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Population Genetic Structure (population + genetic_structure)
Selected AbstractsPOPULATION GENETIC STRUCTURE OF FINLESS PORPOISES, NEOPHOCAENA PHOCAENOIDES, IN CHINESE WATERS, INFERRED FROM MITOCHONDRIAL CONTROL REGION SEQUENCESMARINE MAMMAL SCIENCE, Issue 2 2002Guang Yang Abstract Seven hundred and twenty base pairs (bp) of the mitochondrial control region from 73 finless porpoises, Neophocaena phocaenoides, in Chinese waters were sequenced. Thirteen variable sites were determined and 17 haplotypes were defined. Of these, 5 and 7 were found only in the Yellow Sea population and the South China Sea population, respectively, whereas no specific haplo-type was found in the Yangtze River population. Phylogenetic analyses using NJ and ML algorithm did not divide the haplotypes into monophyletic clades representing recognized geographic populations of finless porpoises in Chinese waters, suggesting the existence of migration and gene flow among populations. Analysis of molecular variance showed the obvious population genetic structure (,st= 0.41, P < 0.05); however, the structure was mainly between either the Yangtze River population or the Yellow Sea population and the South China Sea population. The genetic diversity (nucleotide diversity and haplotypic diversity) of the Yellow Sea population was significantly higher than those of the Yangtze River population and the South China Sea population, suggesting the relatively later divergence of the latter two populations and supporting the Yellow Sea population as the original center of Neophocaena. [source] Population Genetic Structure of the Medicinal Plant Vitex rotundifolia in China: Implications for its Use and ConservationJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2008Yuan Hu Abstract Vitex rotundifolia L. is an important plant species used in traditional Chinese medicine. For its efficient use and conservation, genetic diversity and clonal variation of V. rotundifolia populations in China were investigated using inter-simple sequence repeat markers. Fourteen natural populations were included to estimate genetic diversity, and a large population with 135 individuals was used to analyze clonal variation and fine-scale spatial genetic structure. The overall genetic diversity (GD) of V. rotundifolia populations in China was moderate (GD = 0.190), with about 40% within-population variation. Across all populations surveyed, the average within-population diversity was moderate (P = 22.6%; GD = 0.086). A relatively high genetic differentiation (Gst = 0.587) among populations was detected based on the analysis of molecular variance data. Such characteristics of V. rotundifolia are likely attributed to its sexual/asexual reproduction and limited gene flow. The genotypic diversity (D = 0.992) was greater than the average values of a clonal plant, indicating its significant reproduction through seedlings. Spatial autocorrelation analysis showed a clear within-population structure with gene clusters of approximately 20 m. Genetic diversity patterns of V. rotundifolia in China provide a useful guide for its efficient use and conservation by selecting particular populations displaying greater variation that may contain required medicinal compounds, and by sampling individuals in a population at >20 m spatial intervals to avoid collecting individuals with identical or similar genotypes. [source] Population genetic structure reveals terrestrial affinities for a headwater stream insectFRESHWATER BIOLOGY, Issue 10 2007DEBRA S. FINN Summary 1. The spatial distribution of stream-dwelling organisms is often considered to be limited primarily according to the hierarchical structure of the hydrologic network, and previous conceptual models of population genetic structure have reflected this generality. Headwater specialists, however, are confined to short upstream sections of the network, and therefore are unlikely to respond in the same way as species with a broader range of habitat tolerance. 2. Here, we propose a model to describe spatial patterns of genetic diversity in headwater specialists with a limited ability for among-stream dispersal. The headwater model predicts a partitioning of genetic variance according to higher-elevation ,islands' of terrestrial habitat that provide required headwater stream conditions. The model therefore expects a geographic pattern of genetic variance similar to that expected for low-dispersal terrestrial species occupying the adjacent habitat. 3. Using a 1032-bp mitochondrial DNA fragment encompassing parts of the COI and COII genes, we demonstrate that Madrean Sky Islands populations of the giant water bug Abedus herberti conform to the proposed headwater model. Furthermore, they exhibit phylogeographic patterns broadly concordant with those shown for several terrestrial species in the region, including a major zone of discontinuity in the Chiricahua mountain range. 4. Overall, populations are highly isolated from one another, and a nested clade analysis suggested that A. herberti population structure, similarly to terrestrial Sky Islands species studied previously, has been influenced by Pleistocene climatic cycles causing expansion and contraction of temperate woodland habitat. 5. Because they have no ability to disperse among present-day mountaintop habitat islands, A. herberti and other headwater species with limited dispersal ability are vulnerable to the projected increasing rate of climatic warming in this region. [source] Population genetic structure of three freshwater mussel (Unionidae) species within a small stream system: significant variation at local spatial scalesFRESHWATER BIOLOGY, Issue 8 2007DAVID J. BERG Summary 1. Unionid mussels are highly threatened, but little is known about genetic structure in populations of these organisms. We used allozyme electrophoresis to examine partitioning of genetic variation in three locally abundant and widely distributed species of mussels from a catchment in Ohio. 2. Within-population variation was similar to that previously reported for freshwater mussels, but genotype frequencies exhibited heterozygote deficiencies in many instances. All three species exhibited significant among-population variation. Evidence of isolation-by-distance was found in Elliptio dilatata and Ptychobranchus fasciolaris, while Lampsilis siliquoidea showed no geographical pattern of among-population variation. 3. Our results suggest that the isolating effects of genetic drift were greater in L. siliquoidea than in the other species. Differentiation of populations occurred at a much smaller spatial scale than has previously been found in freshwater mussels. Differences among species may reflect differences in the dispersal abilities of fishes that serve as hosts for the glochidia larvae of mussels. 4. Based on our results, we hypothesise that species of mussels that are common to large rivers exhibit relatively large amounts of within-population genetic variation and little differentiation over large geographical distances. Conversely, species typical of small streams show lower within-population genetic variation and populations will be more isolated. If this hypothesis can be supported, it may prove useful in the design of conservation strategies that maintain the genetic structure of target species. [source] Range-wide genetic structure in a north-east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markersJOURNAL OF BIOGEOGRAPHY, Issue 5 2009Mineaki Aizawa Abstract Aim, We used microsatellite markers to determine the range-wide genetic structure of Picea jezoensis and to test the hypothesis that the past population history of this widespread cold-temperate spruce has resulted in a low level of genetic variation and in imprints of inbreeding and bottlenecks in isolated marginal populations. Location, The natural range of the three infraspecific taxa of P. jezoensis throughout north-east Asia, including isolated marginal populations. Methods, We analysed a total of 990 individuals across 33 natural populations using four nuclear microsatellite loci. Population genetic structure was assessed by analysing genetic diversity indices for each population, examining clustering (model-based and distance-based) among populations, evaluating signals of recent bottlenecks, and testing for isolation by distance (IBD). Results, The 33 populations were clustered into five groups. The isolated marginal groups of populations (in Kamchatka, Kii in Japan and South Korea) exhibited low levels of allelic richness and gene diversity and a complete or almost complete loss of rare alleles. A recent bottleneck was detected in the populations in Hokkaido across to mid-Sakhalin. The IBD analysis revealed that genetic divergence between populations was higher for populations separated by straits. Main conclusions,Picea jezoensis showed a higher level of genetic differentiation among populations (FST = 0.101) than that observed in the genus Picea in general. This might be attributable to the fact that historically the straits around Japan acted as barriers to the movement of seeds and pollen. The low levels of genetic diversity in the isolated marginal population groups may reflect genetic drift that has occurred after isolation. Evidence of a significant bottleneck between the Hokkaido and mid-Sakhalin populations implies that the cold, dry climate in the late Pleistocene resulted in the decline and contraction of populations, and that there was a subsequent expansion followed by a founder effect when conditions improved. The high polymorphism observed in P. jezoensis nuclear microsatellites revealed cryptic genetic structure that organellar DNA markers failed to identify in a previous study. [source] Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of CaliforniaJOURNAL OF FISH BIOLOGY, Issue 2 2010S. M. Plank The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small FST values (,0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep-water channel from the coastal sites, however, was significantly divergent (large FST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size. [source] Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)MOLECULAR ECOLOGY, Issue 15 2008BEATA UJVARI Abstract By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark,recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal. [source] Phylogeography of the olive sea snake, Aipysurus laevis (Hydrophiinae) indicates Pleistocene range expansion around northern Australia but low contemporary gene flowMOLECULAR ECOLOGY, Issue 16 2007V. LUKOSCHEK Abstract Pleistocene sea-level fluctuations profoundly changed landmass configurations around northern Australia. The cyclic emergence of the Torres Strait land bridge and concomitant shifts in the distribution of shallow-water marine habitats repeatedly sundered east and west coast populations. These biogeographical perturbations invoke three possible scenarios regarding the directions of interglacial range expansion: west to east, east to west, or bidirectional. We evaluated these scenarios for the olive sea snake, Aipysurus laevis, by exploring its genetic structure around northern Australia based on 354 individuals from 14 locations in three regions (Western Australia, WA; Gulf of Carpentaria, GoC; Great Barrier Reef, GBR). A 726-bp fragment of the mitochondrial DNA ND4 region revealed 41 variable sites and 38 haplotypes, with no shared haplotypes among the three regions. Population genetic structure was strong overall, ,ST = 0.78, P < 0.001, and coalescent analyses revealed no migration between regions. Genetic diversity was low in the GBR and GoC and the genetic signatures of these regions indicated range or population expansions consistent with their recent marine transgressions around 7000 years ago. By contrast, genetic diversity on most WA reefs was higher and there were no signals of recent expansion events on these reefs. Phylogenetic analyses indicated that GBR and GoC haplotypes were derived from WA haplotypes; however, statistical parsimony suggested that recent range expansion in the GBR-GoC probably occurred from east coast populations, possibly in the Coral Sea. Levels of contemporary female-mediated gene flow varied within regions and reflected potential connectivity among populations afforded by the different regional habitat types. [source] Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservationMOLECULAR ECOLOGY, Issue 11 2003Maristerra R. Lemes Abstract Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754,0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, , = 0.097 and , = 0.147, respectively. Estimates of , and , were significantly greater than zero for all pairwise population comparisons. Pairwise ,-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil. [source] Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequencesMOLECULAR ECOLOGY, Issue 10 2003A. J. Crawford Abstract Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c- myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c- myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c- myc. Nuclear FST estimates were , 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models. [source] Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapesMOLECULAR ECOLOGY, Issue 9 2003Alain Caizergues Abstract We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as ,, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities. [source] The role of environment in shaping the genetic diversity of the subalpine mosquito, Aedes rusticus (Diptera, Culicidae)MOLECULAR ECOLOGY, Issue 7 2003J. P. David Abstract The relative involvement of larval dietary tolerance to the leaf-litter toxic polyphenols in shaping population genetic structure of the subalpine mosquito Aedes rusticus was examined. This was compared with other parameters such as geographical range, type of vegetation surrounding the breeding site, and occurrence of annual larvicidal treatments. Population genetic structure was analysed at 10 presumed neutral polymorphic isoenzyme loci. Toxicological comparisons involved standard bioassays performed on larvae fed on toxic decomposed leaf litter. Significant overall genetic differentiation was observed among the 22 studied populations and within the five defined geographical groups. Analysis of molecular variance revealed an absence of relation between genetic and environmental parameters, genetic variance being essentially found within populations. This suggested that the larval dietary tolerance to the toxic leaf litter and the other studied parameters poorly influence population genetic structure. The local adaptation of subalpine mosquito populations to the surrounding vegetation thus appears as a labile trait. Such a dynamic adaptation is also suggested by the correlation between geographical and toxicological distances and the correlation between dietary tolerance to the leaf-litter toxic polyphenols and annual larvicidal treatments. [source] Population genetic structure of the malaria mosquito Anopheles arabiensis across Nigeria suggests range expansionMOLECULAR ECOLOGY, Issue 11 2001D. Y. Onyabe Abstract Ten microsatellite loci, four located within and six outside chromosome inversions, were employed to study the genetic structure of Anopheles arabiensis across the ecological zones of Nigeria (arid savannah in the north gradually turns into humid forest in the south). Regardless of location within or outside inversions, genetic variability at all loci was characterized by a reduction in both the number of alleles per locus and heterozygosity from savannah to forest. Across all loci, all but one allele in the forest also occurred in the savannah, whereas at least 78 alleles in the savannah were missing in the forest. Genetic differentiation increased with geographical distance; consequently, genetic distances between zones exceeded those within zones. The largest genetic distances were between localities at the extremes of the transect (range FST = 0.196,0.258 and RST = 0.183,0.468) and were as large as those between A. arabiensis and Anopheles gambiae s.s. Gene flow across the country was very low, so that Nm between the extremes of the transect was < 1. These data suggest that A. arabiensis has extended its range from the savannah into the forest during which it experienced a reduction in effective population size due to sequential founder effects. Gene flow post range expansion appears too restricted by geographical distance to homogenize the gene pool of A. arabiensis across Nigeria. [source] Population genetic structure of Plasmopara viticola in the Western Cape Province of South AfricaMOLECULAR PLANT PATHOLOGY, Issue 6 2007TREVOR KOOPMAN SUMMARY Plasmopara viticola populations in South Africa were studied for two consecutive grape growing seasons, in an organically managed and a conventional fungicide-sprayed vineyard. Three to four samplings in each season were genotyped with four microsatellite markers (GOB, CES, ISA and BER). Population differentiation (Fst) between the conventional fungicide-sprayed vineyard and organically managed vineyard was low (0.004 and 0.016) in both growing seasons, suggesting one metapopulation. However, differences in the relative contribution of the predominant and new genotypes to epidemics in the two vineyards suggested that fungicide applications may have selected for reduced pathogen diversity. In both years and vineyards, sexual (oosporic) reproduction and/or migration occurred throughout the year and contributed between 12 and 74% to the epidemic. Hardy,Weinberg analyses suggest that South African P. viticola populations are randomly mating. Epidemics in both years and vineyards were dominated by one or two genotypes that each contributed between 14 and 67% to the epidemic through asexual reproduction. The remaining genotypes showed low levels of asexual reproduction, with most genotypes never being able to reproduce asexually. However, for some genotypes asexual reproduction was important, as it enabled survival of the genotypes from one season to the next. In total, ten genotypes were able to survive asexually or vegetatively from one season to the next. The populations were further characterized by the presence of a high frequency of isolates that most likely have elevated ploidy levels. [source] Population genetic structure of rock ptarmigan in the ,sky islands' of French Pyrenees: implications for conservationANIMAL CONSERVATION, Issue 2 2009N. Bech Abstract Expected consequences of global warming include habitat reduction in many cool climate species. Rock ptarmigan is a Holarctic grouse that inhabits arctic and alpine tundra. In Europe, the Pyrenean ptarmigan inhabits the southern edge of the species' range and since the last glacial maximum its habitat has been severely fragmented and is restricted to high-alpine zones or ,sky islands'. A recent study of rock ptarmigan population genetic in Europe found that the Pyrenean ptarmigan had very low genetic diversity compared with that found in the Alps and Scandinavia. Habitat fragmentation and reduced genetic diversity raises concerns about the viability of ptarmigan populations in the Pyrenees. However, information on population structuring and gene flow across the Pyrenees, which is essential for designing a sound management plan, is absent. In this study, we use seven microsatellites and mitochondrial control region sequences to investigate genetic variation and differentiation among five localities across the Pyrenees. Our analyses reveal the presence of genetic differentiation among all five localities and a significant isolation-by-distance effect that is likely the result of short dispersal distances and high natal and breeding philopatry of Pyrenean ptarmigan coupled with severe habitat fragmentation. Furthermore, analysis of molecular variance, principal component analysis and Bayesian analysis of genetic structuring identified the greatest amount of differentiation between the eastern and main parts of the Pyrenean chain separated by the Sègre Valley. Our data also show that the Canigou massif may host an isolated population and requires special conservation attention. We propose a management plan which includes the translocation of birds. If a sky island structure affects genetic divergence in rock ptarmigan, it may also affect the genetic structure of other sky island species having low dispersal abilities. [source] Population genetic structure and conservation of Asian elephants (Elephas maximus) across IndiaANIMAL CONSERVATION, Issue 4 2005T. N. C. Vidya This study examines the population genetic structure of Asian elephants (Elephas maximus) across India, which harbours over half the world's population of this endangered species. Mitochondrial DNA control region sequences and allele frequencies at six nuclear DNA microsatellite markers obtained from the dung of free-ranging elephants reveal low mtDNA and typical microsatellite diversity. Both known divergent clades of mtDNA haplotypes in the Asian elephant are present in India, with southern and central India exhibiting exclusively the , clade of Fernando et al. (2000), northern India exhibiting exclusively the , clade and northeastern India exhibiting both, but predominantly the , clade. A nested clade analysis revealed isolation by distance as the principal mechanism responsible for the observed haplotype distributions within the , and , clades. Analyses of molecular variance and pairwise population FST tests based on both mitochondrial and microsatellite DNA suggest that northern-northeastern India, central India, Nilgiris (in southern India) and Anamalai-Periyar (in southern India) are four demographically autonomous population units and should be managed separately. In addition, evidence for female philopatry, male-mediated gene flow and two possible historical biogeographical barriers is described. [source] Population genetic structure of the salmon louse, Lepeophtheirus salmonis (Krøyer) on wild and farmed salmonids around the Pacific coast of CanadaAQUACULTURE RESEARCH, Issue 8 2009Elizabeth G Boulding First page of article [source] Population genetic structure of sea cucumber, Stichopus japonicus in Korea using microsatellite markersAQUACULTURE RESEARCH, Issue 10 2008Mi-Jung Kim Abstract Sea cucumber (Stichopus japonicus) is a commercially valuable species in Korea. We examined the genetic characteristics of sea cucumber populations in Korea using microsatellite markers. A total of 144 sea cucumbers from five populations were typed for nine polymorphic microsatellite loci. A total of 139 different alleles were found over all loci and many alleles were unique. The average number of allele per locus ranged from 6 to 18.4. The average observed and expected heterozygosities ranged from 0.532 to 0.626 and from 0.719 to 0.789 respectively. All populations showed significant departure from Hardy,Weinberg equilibrium at almost all loci except one (Psj2409). This deviation was in the direction of heterozygote deficit. A phylogenetic tree revealed two distinct clusters. One cluster was formed by the eastern sea population. A second cluster consisted of the subpopulations of the western and southern sea populations. The eastern sea population showed genetic differences such as a larger number of alleles per locus, a larger number of unique alleles and a smaller number of the most common alleles, suggesting a higher genetic diversity in this population. These results provide basic information on natural population genetic structure of S. japonicus in Korea. [source] Genetic pattern of the recent recovery of European otters in southern FranceECOGRAPHY, Issue 2 2008Xavier Janssens We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cévennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter. [source] The effect of a pathogen epidemic on the genetic structure and reproductive strategy of the crustacean Daphnia magnaECOLOGY LETTERS, Issue 9 2004Suzanne E. Mitchell Abstract Host,parasite coevolution is potentially of great importance in producing and maintaining biological diversity. However, there is a lack of evidence for parasites directly driving genetic change. We examined the impact of an epidemic of the bacterium Pasteuria ramosa on a natural population of the crustacean Daphnia magna through the use of molecular markers (allozymes) and laboratory experiments to determine the susceptibility of hosts collected during and after the epidemic. Some allozyme genotypes were more heavily infected than others in field samples, and the population genetic structure differed during and after the epidemic, consistent with a response to parasite-mediated selection. Laboratory studies showed no evidence for the evolution of higher resistance, but did reveal an intriguing life-history pattern: host genotypes that were more susceptible also showed a greater tendency to engage in sex. In light of this, we suggest a model of host,parasite dynamics that incorporates the cycles of sex and parthenogenesis that Daphnia undergo in the field. [source] Effects of environmental pollution on microsatellite DNA diversity in wood mouse (Apodemus sylvaticus) populationsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Veerle Berckmoes Abstract Ten microsatellite DNA loci were surveyed to investigate the effects of heavy metal pollution on the genetic diversity and population genetic structure of seven wood mouse (Apodemus sylvaticus) populations along a heavy metal pollution gradient away from a nonferrous smelter in the south of Antwerp (Flanders, Belgium). Analysis of soil heavy metal concentrations showed that soil Ag, As, Cd, Cu, and Pb decreased with increasing distance from the smelter. Genetic analyses revealed high levels of genetic variation in all populations, but populations from the most polluted sites in the gradient did not differ from those of less-polluted sites in terms of mean observed and expected heterozygosity level and mean allelic richness. No correlation was found between measures of genetic diversity and the degree of heavy metal pollution. However, an analysis of molecular variance and a neighbor-joining tree suggested a contamination-related pattern of genetic structuring between the most polluted and less polluted sites. Pairwise FST values indicated that populations were significantly genetically differentiated, and assignment tests and direct estimates of recent migration rates suggested restricted gene flow among populations. Additionally, genetic differentiation increased significantly with geographical distance, which is consistent with an isolation-by-distance model. We conclude that, at least for our microsatellite DNA markers, genetic diversity in the studied wood mouse populations is not affected greatly by the heavy metal pollution. [source] Cryptic Kin Selection: Kin Structure in Vertebrate Populations and Opportunities for Kin-Directed CooperationETHOLOGY, Issue 3 2010Ben J. Hatchwell Animal societies of varying complexity have been the favoured testing ground for inclusive fitness theory, and there is now abundant evidence that kin selection has played a critical role in the evolution of cooperative behaviour. One of the key theoretical and empirical findings underlying this conclusion is that cooperative systems have a degree of kin structure, often the product of delayed dispersal, that facilitates interactions with relatives. However, recent population genetic studies have revealed that many non-cooperative animals also have kin-structured populations, providing more cryptic opportunities for kin selection to operate. In this article, I first review the evidence that kin structure is widespread among non-cooperative vertebrates, and then consider the various contexts in which kin selection may occur in such taxa, including: leks, brood parasitism, crèches, breeding associations, territoriality and population dynamics, foraging and predator deterrence. I describe the evidence that kin-selected benefits arise from interacting with kin in each of these contexts, notwithstanding the potential costs of kin competition and inbreeding. I conclude that as the tools required to determine population genetic structure are readily available, measurement of kin structure and the potential for kin selection on a routine basis is likely to reveal that this process has been an important driver of evolutionary adaptation in many non-cooperative as well as cooperative species. [source] EVALUATION OF ELEVATED PLOIDY AND ASEXUAL REPRODUCTION AS ALTERNATIVE EXPLANATIONS FOR GEOGRAPHIC PARTHENOGENESIS IN EUCYPRIS VIRENS OSTRACODSEVOLUTION, Issue 4 2010Sofia Adolfsson Transitions from sexual to asexual reproduction are often coupled with elevations in ploidy. As a consequence, the importance of ploidy per se for the maintenance and spread of asexual populations is unclear. To examine the effects of ploidy and asexual reproduction as independent determinants of the success of asexual lineages, we sampled diploid sexual, diploid asexual, and triploid asexual Eucypris virens ostracods across a European wide range. Applying nuclear and mitochondrial markers, we found that E. virens consists of genetically highly differentiated diploid sexual populations, to the extent that these sexual clades could be considered as cryptic species. All sexual populations were found in southern Europe and North Africa and we found that both diploid asexual and triploid asexual lineages have originated multiple times from several sexual lineages. Therefore, the asexual lineages show a wide variety of genetic backgrounds and very strong population genetic structure across the wide geographic range. Finally, we found that triploid, but not diploid, asexual clones dominate habitats in northern Europe. The limited distribution of diploid asexual lineages, despite their shared ancestry with triploid asexual lineages, strongly suggests that the wider geographic distribution of triploids is due to elevated ploidy rather than to asexuality. [source] BACKGROUND MATCHING AND COLOR-CHANGE PLASTICITY IN COLONIZING FRESHWATER SCULPIN POPULATIONS FOLLOWING RAPID DEGLACIATIONEVOLUTION, Issue 6 2009Andrew R. Whiteley Anthropogenic-induced change is forcing organisms to shift their distributions and colonize novel habitats at an increasing rate, which leads to complex interactions among evolutionary processes. Coastrange sculpin (Cottus aleuticus) have colonized recently deglaciated streams of Glacier Bay in Alaska within the last 220 years. We examined divergence among populations in background matching coloration and tested the hypothesis that observed variation is due to morphological color plasticity. To examine how color-change plasticity has interacted with other evolutionary processes, we also determined the influence of colonization on neutral genetic diversity. We observed clinal variation in substrate-matching fish color along the chronological continuum of streams. Microsatellites provided little evidence of genetic subdivision among sculpin populations. Fish color was significantly correlated to substrate color, but was not correlated to neutral population genetic structure. Furthermore, a laboratory experiment revealed that morphological color plasticity could explain much, but not all, of the observed fish color divergence. Our study demonstrates that sculpin in Glacier Bay have colonized and adapted to recently deglaciated habitat and suggests that color change plasticity has aided in this process. This research, therefore, highlights the important role phenotypic plasticity may play in the adaptation of species to rapid climate change. [source] EFFECTIVE POPULATION SIZES AND TEMPORAL STABILITY OF GENETIC STRUCTURE IN RANA PIPIENS, THE NORTHERN LEOPARD FROGEVOLUTION, Issue 11 2004Eric A. Hoffman Abstract Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipens, over a 22,30 year time interval (11,15 generations). Genetic structure among the populations was very stable, suggesting that these population were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) that toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Nee/Nc ratios in the range of 0.1,1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly. [source] LINKING COEVOLUTIONARY HISTORY TO ECOLOGICAL PROCESS: DOVES AND LICEEVOLUTION, Issue 10 2003Dale H. Clayton Abstract Many host-specific parasites are restricted to a limited range of host species by ecological barriers that impede dispersal and successful establishment. In some cases, microevolutionary differentiation is apparent on top of host specificity, as evidenced by significant parasite population genetic structure among host populations. Ecological barriers responsible for specificity and genetic structure can, in principle, reinforce macroevolutionary processes that generate congruent host-parasite phylogenies. However, few studies have explored both the micro- and macroevolutionary ramifications of close association in a single host-parasite system. Here we compare the macroevolutionary histories of two genera of feather lice (Phthiraptera: Ischnocera) that both parasitize New World pigeons and doves (Aves: Columbiformes). Earlier work has shown that dove body lice (genus Physconelloides) are more host specific and have greater population genetic structure than dove wing lice (Columbicola). We reconstructed phylogenies for representatives of the two genera of lice and their hosts, using nuclear and mitochondrial DNA sequences. The phylogenies were well resolved and generally well supported. We compared the phylogenies of body lice and wing lice to the host phylogeny using reconciliation analyses. We found that dove body lice show strong evidence of cospeciation whereas dove wing lice do not. Although the ecology of body and wing lice is very similar, differences in their dispersal ability may underlie these joint differences in host specificity, population genetic structure, and coevolutionary history. [source] CONTEMPORARY PATTERNS IN A HISTORICAL CONTEXT: PHYLOGEOGRAPHIC HISTORY OF THE PIPEVINE SWALLOWTAIL, BATTUS PHILENOR (PAPILIONIDAE)EVOLUTION, Issue 5 2003James A. Fordyce Abstract We examined mitochondrial DNA (mtDNA) variation in pipevine swallowtail butterflies (Battus philenor) from throughout its extant range to provide a historical, phylogeographical context for ecological studies of the disjunct population in California. We evaluate current hypotheses regarding host plant use, behavior, and mimetic relationships of B. philenor populations and generate alternative hypotheses. Compared to populations throughout the rest of the species' range, California populations are ecologically distinct in that they lack mimics, lay significantly larger clutches of eggs, and exclusively use a unique, endemic larval host plant. Analysis of molecular variance, tests of population differentiation, and nested clade analysis of mtDNA variation indicate that, despite low levels of population genetic structure across the species' range, there is evidence of recent range expansion from presumed Pleistocene refuge(s) in southeastern North America. Colonization of California appears to have been a recent event. This phylogeographic investigation also suggests that the evolution of life-history adaptations to a novel larval host has occurred rapidly in California and the lack of mimics in California may be attributable to the recency of colonization. [source] Genetic diversity and migration patterns of the aquatic macrophyte Potamogeton malaianus in a potamo-lacustrine systemFRESHWATER BIOLOGY, Issue 6 2009YUANYUAN CHEN Summary 1.,Previously, the Yangtze River connected thousands of shallow lakes which together formed a potamo-lacustrine system capable of sustaining a rich variety of submerged macrophytes. 2.,Potamogeton malaianus is one of the dominant submerged macrophytes in many lakes of this area. Genetic variation and population structure of P. malaianus populations from ten lakes in the potamo-lacustrine system were assessed using inter-simple sequence repeat markers. 3.,Twelve primer combinations produced a total of 166 unambiguous bands of which 117 (70.5%) were polymorphic. Potamogeton malaianus exhibited a moderate level of population genetic diversity (PP = 70.5%, HE = 0.163 and I = 0.255), as compared with that of plants in the same habitat and range. The main factors responsible for this moderate value were the plant's mixed breeding system (both sexual and asexual) and the hydrological connectivity among habitats. 4.,F statistics, calculated using different approaches, consistently revealed a moderate genetic differentiation among populations, contributing about 20% of total genetic diversity. An estimate of gene flow (using FST) suggested that gene flow played a more important role than genetic drift in the current population genetic structure of P. malaianus (Nm = 1.131). 5.,The genetic diversity of P. malaianus did not increase downstream. A high level of linkage,disequilibrium at the whole population level suggested that metapopulation processes may affect genetic structure. The migration pattern of P. malaianus was best explained by a two-dimensional stepping stone model, indicating that bird-mediated dispersal could greatly influence gene movements among lakes. [source] Population genetic structure reveals terrestrial affinities for a headwater stream insectFRESHWATER BIOLOGY, Issue 10 2007DEBRA S. FINN Summary 1. The spatial distribution of stream-dwelling organisms is often considered to be limited primarily according to the hierarchical structure of the hydrologic network, and previous conceptual models of population genetic structure have reflected this generality. Headwater specialists, however, are confined to short upstream sections of the network, and therefore are unlikely to respond in the same way as species with a broader range of habitat tolerance. 2. Here, we propose a model to describe spatial patterns of genetic diversity in headwater specialists with a limited ability for among-stream dispersal. The headwater model predicts a partitioning of genetic variance according to higher-elevation ,islands' of terrestrial habitat that provide required headwater stream conditions. The model therefore expects a geographic pattern of genetic variance similar to that expected for low-dispersal terrestrial species occupying the adjacent habitat. 3. Using a 1032-bp mitochondrial DNA fragment encompassing parts of the COI and COII genes, we demonstrate that Madrean Sky Islands populations of the giant water bug Abedus herberti conform to the proposed headwater model. Furthermore, they exhibit phylogeographic patterns broadly concordant with those shown for several terrestrial species in the region, including a major zone of discontinuity in the Chiricahua mountain range. 4. Overall, populations are highly isolated from one another, and a nested clade analysis suggested that A. herberti population structure, similarly to terrestrial Sky Islands species studied previously, has been influenced by Pleistocene climatic cycles causing expansion and contraction of temperate woodland habitat. 5. Because they have no ability to disperse among present-day mountaintop habitat islands, A. herberti and other headwater species with limited dispersal ability are vulnerable to the projected increasing rate of climatic warming in this region. [source] Morphological clines in dendritic landscapesFRESHWATER BIOLOGY, Issue 9 2007A. CHAPUT-BARDY Summary 1. In complex landscapes such as river networks, organisms usually face spatio-temporal heterogeneity and gradients in geomorphological, water, ecological or landscape characteristics are often observed at the catchment scale. These environmental variables determine developmental conditions for larval stages of freshwater insects and influence adult phenotypic characteristics. Environmental clines are therefore expected to generate morphological clines. Such a process has the potential to drive gradual geographical change in morphology-dependent life history traits, such as dispersal. 2. We studied the influence of aquatic and terrestrial environmental factors on morphological variations in Calopteryx splendens across the Loire drainage. To investigate these effects we took explicitly into account the hierarchical structure of the river network. 3. We analysed eight morphological traits. Results showed significant body size variation between tributaries and the presence of a morphological cline at the drainage scale. We observed an effect of pH and water temperature on body size. Individuals in downstream sites were larger than individuals in upstream sites, and adults whose larval stages were exposed to alkaline pH and high temperatures during summer were larger. 4. Body size affects flight abilities in insects. Thus, our results suggest that morphological clines may generate an asymmetric dispersal pattern along the downstream,upstream axis, downstream populations dispersing farther than upstream ones. Such a process is expected to influence population genetic structure at the drainage scale if larval drift and floods do not balance an asymmetrical dispersal pattern of adults along the downstream,upstream gradient. To assess the influence of environmental gradients on the variation of life history traits it is important to understand the population biology of freshwater insects, and more generally of riverine organisms. It is also essential to integrate such data in conservation or restoration programmes. [source] | |||||||||||||||||||||||||||||||