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Genetic Patterns (genetic + pattern)
Kinds of Genetic Patterns Selected AbstractsGenetic 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] Genetic patterns and pollination in Ophrys iricolor and O. mesaritica (Orchidaceae): sympatric evolution by pollinator shiftBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009PHILIPP M. SCHLÜTER Ophrys iricolor and O. mesaritica are a pair of morphologically similar, closely related sexually deceptive orchids from the eastern Mediterranean. Ophrys iricolor is known to be pollinated by Andrena morio males and the specific pollinator of Ophrys mesaritica is determined as Andrena nigroaenea. Amplified fragment length polymorphism revealed O. iricolor and O. mesaritica to be genetically intermixed on the whole, although populations of O. iricolor and O. mesaritica in geographical proximity are strongly differentiated, suggesting that specific pollinators locally differentiate these taxa. Based on the available biological data and the system of pollinator attraction operative in Ophrys, we hypothesize that O. mesaritica may have arisen from O. iricolor by pollinator shift and that this is more probable than scenarios invoking hybridization as a result of mispollination by rare, non-specific flower visitors or specifically attracted insects. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 583,598. [source] Phylogeographic information systems: putting the geography into phylogeographyJOURNAL OF BIOGEOGRAPHY, Issue 11 2006David M. Kidd Abstract Phylogeography is concerned with the observation, description and analysis of the spatial distribution of genotypes and the inference of historical scenarios. In the past, the discipline has concentrated on the historical ,phylo- ' component through the utilization of phylogenetic analyses. In contrast, the spatial , -geographic' component is not a prominent feature of many existing phylogenetic approaches and has often been dealt with in a relatively naive fashion. Recently, there has been a resurgence of interest in the importance of geography in evolutionary biology. Thus, we believe that it is time to assess how geographic information is currently handled and incorporated into phylogeographical analysis. Geographical information systems (GISs) are computer systems that facilitate the integration and interrelation of different geographically referenced data sets; however, so far they have been little utilized by the phylogeographical community to manage, analyse and disseminate phylogeographical data. However, the growth in individual studies and the resurgence of interest in the geographical components of genetic pattern and biodiversity should stimulate further uptake. Some advantages of GIS are the integration of disparate data sets via georeferencing, dynamic data base design and update, visualization tools and data mining. An important step in linking GIS to existing phylogeographical and historical biogeographical analysis software and the dissemination of spatial phylogenies will be the establishment of ,GeoPhylo' data standards. We hope that this paper will further stimulate the resurgence of geography as an equal partner in the symbiosis that is phylogeography as well as advertise some benefits that can be obtained from the application of GIS practices and technologies. [source] Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellitesMOLECULAR ECOLOGY, Issue 11 2006SILVIO SCHUELER Abstract Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S -locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S -locus. The S -locus revealed a higher diversity (15 alleles) than the eight microsatellites (4,12 alleles). Although the frequency distribution of S -alleles differed significantly from the expected equal distribution, the S -locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S -locus: E = 0.91; for the microsatellites: E = 0.48,0.83). Also, highly significant deviations from neutrality were found for the S -locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S -alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S -locus or on S- linked sites might also affect the distribution and dynamics of S -alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S -locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (,g = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S -locus. [source] Dispersal and genetic structure in the American marten, Martes americanaMOLECULAR ECOLOGY, Issue 6 2006T. BROQUET Abstract Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using FST indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent,offspring axial distance (,2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow. [source] Fine-scale genetic pattern and evidence for sex-biased dispersal in the túngara frog, Physalaemus pustulosusMOLECULAR ECOLOGY, Issue 12 2003Kathrin P. Lampert Abstract Túngara frogs (Physalaemus pustulosus) are a model system for sexual selection and communication. Population dynamics and gene flow are of major interest in this species because they influence speciation processes and microevolution, and could consequently provide a deeper understanding of the evolutionary processes involved in mate recognition. Although earlier studies have documented genetic variation across the species' range, attempts to investigate dispersal on a local level have been limited to mark,recapture studies. These behavioural studies indicated high mobility at a scale of several hundred metres. In this study we used seven highly polymorphic microsatellite loci to investigate fine-scaled genetic variation in the túngara frog. We analysed the influence of geographical distance on observed genetic patterns, examined the influence of a river on gene flow, and tested for sex-biased dispersal. Data for 668 individuals from 17 populations ranging in distance from 0.26 to 11.8 km revealed significant levels of genetic differentiation among populations. Genetic differentiation was significantly correlated with geographic distance. A river acted as an efficient barrier to gene flow. Several tests of sex-biased dispersal were conducted. Most of them showed no difference between the sexes, but variance of Assignment Indices exhibited a statistically significant male bias in dispersal. [source] Population structure and paternal admixture landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypesAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 3 2010J. Salazar-Flores Mestizos currently represent most of the Mexican population (>90%); they are defined as individuals born in the country having a Spanish-derived last name, with family antecedents of Mexican ancestors back at least to the third generation. Mestizos are result of 500 years of admixture mainly among Spaniards, Amerindians, and African slaves. Consequently, a complex genetic pattern has been generated throughout the country that has been scarcely studied from the paternal point of view. This fact is important, taking into account that gene flow toward the New World comprised largely males. We analyzed the population structure and paternal admixture of present-day Mexican-Mestizo populations based on Y-STRs. We genotyped at least 12 Y-STRs in DNA samples of 986 males from five states: Aguascalientes (n = 293); Jalisco (n = 185); Guanajuato (n = 168); Chiapas (n = 170); and Yucatán (n = 170). AmpF,STR Y-filer and Powerplex-Y® kits were used. Inclusion of North and Central Y-STR databases in the analyses allowed obtaining a Y-STR variability landscape from Mexico. Results confirmed the population differentiation gradient previously noted in Mestizos with SNPs and autosomal STRs throughout the Mexican territory: European ancestry increments to the Northwest and, correspondingly, Amerindian ancestry increments to the Center and Southeast. In addition, SAMOVA test and Autocorrelation Index for DNA Analysis autocorrelogram plot suggested preferential gene flow of males with neighboring populations in agreement with the isolation-by-distance model. Results are important for disease-risk studies (principally male-related) and for human identification purposes, because Y-STR databases are not available on the majority of Mexican-Mestizo populations. Am. J. Hum. Biol., 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] Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western MediterraneanANNALS OF HUMAN GENETICS, Issue 4 2003S. Plaza Summary Phylogenetic analysis of mitochondrial DNA (mtDNA) performed in Western Mediterranean populations has shown that both shores share a common set of mtDNA haplogroups already found in Europe and the Middle East. Principal co-ordinates of genetic distances and principal components analyses based on the haplotype frequencies show that the main genetic difference is attributed to the higher frequency of sub-Saharan L haplogroups in NW Africa, showing some gene flow across the Sahara desert, with a major impact in the southern populations of NW Africa. The AMOVA demonstrates that SW European populations are highly homogeneous whereas NW African populations display a more heterogeneous genetic pattern, due to an east-west differentiation as a result of gene flow coming from the East. Despite the shared haplogroups found in both areas, the European V and the NW African U6 haplogroups reveal the traces of the Mediterranean Sea permeability to female migrations, and allowed for determination and quantification of the genetic contribution of both shores to the genetic landscape of the geographic area. Comparison of mtDNA data with autosomal markers and Y-chromosome lineages, analysed in the same populations, shows a congruent pattern, although female-mediated gene flow seems to have been more intense than male-mediated gene flow. [source] Achromobacter xylosoxidans respiratory tract infections in cystic fibrosis patients,APMIS, Issue 9 2008TIZIANA RASO Achromobacter xylosoxidans is a ubiquitous Gram-negative non-fermenting rod, recently characterized as an emerging pathogen in cystic fibrosis (CF) patients. Its pathogenic potential and prevalent transmission routes are still unclear. This study investigated the PFGE genetic pattern and antimicrobial resistance profile of 42 A. xylosoxidans isolates obtained over 4 years from the respiratory tract of 22 CF patients. By genotypic analysis, 31 isolates were attributed to 8 distinct PFGE patterns (A,H), whereas 11 isolates were not typable because their DNA was not restricted by XbaI and DraI restriction enzymes. The majority of the isolates showed multidrug resistance; imipenem and piperacillin were the most active drugs. During the course of A. xylosoxidans chronic infection forced expiratory volume and body mass index values were not significantly lowered. The demonstration of widespread antibiotic resistance underscores the importance of antibiogram-directed therapy. Our data suggest that in some cases the infection may have been acquired from other patients or from a common contaminated source. Further epidemiological studies may be important for the design and implementation of prophylactic measures in CF centers. [source] DISPERSAL, PHILOPATRY, AND INFIDELITY: DISSECTING LOCAL GENETIC SWTRUCTURE IN SUPERB FAIRY-WRENS (MALURS CYANEUS)EVOLUTION, Issue 3 2005M. C. Double Abstract Dispersal influences evolution, demography, and social characteristics but is generally difficult to study. Here we combine long-term demographic data from an intensively studied population of superb fairy-wrens(Malurus cyaneus) and multivariate spatial autocorrelation analyses of microsatellite genotypes to describe dispersal behavior in this species. The demographic data revealed: (1) sex-biased dispersal: almost all individuals that dispersed into the study area over an eight-year period were female (93%; n 5 153); (2) high rates of extragroup infidelity (66% of offspring), which also facilitated local gene dispersal; and (3) skewed lifetime reproductive success in both males and females. These data led to three expectations concerning the patterns of fine-scale genetic structure: (1) little or no spatial genetic autocorrelation among females, (2) positive spatial genetic autocorrelation among males, and (3) a heterogeneous genetic landscape. Global autocorrelation analysis of the genotypes present in the study population confirmed the first two expectations. A novel two-dimensional local autocorrelation analysis confirmed the third and provided new insight into the patterns of genetic structure across the two-dimensional landscape. We highlight the potential of autocorrelation analysis to infer evolutionary processes but also emphasize that genetic patterns in space cannot be fully understood without an appropriate and intensive sampling regime and detailed knowledge of the individuals genotyped. [source] Heritability of human cranial dimensions: comparing the evolvability of different cranial regionsJOURNAL OF ANATOMY, Issue 1 2009Neus Martínez-Abadías Abstract Quantitative craniometrical traits have been successfully incorporated into population genetic methods to provide insight into human population structure. However, little is known about the degree of genetic and non-genetic influences on the phenotypic expression of functionally based traits. Many studies have assessed the heritability of craniofacial traits, but complex patterns of correlation among traits have been disregarded. This is a pitfall as the human skull is strongly integrated. Here we reconsider the evolutionary potential of craniometric traits by assessing their heritability values as well as their patterns of genetic and phenotypic correlation using a large pedigree-structured skull series from Hallstatt (Austria). The sample includes 355 complete adult skulls that have been analysed using 3D geometric morphometric techniques. Heritability estimates for 58 cranial linear distances were computed using maximum likelihood methods. These distances were assigned to the main functional and developmental regions of the skull. Results showed that the human skull has substantial amounts of genetic variation, and a t -test showed that there are no statistically significant differences among the heritabilities of facial, neurocranial and basal dimensions. However, skull evolvability is limited by complex patterns of genetic correlation. Phenotypic and genetic patterns of correlation are consistent but do not support traditional hypotheses of integration of the human shape, showing that the classification between brachy- and dolicephalic skulls is not grounded on the genetic level. Here we support previous findings in the mouse cranium and provide empirical evidence that covariation between the maximum widths of the main developmental regions of the skull is the dominant factor of integration in the human skull. [source] Patterns of population genetic diversity in riparian and aquatic plant species along riversJOURNAL OF BIOGEOGRAPHY, Issue 9 2010Olivier Honnay Abstract Aim, The downstream hydrochoric spread of seeds of aquatic and riparian plant species, without upstream compensation, can be expected to result in downstream accumulation of population genetic diversity. This idea has been termed the ,unidirectional dispersal hypothesis' and is the genetic equivalent of the more generally known ,drift paradox'. Our aim was to test this unidirectional diversity hypothesis, and to present a general synthesis of the patterns of population genetic variation across different riparian and aquatic plant species along rivers. Location, The Meuse River (Belgium) and rivers world-wide. Methods, First, we used amplified fragment length polymorphism markers to compare patterns of within- and between-population genetic diversity among three riparian plant species (Sisymbrium austriacum, Erysimum cheiranthoides and Rorippa sylvestris), typically occurring in different habitats along a gradient perpendicular to the Meuse River. Second, we performed a meta-analysis on studies reporting on the population genetic structure of riparian and aquatic plant species along rivers. Results, Along the Meuse River, we found significant genetic differentiation among populations of all three riparian species, and significant isolation by distance for one of them (R. sylvestris). There was no clear association between the typical habitat of a species and its population genetic structure. None of the three species provided evidence for the unidirectional dispersal hypothesis. The meta-analysis, based on 21 data records, did not support the unidirectional dispersal hypothesis either. Average weighted population genetic differentiation across species was significant. Main conclusions, Important mechanisms of upstream seed dispersal, probably through zoochory, together with higher seed recruitment opportunities in upstream habitats due to density dependence of recruitment, may explain the absence of downstream accumulation of genetic diversity. Also, it seems difficult to find consistent patterns in genetic variation in species from aquatic and riparian habitats. We argue that this is due to the recurrent extinctions and colonizations characteristic of these habitats, resulting in complex genetic patterns. Our results strongly support previous suggestions that stream ecology should consistently embrace metapopulation theory to be able to understand patterns of genetic diversity, as well as species diversity. [source] Eastern Beringian biogeography: historical and spatial genetic structure of singing voles in AlaskaJOURNAL OF BIOGEOGRAPHY, Issue 8 2010Marcelo Weksler Abstract Aim Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high-latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high-latitude arvicoline rodents. Location Continental Alaska (alpine and arctic tundra) and the St Matthew Archipelago (Bering Sea). Methods We generated and analysed cytochrome b sequences of 97 singing and insular voles (M. miurus and M. abbreviatus) from Alaska. Deep evolutionary structure was inferred by phylogenetic analysis using parsimony, maximum likelihood and Bayesian approaches; the geographical structure of genetic diversity was assessed using analysis of molecular variance and network analysis; ages of cladogenetic and coalescent events were estimated using a relaxed molecular clock model with Bayesian approximation. Results Regional nucleotide diversity in singing voles is higher than in other high-latitude arvicoline species, but intra-population diversity is within the observed range of values for arvicolines. Microtus abbreviatus specimens are phylogenetically nested within M. miurus. Molecular divergence date estimates indicate that current genetic diversity was formed in the last glacial (Wisconsinan) and previous interglacial (Sangamonian) periods, with the exception of a Middle Pleistocene split found between samples collected in the Wrangell Mountains region and all other singing vole samples. Main conclusions High levels of phylogenetic and spatial structure are observed among analysed populations. This pattern is consistent with that expected for a taxon with a long history in Beringia. The spatial genetic structure of continental singing voles differs in its northern and southern ranges, possibly reflecting differences in habitat distribution between arctic and alpine tundra. Our phylogenetic results support the taxonomic inclusion of M. miurus in its senior synonym, M. abbreviatus. [source] Spatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary historiesJOURNAL OF BIOGEOGRAPHY, Issue 11 2004Sophia A. Bickford Abstract Aim, The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro-scaled evolutionary processes. Location, The range occupied by Pultenaea species in temperate and sub-tropical eastern Australia, extending from western South Australia (133° E,32° S) to Tasmania (146° E,43° S) to coastal central Queensland (148° E,20° S). Methods, We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL-F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi-scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results, Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions, The combined analysis of diversity, phylogeny and geography has potential to reveal macro-scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple-index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large-scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus. [source] Stocking-related patterns of genetic variation at enzymatic loci in south European Atlantic salmon populationsJOURNAL OF FISH BIOLOGY, Issue 2005P. Morán Genetic variation at 24 enzymatic loci was investigated in eight south European Atlantic salmon populations from the rivers Nivelle, Cares, Sella, Narcea, Esva, Navia, Porcia and Eo. In these rivers, management based on supplementation of native populations with foreign stocks was carried out for more than one decade. Population genetic patterns expressed in terms of allele frequencies, mean heterozygosity and conformity to Hardy-Weinberg equilibrium, were significantly different between populations. Relevant temporal changes of genetic variability were reported. Evidence that foreign stocking has disturbed the genetic patterns of some of the studied populations is presented. [source] Genetic variability and differentiation in red deer (Cervus elaphus) from Scotland and EnglandJOURNAL OF ZOOLOGY, Issue 3 2006S. S. Hmwe Abstract Samples from 69 British red deer Cervus elaphus scoticus from seven populations in Scotland and England were analysed with respect to variability within and differentiation among stocks using 11 polymorphic microsatellite loci and 439 bp of the mitochondrial control region. The results clearly showed the effects of anthropogenic factors on British red deer. On the whole, variability values were within the species' reported range. The island population of Islay, Scotland, however, while showing average microsatellite variability, exhibited no mitochondrial variation at all. One microsatellite locus was monomorphic in three Scottish populations (Islay, Dunachton and Achnacarry). Overall and pairwise FST values indicate considerable differentiation among the populations studied, but Dunachton and Achnacarry, two adjacent populations free from recorded introductions, showed only a little differentiation and were paired in trees based on genetic distances. In terms of variability, no statistically significant differences were observed between island and mainland populations and the overall test of isolation by distance was negative. Possible reasons for the genetic patterns observed, such as differences in human impact on the populations, are discussed. [source] Genetic tests of the taxonomic status of the ring-tailed lemur (Lemur catta) from the high mountain zone of the Andringitra Massif, MadagascarJOURNAL OF ZOOLOGY, Issue 1 2000Anne D. Yoder Abstract A recent survey of the high-mountain zone of the Madagascar Parc National (PN) d'Andringitra revealed the presence of an apparently isolated troop of the ring-tailed lemur Lemur catta. These animals display phenotypic and ecological characteristics that are unusual for the monotypic genus Lemur, thus raising the possibility that they are members of a different undescribed species. We present analyses of two mitochondrial genes to test the hypothesis that L. catta from Andringitra should be considered a distinct species. The results indicate that taxonomic revision is not warranted under the expectations of the phylogenetic, coalescent, or biological species concepts. Rather, the genetic patterns observed among the Andringitra and lowland mitochondrial haplotypes are consistent with those expected for a single species. [source] Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersalMOLECULAR ECOLOGY, Issue 17 2010HEATHER M. GALINDO Abstract Coupled biological and physical oceanographic models are powerful tools for studying connectivity among marine populations because they simulate the movement of larvae based on ocean currents and larval characteristics. However, while the models themselves have been parameterized and verified with physical empirical data, the simulated patterns of connectivity have rarely been compared to field observations. We demonstrate a framework for testing biological-physical oceanographic models by using them to generate simulated spatial genetic patterns through a simple population genetic model, and then testing these predictions with empirical genetic data. Both agreement and mismatches between predicted and observed genetic patterns can provide insights into mechanisms influencing larval connectivity in the coastal ocean. We use a high-resolution ROMS-CoSINE biological-physical model for Monterey Bay, California specifically modified to simulate dispersal of the acorn barnacle, Balanus glandula. Predicted spatial genetic patterns generated from both seasonal and annual connectivity matrices did not match an observed genetic cline in this species at either a mitochondrial or nuclear gene. However, information from this mismatch generated hypotheses testable with our modelling framework that including natural selection, larval input from a southern direction and/or increased nearshore larval retention might provide a better fit between predicted and observed patterns. Indeed, moderate selection and a range of combined larval retention and southern input values dramatically improve the fit between simulated and observed spatial genetic patterns. Our results suggest that integrating population genetic models with coupled biological-physical oceanographic models can provide new insights and a new means of verifying model predictions. [source] Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef speciesMOLECULAR ECOLOGY, Issue 17 2010KIMBERLY A. SELKOE Abstract Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as ,chaotic' genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet's whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information,theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure. [source] Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate changeMOLECULAR ECOLOGY, Issue 17 2010VICTORIA L. SORK Abstract Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971,2000) and future (2070,2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. [source] Inferring ancient Agave cultivation practices from contemporary genetic patternsMOLECULAR ECOLOGY, Issue 8 2010KATHLEEN C. PARKER Abstract Several Agave species have played an important ethnobotanical role since prehistory in Mesoamerica and semiarid areas to the north, including central Arizona. We examined genetic variation in relict Agave parryi populations northeast of the Mogollon Rim in Arizona, remnants from anthropogenic manipulation over 600 years ago. We used both allozymes and microsatellites to compare genetic variability and structure in anthropogenically manipulated populations with putative wild populations, to assess whether they were actively cultivated or the result of inadvertent manipulation, and to determine probable source locations for anthropogenic populations. Wild populations were more genetically diverse than anthropogenic populations, with greater expected heterozygosity, polymorphic loci, effective number of alleles and allelic richness. Anthropogenic populations exhibited many traits indicative of past active cultivation: fixed heterozygosity for several loci in all populations (nonexistent in wild populations); fewer multilocus genotypes, which differed by fewer alleles; and greater differentiation among populations than was characteristic of wild populations. Furthermore, manipulated populations date from a period when changes in the cultural context may have favoured active cultivation near dwellings. Patterns of genetic similarity among populations suggest a complex anthropogenic history. Anthropogenic populations were not simply derived from the closest wild A. parryi stock; instead they evidently came from more distant, often more diverse, wild populations, perhaps obtained through trade networks in existence at the time of cultivation. [source] Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in CaliforniaMOLECULAR ECOLOGY, Issue 3 2010PHILLIP Q. SPINKS Abstract The historical biogeography of California's taxa has been the focus of extensive research effort. The western pond turtle (Emys marmorata) is an example of a wide-ranging taxon that spans several well-known California diversity hotspots. Using a dataset comprised of one mitochondrial and five nuclear loci, we elucidate the major biogeographic patterns of the western pond turtle across the California landscape. By employing a combination of phylogenetic and network-based approaches, we recovered a relatively ancient (c. 2,8 Ma) north/south split among populations of E. marmorata and find an area of intergradation centred in the Central Coast Ranges of California. In addition, discordant mitochondrial/nuclear genetic patterns suggest subsequent gene flow from northern populations and from San Joaquin Valley populations into the Central Coast Ranges after the Pliocene-Pleistocene marine embayment of the Great Central Valley subsided. Our results emphasize the utility of nuclear DNA phylogeography for recovering the impact of relatively ancient biogeographic events, and suggest that the Central Coast Ranges of California have played a major role in the geographic structuring of the western pond turtle, and possibly other co-distributed taxa. [source] Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonidsMOLECULAR ECOLOGY, Issue 23 2009DANIEL GOMEZ-UCHIDA Abstract Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (,) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies. [source] Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagleMOLECULAR ECOLOGY, Issue 3 2007B. MARTÍNEZ-CRUZ Abstract The fragmentation of a population may have important consequences for population genetic diversity and structure due to the effects of genetic drift and reduced gene flow. We studied the genetic consequences of the fragmentation of the Spanish imperial eagle (Aquila adalberti) population into small patches through a temporal analysis. Thirty-four museum individuals representing the population predating the fragmentation were analysed for a 345-bp segment of the mitochondrial control region and a set of 10 nuclear microsatellite loci. Data from a previous study on the current population (N = 79) were re-analysed for this subset of 10 microsatellite markers and results compared to those obtained from the historical sample. Three shared mitochondrial haplotypes were found in both populations, although fluctuations in haplotype frequencies and the occurrence of a fourth haplotype in the historical population resulted in lower current levels of haplotype and nucleotide diversity. However, microsatellite markers revealed undiminished levels of nuclear diversity. No evidence for genetic structure was observed for the historical Spanish imperial eagle population, suggesting that the current pattern of structure is the direct consequence of population fragmentation. Temporal fluctuations in mitochondrial and microsatellite allelic frequencies were found between the historical and the current population as well as for each pairwise comparison between historical and current Centro and historical and current Parque Nacional de Doñana nuclei. Our results indicate an ancestral panmictic situation for the species that management policies should aim to restore. A historical analysis like the one taken here provides the baseline upon which the relative role of recent drift in shaping current genetic patterns in endangered species can be evaluated and this knowledge is used to guide conservation actions. [source] Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypesMOLECULAR ECOLOGY, Issue 14 2006H. M. NEVILLE Abstract Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of fine-scale genetic structuring due to the spatial clustering of related individuals on spawning grounds. Thus, we explored the spatial resolution of natal homing using genetic associations among individual Chinook salmon (Oncorhynchus tshawytscha) in an interconnected stream network. We also investigated the relationship between genetic patterns and two factors hypothesized to influence natal homing and localized movements at finer scales in this species, localized patterns in the distribution of spawning gravels and sex. Spatial autocorrelation analyses showed that spawning locations in both sub-basins of our study site were spatially clumped, but the upper sub-basin generally had a larger spatial extent and continuity of redd locations than the lower sub-basin, where the distribution of redds and associated habitat conditions were more patchy. Male genotypes were not autocorrelated at any spatial scale in either sub-basin. Female genotypes showed significant spatial autocorrelation and genetic patterns for females varied in the direction predicted between the two sub-basins, with much stronger autocorrelation in the sub-basin with less continuity in spawning gravels. The patterns observed here support predictions about differential constraints and breeding tactics between the two sexes and the potential for fine-scale habitat structure to influence the precision of natal homing and localized movements of individual Chinook salmon on their breeding grounds. [source] Fine-scale spatial genetic correlation analyses reveal strong female philopatry within a brush-tailed rock-wallaby colony in southeast QueenslandMOLECULAR ECOLOGY, Issue 12 2004S. L. HAZLITT Abstract We combine spatial data on home ranges of individuals and microsatellite markers to examine patterns of fine-scale spatial genetic structure and dispersal within a brush-tailed rock-wallaby (Petrogale penicillata) colony at Hurdle Creek Valley, Queensland. Brush-tailed rock-wallabies were once abundant and widespread throughout the rocky terrain of southeastern Australia; however, populations are nearly extinct in the south of their range and in decline elsewhere. We use pairwise relatedness measures and a recent multilocus spatial autocorrelation analysis to test the hypotheses that in this species, within-colony dispersal is male-biased and that female philopatry results in spatial clusters of related females within the colony. We provide clear evidence for strong female philopatry and male-biased dispersal within this rock-wallaby colony. There was a strong, significant negative correlation between pairwise relatedness and geographical distance of individual females along only 800 m of cliff line. Spatial genetic autocorrelation analyses showed significant positive correlation for females in close proximity to each other and revealed a genetic neighbourhood size of only 600 m for females. Our study is the first to report on the fine-scale spatial genetic structure within a rock-wallaby colony and we provide the first robust evidence for strong female philopatry and spatial clustering of related females within this taxon. We discuss the ecological and conservation implications of our findings for rock-wallabies, as well as the importance of fine-scale spatial genetic patterns in studies of dispersal behaviour. [source] Fine-scale genetic pattern and evidence for sex-biased dispersal in the túngara frog, Physalaemus pustulosusMOLECULAR ECOLOGY, Issue 12 2003Kathrin P. Lampert Abstract Túngara frogs (Physalaemus pustulosus) are a model system for sexual selection and communication. Population dynamics and gene flow are of major interest in this species because they influence speciation processes and microevolution, and could consequently provide a deeper understanding of the evolutionary processes involved in mate recognition. Although earlier studies have documented genetic variation across the species' range, attempts to investigate dispersal on a local level have been limited to mark,recapture studies. These behavioural studies indicated high mobility at a scale of several hundred metres. In this study we used seven highly polymorphic microsatellite loci to investigate fine-scaled genetic variation in the túngara frog. We analysed the influence of geographical distance on observed genetic patterns, examined the influence of a river on gene flow, and tested for sex-biased dispersal. Data for 668 individuals from 17 populations ranging in distance from 0.26 to 11.8 km revealed significant levels of genetic differentiation among populations. Genetic differentiation was significantly correlated with geographic distance. A river acted as an efficient barrier to gene flow. Several tests of sex-biased dispersal were conducted. Most of them showed no difference between the sexes, but variance of Assignment Indices exhibited a statistically significant male bias in dispersal. [source] Isolation and characterization of microsatellite markers in Pterocarpus officinalis Jacq.MOLECULAR ECOLOGY RESOURCES, Issue 2 2006FÉLIX MULLER Abstract The leguminous Pterocarpus officinalis Jacq. is one of the dominant freshwater wetland tree species in the Caribbean basin. Anthromorphic factors threaten to reduce its population. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred ninety-one individuals were analysed within nine Caribbean and continental populations. These loci were polymorphic in all the populations, with four to 20 alleles per locus. Significant Hardy,Weinberg deviation was detected and was interpreted as a result of Wahlund effect. These loci constitute a powerful tool to investigate the genetic patterns within populations of the swamp species P. officinalis. [source] Genetic variation and biogeography of Mertensia maritima (Boraginaceae)NORDIC JOURNAL OF BOTANY, Issue 5 2004Olav Skarpaas To elucidate the population dynamics and biogeographic connections of Mertensia maritima in the North Atlantic we studied the genetic variation within and among 16 local populations in the Oslofjord region (south-east Norway), Finnmark (northern Norway), Iceland and Svalbard, using starch gel isozyme electrophoresis. We also tested the self-compatibility experimentally. Mertensia maritima was found to be self-compatible and able to self-pollinate by autodeposition. The total level of genetic variation was extremely low. All the screened individuals were homozygous at all loci. All individuals from the populations of mainland Norway and Iceland were isozymatically identical, whereas individuals from Svalbard differed from these at three loci (AAT-1, PGM-3 and SKD-2). The genetic identity between any population at Svalbard and any population on the mainland was 0.86. These genetic patterns may have resulted from a combination of inbreeding, frequent local population extinctions, and long-distance dispersal. The isozymatic distinctness of the Svalbard populations is consistent with the arctic distribution of the morphologically based var. tenella, here raised to subspecific rank as Mertensia maritima ssp. tenella. [source] | ||||||||||||||||||||||||||||