relationships among populations, and to clarify systematics of the genus, using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. We found four deeply diverged clades within this genus, with a basal split that approximately coincided with the Cretaceous,Tertiary boundary. Divergence events within the four base clades were much more recent, corresponding to geographically disjunct sets of populations, which might represent species complexes. Across all taxa, populations of Dreissena shared a common pattern of genetic signatures indicating historical population bottlenecks and expansions. Haplotype diversity was relatively low in Ponto-Caspian drainages relative to more stable tectonic lakes in Greece, Macedonia, and Turkey. The phylogeographic and demographic patterns in the endemic range of Dreissena might have resulted from vicariance events, habitat instability, and the high fecundity and passive dispersal of these organisms. [source] Detecting past population bottlenecks using temporal genetic dataMOLECULAR ECOLOGY, Issue 10 2005UMA RAMAKRISHNAN Abstract Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations. [source] Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptationsMOLECULAR ECOLOGY, Issue 11 2004SABINE FINK Abstract The phylogeography of the common vole (Microtus arvalis) was examined by analysing mitochondrial DNA (mtDNA) sequence variation in 1044 base pairs (bp) of the cytochrome b (cytb) gene and in 322 bp of the control region (ctr) among 106 individuals from 58 locations. The geographical distribution of four previously recognized cytb evolutionary lineages in Europe was refined and a new lineage was found in southern Germany. All lineages were distributed allopatrically, except in one sample that was probably located in a contact zone. The occurrence of several lineages in the Alps is in keeping with their recent recolonization from distinct sources. The translation of 84 cytb DNA sequences produced 33 distinct proteins with relationships that differed from those of the DNA haplotypes, suggesting that the mtDNA lineages did not diverge in response to selection. In comparison with M. agrestis, a neutrality test detected no overall evidence for selection in the cytb gene, but a closer examination of a structural model showed that evolutionarily conserved and functionally important positions were often affected. A new phylogeographical test of random accumulation of nonsynonymous mutations generated significant results in three lineages. We therefore conclude that the molecular diversity of cytb in M. arvalis is overall the result of the demographic history of the populations, but that there have been several episodes of local adaptation to peculiar environments. [source] Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelagoMOLECULAR ECOLOGY, Issue 6 2001Simon J. Goodman Abstract We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size. [source] Isolation and characterization of microsatellite loci in the icefish Chionodraco rastrospinosus (Perciformes, Notothenioidea, Channichthyidae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006CHIARA PAPETTI Abstract We characterized eight polymorphic microsatellites in the icefish Chionodraco rastrospinosus (Perciformes, Notothenioidea, Channichthyidae). Microsatellites were isolated from a partial genomic library enriched for an AC motif. Chionodraco rastrospinosus is an endemic species inhabiting southern ocean waters surrounding the Antarctic Peninsula, the South Shetland Islands, and the South Orkney Islands. An excess of homozygotes was observed in seven out of the eight investigated loci; however, presence of null alleles was detected only for three of them suggesting that other factors may act in reducing heterozygosity. These molecular markers will be useful to investigate icefish genetic structure, possibly providing insights on its effective population size and demographic history. [source] Brief communication: Patterns of linkage disequilibrium and haplotype diversity at Xq13 in six Native American populationsAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010Sijia Wang Abstract Comparative studies of linkage disequilibrium (LD) can provide insights into human demographic history. Here, we characterize LD in six Native American populations using seven microsatellite markers in Xq13, a region of the genome extensively studied in populations around the world. Native Americans show relatively low diversity and high LD, in agreement with recent genome-wide survey and a scenario of sequential founder effects accompanying human population dispersal around the globe. LD in Native Americans is similar to that observed in some recently described small population isolates and higher than in large European isolates (e.g., Finns), which have been extensively analyzed in medical genetics studies. Haplotype analyses are consistent with a colonization of the New World by a differentiated East Asian population, followed by extensive genetic drift in the Americas. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source] A multi-perspective view of genetic variation in CameroonAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009V. Coia Abstract In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration N, ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source] Dissecting the molecular architecture and origin of Bayash Romani patrilineages: Genetic influences from South-Asia and the BalkansAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Irena Martinovi, Klari Abstract The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift. Am J Phys Anthropol, 2009. © 2008 Wiley-Liss, Inc. [source] Conservation genetics of a critically endangered Iberian minnow: evidence of population decline and extirpationsANIMAL CONSERVATION, Issue 2 2010V. Sousa Abstract The endangered minnow Iberochondrostoma almacai is an endemic Iberian cyprinid with a restricted and fragmented distribution. Here, we describe the genetic structure of the species and infer its demographic history from six nuclear-encoded microsatellite loci and mitochondrial cytochrome b sequences. Genetic diversity was low (microsatellite He<0.45; mtDNA ,<0.0015), and both markers resolved two groups: one from the northern Mira drainage and one from the Arade and Bensafrim drainages. The relatively low differentiation between these groups (0.09 The population genetic effects of ancestry and admixture in a subdivided cattle breedANIMAL GENETICS, Issue 4 2009T. C. Bray Summary The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability (HE = 0.63,0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations (HE = 0.52,0.55) and higher differentiation (FST > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method-based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data. [source] Frequency of the AGT Pro11Leu Polymorphism in Humans: does Diet Matter?ANNALS OF HUMAN GENETICS, Issue 1 2010Laure Ségurel Summary The Pro11Leu substitution in the AGXT gene, which causes primary hyperoxaluria type 1, is found with high frequency in some human populations (e.g., 5,20% in Caucasians). It has been suggested that this detrimental mutation could have been positively selected in populations with a meat-rich diet. In order to test this hypothesis, we investigated the occurrence of Pro11Leu in both herder and agriculturalist populations from Central Asia. We found a lower frequency of this detrimental mutation in herders, whose diet is more meat-rich, as compared to agriculturalists, which therefore challenges the universality of the previous claim. Furthermore, when combining our original data with previously published results, we could show that the worldwide genetic differentiation measured at the Pro11Leu polymorphism does not depart from neutrality. Hence, the distribution of the variation observed in the AGXT gene could be due to demographic history, rather than local adaptation to diet. [source]
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