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Population Genetic Data (population + genetic_data)
Selected AbstractsOptimizing dispersal and corridor models using landscape geneticsJOURNAL OF APPLIED ECOLOGY, Issue 4 2007CLINTON W. EPPS Summary 1Better tools are needed to predict population connectivity in complex landscapes. ,Least-cost modelling' is one commonly employed approach in which dispersal costs are assigned to distinct habitat types and the least-costly dispersal paths among habitat patches are calculated using a geographical information system (GIS). Because adequate data on dispersal are usually lacking, dispersal costs are often assigned solely from expert opinion. Spatially explicit, high-resolution genetic data may be used to infer variation in animal movements. We employ such an approach to estimate habitat-specific migration rates and to develop least-cost connectivity models for desert bighorn sheep Ovis canadensis nelsoni. 2Bighorn sheep dispersal is thought to be affected by distance and topography. We incorporated both factors into least-cost GIS models with different parameter values and estimated effective geographical distances among 26 populations. We assessed which model was correlated most strongly with gene flow estimates among those populations, while controlling for the effect of anthropogenic barriers. We used the best-fitting model to (i) determine whether migration rates are higher over sloped terrain than flat terrain; (ii) predict probable movement corridors; (iii) predict which populations are connected by migration; and (iv) investigate how anthropogenic barriers and translocated populations have affected landscape connectivity. 3Migration models were correlated most strongly with migration when areas of at least 10% slope had 1/10th the cost of areas of lower slope; thus, gene flow occurred over longer distances when ,escape terrain' was available. Optimal parameter values were consistent across two measures of gene flow and three methods for defining population polygons. 4Anthropogenic barriers disrupted numerous corridors predicted to be high-use dispersal routes, indicating priority areas for mitigation. However, population translocations have restored high-use dispersal routes in several other areas. Known intermountain movements of bighorn sheep were largely consistent with predicted corridors. 5Synthesis and applications. Population genetic data provided sufficient resolution to infer how landscape features influenced the behaviour of dispersing desert bighorn sheep. Anthropogenic barriers that block high-use dispersal corridors should be mitigated, but population translocations may help maintain connectivity. We conclude that developing least-cost models from similar empirical data could significantly improve the utility of these tools. [source] Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanusMOLECULAR ECOLOGY, Issue 8 2009ELLEN L. KENCHINGTON Abstract A north/south discontinuity along the northeastern coast of North America in the genetic structure of the American lobster (Homarus americanus) was detected using a suite of 13 microsatellite loci assessed using spatial analyses. Population genetic data laid over existing data on physiographic changes and sea-surface temperatures were used to reconstruct the Pleistocene distribution of this species. A postglacial northern-edge colonization model best explains the relative genetic homogeneity of the northern region compared to the southern region centred in the Gulf of Maine. Population genetic analyses identified significant structure (range of standardized theta 0,0.02) but no significant evidence for isolation by distance. The novel application of spatial genetic analyses to a marine species allowed us to interpret these results by providing a greater insight into the evolutionary factors responsible for shaping the genetic structure of this species throughout is natural range. [source] LIKELIHOOD-BASED INFERENCE IN ISOLATION-BY-DISTANCE MODELS USING THE SPATIAL DISTRIBUTION OF LOW-FREQUENCY ALLELESEVOLUTION, Issue 11 2009John Novembre Estimating dispersal distances from population genetic data provides an important alternative to logistically taxing methods for directly observing dispersal. Although methods for estimating dispersal rates between a modest number of discrete demes are well developed, methods of inference applicable to "isolation-by-distance" models are much less established. Here, we present a method for estimating ,,2, the product of population density (,) and the variance of the dispersal displacement distribution (,2). The method is based on the assumption that low-frequency alleles are identical by descent. Hence, the extent of geographic clustering of such alleles, relative to their frequency in the population, provides information about ,,2. We show that a novel likelihood-based method can infer this composite parameter with a modest bias in a lattice model of isolation-by-distance. For calculating the likelihood, we use an importance sampling approach to average over the unobserved intraallelic genealogies, where the intraallelic genealogies are modeled as a pure birth process. The approach also leads to a likelihood-ratio test of isotropy of dispersal, that is, whether dispersal distances on two axes are different. We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana. [source] Genetic population structure of marine fish: mismatch between biological and fisheries management unitsFISH AND FISHERIES, Issue 4 2009Henning Reiss Abstract An essential prerequisite of a sustainable fisheries management is the matching of biologically relevant processes and management action. In fisheries management and assessment, fish stocks are the fundamental biological unit, but the reasoning for the operational management unit is often indistinct and mismatches between the biology and the management action frequently occur. Despite the plethora of population genetic data on marine fishes, to date little or no use is made of the information, despite the fact that the detection of genetic differentiation may indicate reproductively distinct populations. Here, we discuss key aspects of genetic population differentiation in the context of their importance for fisheries management. Furthermore, we evaluate the population structure of all 32 managed marine fish species in the north-east Atlantic and relate this structure to current management units and practice. Although a large number of studies on genetic population structure have been published in the last decades, data are still rare for most exploited species. The mismatch between genetic population structure and the current management units found for six species (Gadus morhua, Melanogrammus aeglefinus, Merlangius merlangus, Micromesistius poutassou, Merluccius merluccius and Clupea harengus), emphasizes the need for a revision of these units and questions the appropriateness of current management measures. The implementation of complex and dynamic population structures into novel and less static management procedures should be a primary task for future fisheries management approaches. [source] Long-standing environmental conditions, geographic isolation and host,symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus SymbiodiniumJOURNAL OF BIOGEOGRAPHY, Issue 5 2010Todd C. LaJeunesse Abstract Aim, This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral,algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate. Location, Indian Ocean. Methods, Community assemblages of obligate symbiotic invertebrates were sampled at numerous sites from two regions, the north-eastern Indian Ocean (Andaman Sea, western Thailand) and the western Indian Ocean (Zanzibar, Tanzania). Molecular genetic methods, including denaturing gradient gel electrophoresis analysis of the ribosomal internal transcribed spacers, DNA sequencing and microsatellite genotyping, were used to characterize the ,species' diversity and evolutionary relationships of symbiotic dinoflagellates (genus Symbiodinium). Host,symbiont specificity, geographic isolation and local and regional environmental factors were evaluated in terms of their importance in governing the distribution and prevalence of certain symbiont taxa. Results, Host-generalist symbionts (C3u and D1-4, formerly D1a now designated Symbiodinium trenchi) frequently occurred alone and sometimes together in hosts with horizontal modes of symbiont acquisition. However, the majority of Symbiodinium diversity consisted of apparently host-specific ,species'. Clade C Symbiodinium were diverse and dominated host assemblages from sites sampled in the western Indian Ocean, a pattern analogous to symbiont communities on the Great Barrier Reef with similar environmental conditions. Clade D Symbiodinium were diverse and occurred frequently in hosts from the north-eastern Indian Ocean, especially at inshore locations, where temperatures are warmer, water turbidity is high and large tidal exchanges commonly expose coral populations to aerial desiccation. Main conclusions, Regional and local differences in cnidarian,algal combinations indicate that these symbioses are ecologically and evolutionarily responsive and can thrive under various environmental conditions. The high temperatures and turbid conditions of the north-eastern Indian Ocean partly explain the ecological success of Clade D Symbiodinium relative to Clade C. Phylogenetic, ecological and population genetic data further indicate that Clade D has undergone an adaptive radiation, especially in regions around Southeast Asia, during the Pleistocene. [source] Statistical methods in spatial geneticsMOLECULAR ECOLOGY, Issue 23 2009GILLES GUILLOT Abstract The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls. [source] Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesaeMOLECULAR ECOLOGY, Issue 7 2008C. R. YOUNG Abstract This study examined relationships between bathymetrically induced deep-ocean currents and the dispersal of the hydrothermal vent tubeworm Ridgeia piscesae along the northeast Pacific ridge system. A robust diagnostic model of deep-ocean circulation in this region predicted strong southeasterly currents following contours of the Blanco Transform Fault, a 450-km lateral offset that separates the Gorda and Juan de Fuca ridge systems. Such currents should facilitate the southward dispersal of R. piscesae larvae. Immigration rates for populations north and south of the Blanco Transform Fault were estimated from molecular population genetic data. Mitochondrial DNA evidence revealed population subdivision across the Blanco Transform Fault, and a strong directional bias in gene flow that was consistent with predictions of the circulation model. The distribution of mitochondrial diversity between the northern and southern populations of R. piscesae suggests that the Gorda Ridge tubeworms have maintained larger effective population sizes than the northern populations, a pattern that also exists in co-occurring limpets. Together, these data suggest that the northern vent fields may experience a higher frequency of habitat turnover and consequently more rapid losses of genetic diversity. [source] Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?MOLECULAR ECOLOGY, Issue 10 2005CHRISTOPHER IRWIN SMITH Abstract Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert-dwelling species of Moneilema. [source] | ||||||||||