Genetic Structure (genetic + structure)

Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Genetic Structure

  • colony genetic structure
  • fine-scale genetic structure
  • fine-scale spatial genetic structure
  • population genetic structure
  • significant spatial genetic structure
  • spatial genetic structure
  • strong genetic structure

  • Selected Abstracts


    EVOLUTION, Issue 3 2006
    Charles D. Criscione
    Abstract Little is known about actual mating systems in natural populations of parasites or about what constitutes the limits of a parasite deme. These parameters are interesting because they affect levels of genetic diversity, opportunities for local adaptation, and other evolutionary processes. We expect that transmission dynamics and the distribution of parasites among hosts should have a large effect on mating systems and demic structure, but currently we have mostly speculation and very few data. For example, infrapopulations (all the parasites in a single host) should behave as demes if parasite offspring are transmitted as a clump from host to host over several generations. However, if offspring are well mixed, then the parasite component population (all the parasites among a host population) would function as the deme. Similarly, low mean intensities or a high proportion of worms in single infections should increase the selfing rate. For species having an asexual amplification stage, transmission between intermediate and definitive (final) hosts will control the variance in clonal reproductive success, which in turn could have a large influence on effective sizes and rates of inbreeding. We examined demic structure, selfing rates, and the variance in clonal reproductive success in natural populations of Plagioporus shawi, a hermaphroditic trematode that parasitizes salmon. Overall levels of genetic diversity were very high. An a posteriori inference of population structure overwhelmingly supports the component population as the deme, rather than individual infrapopulations. Only a single pair of 597 adult individuals was identified as clones. Thus, the variance in clonal reproductive success was almost zero. Despite being hermaphroditic, P. shawi appears to be almost entirely outcrossing. Genetic estimates of selfing (<5%) were in accordance with the proportion of parasites from single infections. Thus, it appears that individual flukes outcross whenever possible and only resort to selfing when alone. Finally, our data support the hypothesis that aquatic transmission and the use of several intermediate hosts promotes high genetic diversity and well-mixed infrapopulations. [source]


    EVOLUTION, Issue 11 2004
    Eric 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]


    Marila Lázaro
    Abstract The franciscana, Pontoporia blainvillei, is endemic to the South Atlantic coast of South America. The species is of conservation concern because it suffers elevated mortality rates due to incidental captures in fishing nets, and perhaps it is one of the most threatened small cetaceans in this region. Previous morphological and genetic studies have suggested the existence of at least two distinct stocks to the north and south of Santa Catarina Island in Brazil. Fixed differences were found between a sample from Rio de Janeiro and one from Rio Grande do Sul, in southern Brazil. Using 94 sequences of the control region of mitochondrial DNA, we examined the genetic structure of the species. We found no shared haplotypes between Rio de Janeiro and samples from the southern range of the species distribution. However, a phylogenetic analysis suggests that the former population is diphyletic with respect to the southern samples. This suggests that the populations have not been isolated long enough to reach reciprocal monophyly. Furthermore, genetic differentiation is broadly consistent with a simple model of isolation by distance, that therefore appears as an alternative to a model of strict isolation of two stocks. The estimated levels of gene flow are higher among neighboring populations, and decrease as more distant localities are compared. Finally, the molecular data suggest that franciscanas have expanded in Rio de Janeiro. [source]


    Guang 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 Conservation

    Yuan 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]

    Differentiation and Genetic Structure of Sclerophoma pythiophila Strains on Pinus sylvestris in Poland

    Wojciech Kraj
    Abstract Between 1996 and 2006, 97 strains of Sclerophoma pythiophila were isolated from 3 to 10-year-old trees of Pinus sylvestris from three regions of Poland differing by climatic conditions and geographic location. On the basis of 56 random amplified microsatellites (RAMS) markers obtained with the use of five primers, very high level of genetic variability of strains (mean Jaccard's coefficient 0.56) was ascertained. Among the analysed markers only one was completely monomorphic, whereas six were monomorphic in 90%. Greater genetic similarity was ascertained for strains in southern Poland (0.58) in comparison with strains deriving from northern Poland (0.52). Correlation between the percentage share of polymorphic loci and the average annual temperature of places of strain isolation (r = 0.62) were shown, as well as the number of days with snow cover (r = 0.79). On the basis of the amova analysis, it was ascertained that 11.6% of genetic variability was located between regions of the strains origin and 88.4% within the regions. [source]

    Fine-Scale Spatial Genetic Structure of the Distylous Primula veris in Fragmented Habitats

    PLANT BIOLOGY, Issue 3 2007
    F. van Rossum
    Abstract: In Flanders (northern Belgium), the distylous self-incompatible perennial herb Primula veris is common, but mainly occurs in fragmented habitats. Distyly, which favours disassortative mating, is characterized in P. veris by two genetically determined floral morph types (pin or thrum). Using 18 polymorphic loci, we investigated fine-scale spatial genetic structure (SGS) and spatial distribution of the morphs within four populations from two regions that differ in degree of habitat fragmentation. We studied the contributions made by sexual reproduction and clonal propagation and compared the SGS patterns between pin and thrum morph types. Clonal growth was very restricted to a few individuals and to short distances. One population showed a non-random spatial distribution of the morphs. Pin and thrum individuals differed in SGS patterns at a small scale, suggesting intrapin biparental inbreeding, also related to high plant densities. This may be explained by partial self-compatibility of the pin morph combined with restricted seed dispersal and pollinator behaviour. There is an indication of more pronounced SGS when populations occur in highly fragmented habitats. From our findings, we may hypothesize disruption of the gene flow processes if these large populations evolve into patchworks of small remnants, but also a possible risk for long-term population survival if higher intrapin biparental inbreeding leads to inbreeding depression. Our study emphasizes the need for investigating the interactions between the heterostylous breeding system, population demographic and genetic structure for understanding population dynamics in fragmented habitats and for developing sustainable conservation strategies. [source]

    Social Network Analysis of the Genetic Structure of Pacific Islanders

    John Edward Terrell
    Summary Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania. [source]

    Genetic structure of Euphrasia stricta on the Baltic island of Gotland, Sweden

    ECOGRAPHY, Issue 4 2005
    Anna-Karin Kolseth
    Genetic differentiation between and within five varieties of Euphrasia stricta (var. brevipila, var. gotlandica, var. stricta, var. suecica and var. tenuis) on Gotland was investigated, using amplified fragment length polymorphism, AFLP. The varieties are described in the literature by morphology and association to habitat type. We wanted to investigate whether the varieties are locally adapted populations to the typical habitat type for each variety or if they are preadapted to certain habitat types and have colonized Gotland in their present form. A constrained principal coordinate analysis revealed three genetically differentiated subunits within the species. The two early-flowering varieties suecica and tenuis each formed a distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta together formed the third group. A phylogenetic tree confirms the partitioning into three groups. Within the group containing the late-flowering varieties there are populations that pair as each other's closest relatives, but belong to different varieties. These pairs are also geographically adjacent. The phylogenetic tree had a "star-like" appearance indicating a stronger divergence between populations than between varieties. The same pattern was seen in the partitioning of genetic diversity, with a lower amount of genetic variation occurring between varieties, FST=0.14, than between populations within the varieties, FST ranging from 0.26 to 0.60. In Euphrasia stricta the varieties suecica and tenuis and the group containing the varieties stricta/gotlandica/brevipila are likely to have a phylogeographical history outside Gotland, or an ancient and concealed local origin on the island. Within the group stricta/gotlandica/brevipila local evolutionary events seem to determine the variety identity, probably through local adaptation. [source]

    Genetic structure of New Zealand eels Anguilla dieffenbachii and A. australis with allozyme markers

    P. J. Smith
    Abstract , Glass eels and adults of Anguilla australis and A. dieffenbachii were collected from rivers in the North and South Islands of New Zealand and tested for nine and ten allozyme loci, respectively. There was no heterogeneity among glass eel samples, but there was heterogeneity among adult samples within species. The results indicate that there may be single panmictic populations subject to sweepstake events or different selective pressures in the adult environments., [source]

    Genetic structure of Japanese populations of an ambrosia beetle, Xylosandrus germanus (Curculionidae: Scolytinae)

    Masaaki ITO
    Abstract We examined the genetic structures of 13 Japanese populations of an ambrosia beetle, Xylosandrus germanus (Curculionidae: Scolytinae), to understand the effects of geographical barriers on the colonization dynamics of this species. The genetic structure was studied using portions of the mitochondrial cytochrome oxidase I (COI) gene. A phylogenetic analysis revealed three distinct lineages (clades A, B and C) within X. germanus. Clade A contained 21 haplotypes from all 13 populations; whereas clade B contained eight haplotypes from Hokkaido (Sapporo and Furano), Iwate and Nagano populations; and clade C contained only a single a haplotype from the Hokkaido (Furano) population. In the analysis of molecular variance (amova), the greatest amount of genetic variation was detected between populations in Hokkaido and those in Honshu and other southern islands. Between these two groups of populations, all the values of the coefficient of gene differentiation were significantly larger than zero, except for the Hokkaido (Sapporo) versus Nagano comparison. Our results confirm that for X. germanus, gene flow has been interrupted between Hokkaido and Honshu since the last glacial maximum. [source]


    EVOLUTION, Issue 11 2004
    Eric 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]

    Can low densities of carnivores result in genetic depletion?

    An investigation within French polecat populations
    Summary Carnivores as top predators are commonly found in relatively low densities even in optimal habitats. Despite a lack of empirical studies, it could be suspected that long-term low density could result in genetic depletion. The genetic structure of European polecat Mustela putorius natural populations was investigated by allozyme electrophoresis in five distinct areas. Density estimates significantly differed among sites from 0.17 to 0.83 individuals/km2 with an average of 0.56 individuals per km2, resulting in a scattered distribution. Genetic structure varied among distinct populations both in number of polymorphic loci and heterozygosity. Polecats from Brittany revealed a very low observed heterozygosity (HO = 0.028) whereas mean heterozygosity reached HO = 0.072 in Brière. That the lowest heterozygosity levels and highest inbreeding coefficient FIS were significantly associated with the lowest densities suggests that low densities may affect populations of carnivores. Both the loss of polymorphic loci and the reduction in heterozygosity rates suggest a density-dependent effect and population density can be arguably regarded as a factor affecting genetic diversity in top carnivores. [source]

    Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms

    E.M. Ibeagha-Awemu
    Summary Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds. [source]

    Genetic structure of Norwegian horse breeds

    G. Bjørnstad
    The evaluation of the genetic structure of four native Norwegian horse breeds was investigated using 35 genetic markers including nine biochemical loci and 26 microsatellites. The proportion of genetic variation measured as heterozygosity and the number of alleles indicated high variation in Fjord Horse and Coldblooded Trotter, but somewhat reduced variation in Døle Horse. No clear signs of bottleneck effects were found in either of the breeds, but significant inbreeding estimates in Nordland/Lyngen Horse may indicate subdivision of this breed. Significant population differentiation was detected between all breeds, also between the recently diverged Døle Horse and Coldblooded Trotter. The principal component analysis supports the close genetic relationship between these two breeds. Zusammenfassung Die genetische Struktur von vier in Norwegen heimischen Pferderassen wurde mit Hilfe von 35 genetischen Markören bestehend aus neun biochemischen Loci und 26 Mikrosatelliten untersucht. Der Umfang der genetischen Variation, gemessen als Heterozygozität und Anzahl Allelen, deutet eine grosse Variation beim Norwegischen Fjordpferd und Kaltbluttraber an, aber eine geringere beim Dölepferd. In keine der Rassen wurden klare Anzeichen eines Flaschenhalseffektes gefunden, aber hohe Inzuchtschätzwerte des Nordland/Lyngenpferdes lassen eine Unterteilung dieser Rasse vermuten. Zwischen allen Rassen wurde signifikante Populationsunterschiede gefunden, auch zwischen den erst neulich getrennten Dölepferd und Kaltbluttraber. Die enge genetische Beziehung zwischen diesen beiden Rassen wird durch die Hauptkomponentenanalyse unterstützt. [source]

    Genetic structure in Atlantic brown trout (Salmo trutta L.) populations in the Iberian peninsula: evidence from mitochondrial and nuclear DNA analysis

    S. Dunner
    Summary Brown trout (Salmo trutta L.) was sampled in rivers belonging to three different Spanish basins in order to analyse the distribution of genetic variability. The genetic analysis was performed by using two systems and techniques: nuclear DNA was screened through random amplified polymorphic DNAs (screening 2 × 105 bp of the whole genome), and mitochondrial DNA (mtDNA) through sequencing of the hypervariable control region. Genetic distances between the populations were similar using either analysis although some differences arise. For example, some populations of the Tajo basin were very close through nuclear analysis but more distant using mtDNA. Differences between the two DNA sources could be the result of a different evolutionary rate, and the fact that mtDNA is maternally transmitted and differences in sex migration rates will influence the patterns of genetic variation between the transmitted DNAs. Total variation was partitioned using amova showing a clear subdivision among basins although intrapopulation variation remained as high as 62%. A correspondence analysis defined the differences in a three-dimensional way, clustering the populations according to their common basin. When mtDNA was sequenced, higher variability was noted in the segment between 400 and 600bp of the whole D-loop sequence, suggesting that these 200bp improved the analysis of the variability more than sequencing the t-RNA ends of the control region. A comparison was made between the t-RNAPro ends of the 10 populations screened here and the rest of the published sequences found in the literature, leading to a concentration of these populations in group IV which includes all trouts which originate in the Atlantic. The analyses performed suggest that a high genetic variability is present in all populations and that although there has been a probable interference from stocked strains introduced to increase population density, this was only detectable through the variance between rivers which reflect different policies according to the region where the basin is located. However, the genetic analysis using the two approaches allows the control of the natural populations avoiding a loss of their genetic potential. Zusammenfassung In drei verschiedenen spanischen Wassersystemen wurden Bachforellen (Salmo trutta L.) gesammelt, um die genetische Variabilität zu analysieren. Zur Analyse wurden zwei Systeme und zwei Techniken genutzt: Kern-DNA wurde mittels RAPD analysiert (2.105bp des Gesamtgenoms), mitochondriale DNA durch das Sequenzieren der hypervariablen Kontrollregion. Beide Techniken ergaben ähnliche genetische Distanzen zwischen den Populationen, obwohl Unterschiede bei Populationen aus dem Tajo-Gebiet auftraten, deren Kern-DNA eine sehr geringe Distanz aufwiesen, während die über Sequenzierung von mtDNA ermittelte Distanz auf größere Unterschiede hinwies. Diese Differenz könnte das Ergebnis unterschiedlicher Mutationsraten während der Evolution sein, oder auf dieTatsache zurückzuführen sein, daß mtDNA über die Mutterlinien weitergegeben wird, und Migrationsunterschiede zwischen den Geschlechtern die Muster der genetischen Variation der weitergegebenen DNA-Stücke beeinflußt. Die Gesamtvarianz wurde mit Hilfe von AMOVA analysiert, wobei zwischen den Wassersystemen eine eindeutige Unterteilung festgestellt werden konnte, obwohl die Varianz innerhalb der Population bei 62% liegt. Eine Korrespondenzanalyse erklärt die Distanzen dreidimensional, wodurch die Populationen gleicher Herkunft in Cluster zusammenfallen. Bei der Sequenzierung von mtDNA wurde eine größere Variabilität im Sequenzbereich zwischen 400 und 600 bp der gesamten D-Loop Sequenz festgestellt, was darauf schließen läßt, daß diese 200 bp für eine Analyse der Variabilität geeigneter sind als eine Sequenzierung der t-RNA Enden der Kontrollregion. Ein Vergleich der t-RNAPro Enden der zehn hier untersuchten Populationen und der bereits publizierten Sequenzen führen zu einer Konzentration dieser in der Gruppe IV, zu der alle Forellenpopulationen zählen, die aus dem Atlantik stammen. Die Untersuchung deutet auf eine hohe genetische Variabilität in allen Populationen hin und auf Interferenzen durch Aufstockungsmaßnahmen zur Erhöhung der Populationsdichten hin. Dies ist nur durch die Varianz zwischen den Flußsystemen aufzuklären, die von Region zu Region unterschiedliche Maßnahmen wiederspiegelt. Die genetische Analyse mittels dieser zwei Ansätze erlaubt eine Kontrolle der natürlichen Populationen zwecks Vermeidung eines Verlustes ihres genetischen Potentials. [source]

    Genetic structure and gene flow in wild beet populations: the potential influence of habitat on transgene spread and risk assessment

    Summary 1The consequences of the movement of transgenes from genetically modified (GM) crops into wild populations of plants continues to be of concern to ecologists and conservationists because of the possible threat posed to those populations in terms of their continued survival and because of the further knock-on effects that might occur to habitats in which they occur. 2We examined five UK sea beet Beta vulgaris ssp. maritima populations from each of two major habitat types, cliff top and drift line. We assessed population genetic parameters, genetic diversity, gene flow, population differentiation and isolation by distance, to enable determination of the likelihood and consequences of spread to wild populations of genes from cultivated sugar beet group Beta vulgaris ssp. vulgaris, which could in the future be transgenic. 3Drift line populations were more diverse than cliff top populations and also showed greater levels of gene flow. 4Isolation by distance was identified in both habitats, but the relationship between genetic and geographical distance was detectable over longer distances for drift line populations. However, clear indications of vicariance (the subdivision of a population into distinct taxa by the appearance of a geological barrier) between cliff and drift line populations were also evident, because of the restriction of gene flow between the two habitats occurring more in one direction than the other. 5Synthesis and applications. The likelihood of transgene spread from crop to wild populations is habitat dependent and conservation management decisions could therefore vary from one population to another, for example water courses were found to facilitate seed dispersal. This should be taken into account when estimating isolation distances for GM beet, and when predicting transgene frequencies (exposure estimates) for environmental risk assessments of GM beet. [source]

    Phylogeography of the world's tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia

    Paul G. Nevill
    Abstract Aim, There is a need for more Southern Hemisphere phylogeography studies, particularly in Australia, where, unlike much of Europe and North America, ice sheet cover was not extensive during the Last Glacial Maximum (LGM). This study examines the phylogeography of the south-east Australian montane tree species Eucalyptus regnans. The work aimed to identify any major evolutionary divergences or disjunctions across the species' range and to examine genetic signatures of past range contraction and expansion events. Location, South-eastern mainland Australia and the large island of Tasmania. Methods, We determined the chloroplast DNA haplotypes of 410 E. regnans individuals (41 locations) based on five chloroplast microsatellites. Genetic structure was examined using analysis of molecular variance (AMOVA), and a statistical parsimony tree was constructed showing the number of nucleotide differences between haplotypes. Geographic structure in population genetic diversity was examined with the calculation of diversity parameters for the mainland and Tasmania, and for 10 regions. Regional analysis was conducted to test hypotheses that some areas within the species' current distribution were refugia during the LGM and that other areas have been recolonized by E. regnans since the LGM. Results, Among the 410 E. regnans individuals analysed, 31 haplotypes were identified. The statistical parsimony tree shows that haplotypes divided into two distinct groups corresponding to mainland Australia and Tasmania. The distribution of haplotypes across the range of E. regnans shows strong geographic patterns, with many populations and even certain regions in which a particular haplotype is fixed. Many locations had unique haplotypes, particularly those in East Gippsland in south-eastern mainland Australia, north-eastern Tasmania and south-eastern Tasmania. Higher haplotype diversity was found in putative refugia, and lower haplotype diversity in areas likely to have been recolonized since the LGM. Main conclusions, The data are consistent with the long-term persistence of E. regnans in many regions and the recent recolonization of other regions, such as the Central Highlands of south-eastern mainland Australia. This suggests that, in spite of the narrow ecological tolerances of the species and the harsh environmental conditions during the LGM, E. regnans was able to persist locally or contracted to many near-coastal refugia, maintaining a diverse genetic structure. [source]

    Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugium

    Patrik Mráz
    Abstract Aim, The range of the subalpine species Hypochaeris uniflora covers the Alps, Carpathians and Sudetes Mountains. Whilst the genetic structure and post-glacial history of many high-mountain plant taxa of the Alps is relatively well documented, the Carpathian populations have often been neglected in phylogeographical studies. The aim of the present study is to compare the genetic variation of the species in two major European mountain systems , the Alps and the Carpathians. Location, Alps and Carpathians. Methods, The genetic variation of 77 populations, each consisting of three plants, was studied using amplified fragment length polymorphism (AFLP). Results, Neighbour joining and principal coordinate analyses revealed three well-supported phylogeographical groups of populations corresponding to three disjunct geographical regions , the Alps and the western and south-eastern Carpathians. Moreover, two further clusters could be distinguished within the latter mountain range, one consisting of populations from the eastern Carpathians and the second consisting of populations from the southern Carpathians. Populations from the Apuseni Mountains had an intermediate position between the eastern and southern Carpathians. The genetic clustering of populations into four groups was also supported by an analysis of molecular variance, which showed that most genetic variation (almost 46%) was found among these four groups. By far the highest within-population variation was found in the eastern Carpathians, followed by populations from the southern and western Carpathians. Generally, the populations from the Alps were considerably less variable and displayed substantially fewer region-diagnostic markers than those from the south-eastern Carpathians. Although no clear geographical structure was found within the Alps, based on neighbour joining or principal coordinate analyses, some trends were obvious: populations from the easternmost part were genetically more variable and, together with those from the south-western part, exhibited a higher proportion of rare AFLP fragments than populations in other areas. Moreover, the total number of AFLP fragments per population, the percentage of polymorphic loci and the proportion of rare AFLP fragments significantly decreased from east to west. Main conclusions, Deep infraspecific phylogeographical gaps between the populations from the Alps and the western and south-eastern Carpathians suggest the survival of H. uniflora in three separate refugia during the last glaciation. Our AFLP data provide molecular evidence for a long-term geographical disjunction between the eastern and western Carpathians, previously suggested from the floristic composition at the end of 19th century. It is likely that Alpine populations survived the Last Glacial in the eastern part of the Alps, from where they rapidly colonized the rest of the Alps after the ice sheet retreated. Multiple founder effects may explain a gradual loss of genetic variation during westward colonization of the Alps. [source]

    Genetic structure of two populations of the Namibian giraffe, Giraffa camelopardalis angolensis

    Rick A. Brenneman
    Abstract Two geographically distinct populations of giraffe (Giraffa camelopardalis) were sampled for this study, the northern Namib Desert and Etosha National Park. Population genetic parameters and relationships within subpopulations were estimated to better understand the genetic architecture of this isolated subspecies. Gene flow between the geographically separated populations can be attributed to recent translocation of giraffe between the two populations. Inbreeding estimates in the six subpopulations studied were low though we found evidence that genetic drift may be affecting the genetic diversity of the isolated populations in northern Namibia. Population dynamics of the sampling locations was inferred with relationship coefficient analyses. Recent molecular systematics of the Namibian giraffe populations indicates that they are distinct from the subspecies Giraffa camelopardalis giraffa and classified as G. c. angolensis. Based on genetic analyses, these giraffe populations of northern Namibia, the desert-dwelling giraffe and those protected in Etosha National Park, are a distinct subspecies from that previously assumed; thus we add data on G. c. angolensis to our scientific knowledge of this giraffe of southern Africa. Résumé Deux populations de girafes (Giraffa camelopardalis) distinctes sur le plan géographique ont servi d'échantillons pour cette étude, celle du nord du Désert du Namib et celle du Parc National d'Etosha. Nous avons estimé les paramètres génétiques des populations et les relations au sein des sous-populations pour mieux comprendre l'architecture génétique de cette sous-espèce isolée. Les flux génétiques entre les populations séparées géographiquement peuvent être attribués à la récente translocation de girafes entre ces deux populations. L'inbreeding estimé dans les six sous-populations étudiées était faible, encore que nous ayons découvert des preuves que la dérive génétique pourrait bien affecter la diversité génétique des populations isolées dans le nord de la Namibie. La dynamique des populations des endroits où furent faits les échantillonnages fut déduite en fonction de l'analyse des coefficients. La nouvelle systématique moléculaire des populations de girafes de Namibie indique qu'elles sont distinctes de la sous-espèce Giraffa camelopardalis giraffa et classées comme G.c. angolensis. Selon les analyses génétiques, ces populations de girafes du nord de la Namibie, les girafes qui vivent dans le désert et celles qui sont protégées dans le Parc National d'Etosha sont une sous-espèce distincte de celle que l'on croyait auparavant, et nous ajoutons ainsi des données sur G.c. angolensisà la connaissance scientifique de cette girafe d'Afrique australe. [source]

    Gene diversity in a fragmented population of Briza media: grassland continuity in a landscape context

    JOURNAL OF ECOLOGY, Issue 1 2006
    Summary 1We investigated patterns of allozyme variation in demes of the grass Briza media in semi-natural grassland fragments within a mosaic agricultural landscape on the Baltic island of Öland. In the study area, Briza is both a characteristic species of old pastures and an early colonizer of young grasslands developing on previously forested or arable sites. 2Generalized linear models revealed that descriptors of both present landscape structure and past grassland history are significant determinants of genetic variation in the Briza demes. Genetic structure and levels of within-deme diversity are influenced by the size of grassland fragments, the type of habitat surrounding the grasslands, the size/spatial extent of the demes, the geographic position of the demes and the historical continuity of the grassland fragments. 3Gene diversity (H) was higher in demes from grassland polygons with a high proportion of adjacent grassland, higher in the more extensive demes, and decreased northwards within the study area. 4The negative association between the inbreeding coefficient (FIS) and grassland continuity is interpreted in terms of a two-stage colonization process: recruitment into young grasslands leads initially to spatial patchiness, but subsequent selection in maturing pastures occurs within an increasingly uniform and dense sward. 5Despite a weak overall genetic structure (as indicated by Bayesian cluster analysis) the between-deme FST was significant. Linear discriminant analysis of within-deme allele frequencies grouped the demes according to the age and previous land-use history of their grassland polygons. The convergence of the allele frequency profiles in the younger grasslands towards those of the old grasslands is consistent with convergence of selective regimes as pastures mature towards an increasingly uniform, dense sward and characteristic species assemblage. 6The genetic composition of demes of a grassland species appears to be influenced by the process of plant community convergence during grassland development , complementing the recent finding that convergence of species composition in experimental assemblages of grassland plants is dependent on the genotypic composition of the component species. [source]

    Genetic structure of Polytrichum formosum in relation to the breeding system as revealed by microsatellites

    M. Van Der Velde
    Microsatellite variation was determined for three Danish and three Dutch populations of the haploid moss species Polytrichum formosum to gain insight into the relative importance of sexual vs. asexual reproduction for the amount and structure of genetic variation. In general, low levels of microsatellite variation were observed within this species. Even when estimated for polymorphic loci only, the levels of microsatellite variability (P=90.6, A=4.3 and HS=0.468) within populations were on average lower than those reported for most other plant species. In contrast, genotypic diversity was high within each of the examined populations, indicating that sexual reproduction is a very important determinant of the genetic structure of P. formosum within populations. In agreement with previous findings for allozyme data, no significant genetic differentiation (FST=0.028, RST=0.015) was observed neither between populations nor between regions approximately 450 km apart (Denmark vs. the Netherlands). These low levels of population differentiation observed for both types of genetic markers are probably best explained by a high level of effective spore dispersal (gene flow) between populations. Therefore, also on a large geographical scale sexual reproduction is the most important determinant of the genetic structure of P. formosum, despite the high potential to reproduce clonally. [source]

    Impact of rifting and hydrography on the genetic structure of Clarias gariepinus in eastern Africa

    C.S. Giddelo
    In a study of the genetic structure of Clarias gariepinus at the ND5 and ND6 loci of mitochondrial DNA using RFLP,PCR in 16 populations (267 fish), a total of 18 haplotypes was detected. The most common haplotype was EA1 and represented 46% of all genotypes. Three phylogenetic groups characterized the region, with the East African clade occurring between the western rift in the west, Lake Baringo in the north, the Indian Ocean in the east and the Rufiji River in the south. The Lower Tana River (unlike the Upper Tana River) and Lake Kamnarok grouped with the North clade, while the Ruaha River (tributary of the Rufiji River) represented a contact zone between the East and the South-central African clade. Genetic structure was distinct (FST=0·66), with the Lower Tana River and Lake Mtera forming specific units. Within the East clade, the Oloibortoto River, Upper Tana River and Lake Victoria each formed a distinct population. Lake Baringo grouped either with the eastern rift or the western rift depending on the analysis. Lake Jipe, the Pangani River, Rusizi River, Lake Edward, Nyabugogo River and the Luiche River clustered together. Among group variance explained 66·8% of the total variance; the impact of vicariance (rifting and uplifting) on the phylogeography was considerable. A distribution model of the catfish is proposed which combines the separation by rifting several million years ago with a high gene flow in the western rift due to historical connectivity among lakes and rivers. [source]

    Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategies

    JOURNAL OF ZOOLOGY, Issue 1 2006
    C. Pertoldi
    Abstract During the last century, the European polecat Mustela putorius populations in most of Europe declined and survived in fragmented patches, because of habitat alterations and direct persecution. To assess the genetic consequences of the demographic decline and to describe the spatial pattern of genetic diversity, 250 polecats sampled at seven localities from five European countries , Poland, Denmark (southern Denmark and northern Denmark), Spain, Belgium (eastern and western) and the Netherlands , were screened by means of nine microsatellite loci. Genetic diversity estimated by mean expected heterozygosity (HE) and allelic richness (AR) were moderately high within populations [range: 0.50 (northern Denmark) ,HE,0.64 (Poland) and 1.33,AR,7.80] as compared with other carnivores and mustelids. Bottleneck tests suggested that polecat populations in southern Denmark and Poland have declined recently and populations from northern Denmark and the Netherlands have expanded recently, whereas the remaining populations did not show any sign of demographic change. Recent demographic changes could suggest that some of the populations are still not in equilibrium, which could partly explain the relatively high genetic variability observed in polecat populations despite the drastic decline in population size observed in several European countries. A significant heterozygote deficiency [FIS=0.19; 0.01,95% confidence interval (CI),0.32] suggests substructuring within the total European sample. Partitioning of the genetic variation among sampling locations (FST=0.14; 0.06,95% CI,0.23) and pairwise FST between localities (range: 0.01,FST,0.37) without any correlation with the geographic distances between localities were found, suggesting a recent divergence and a restriction of gene flow between populations and the action of genetic drift. An assignment test showed that the Polish and the northern Danish populations were the most unique, whereas the other populations were partially admixed. Factorial component analysis tests indicate a subdivision of the total sample into two distinct groups: one including the samples from Poland and the two Danish localities and the second group comprising the remaining localities investigated. The observed pattern of genetic differentiation is suggested to be due to two main routes of recolonization after the last glacial period. To compare the results obtained with microsatellite data, the most variable region of the mitochondrial DNA (d-loop) was sequenced and different phylogenetic reconstructions and genetic diversity analyses based on nucleotide (,) and haplotype diversity (h) measures within populations were performed using a subsample of populations. The lack of well-defined geographical structure, as well as the reduced level of mitochondrial DNA variability (,: 0.00274±0.00038; h: 0.876±0.028) that was found, has been previously reported in several studies on different carnivores and supports the hypothesis of post-glacial recolonization from southern or eastern refugees of Europe as suggested by the microsatellite data. Implications for conservation strategies of the polecat at the European level are discussed. [source]

    Genetic structure and gene flow in French populations of two Ostrinia taxa: host races or sibling species?

    MOLECULAR ECOLOGY, Issue 20 2007
    Abstract Most models of ecological speciation concern phytophagous insects in which speciation is thought to be driven by host shifts and subsequent adaptations of populations. Despite the ever-increasing number of studies, the current evolutionary status of most models remains incompletely resolved, as estimates of gene flow between taxa remain extremely rare. We studied the population genetics of two taxa of the Ostrinia genus , one feeding mainly on maize and the other on mugwort and hop , occurring in sympatry throughout France. The actual level of divergence of these taxa was unknown because the genetic structure of populations had been investigated over a limited geographical area and the magnitude of gene flow between populations had not been estimated. We used 11 microsatellite markers to investigate the genetic structure of populations throughout France and the extent of gene flow between the two Ostrinia taxa at several sites at which they are sympatric. We observed clear genetic differentiation between most populations collected on the typical respective hosts of each taxon. However, populations displaying intermediate allelic frequencies were found on hop plants in southern France. Individual assignments revealed that this result could be accounted for by the presence of both taxa on the same host. Gene flow, estimated by determining the proportion of hybrids detected, was low: probably < 1% per generation, regardless of site. This indicates that the two Ostrinia taxa have reached a high level of genetic divergence and should be considered sibling species rather than host races. [source]

    Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains

    MOLECULAR ECOLOGY, Issue 12 2007
    Abstract In wide-ranging species, the genetic consequences of range shifts in response to climate change during the Pleistocene can be predicted to differ among different parts of the distribution area. We used amplified fragment length polymorphism data to compare the genetic structure of Arabis alpina, a widespread arctic-alpine and afro-alpine plant, in three distinct parts of its range: the North Atlantic region, which was recolonized after the last ice age, the European Alps, where range shifts were probably primarily altitudinal, and the high mountains of East Africa, where the contemporary mountain top populations result from range contraction. Genetic structure was inferred using clustering analyses and estimates of genetic diversity within and between populations. There was virtually no diversity in the vast North Atlantic region, which was probably recolonized from a single refugial population, possibly located between the Alps and the northern ice sheets. In the European mountains, genetic diversity was high and distinct genetic groups had a patchy and sometimes disjunct distribution. In the African mountains, genetic diversity was high, clearly structured and partially in accordance with a previous chloroplast phylogeography. The fragmented structure in the European and African mountains indicated that A. alpina disperses little among established populations. Occasional long-distance dispersal events were, however, suggested in all regions. The lack of genetic diversity in the north may be explained by leading-edge colonization by this pioneer plant in glacier forelands, closely following the retracting glaciers. Overall, the genetic structure observed corresponded to the expectations based on the environmental history of the different regions. [source]

    Genetic structure of the widespread and common Mediterranean bryophyte Pleurochaete squarrosa (Brid.) Lindb. (Pottiaceae) , evidence from nuclear and plastidic DNA sequence variation and allozymes

    MOLECULAR ECOLOGY, Issue 4 2007
    Abstract The Mediterranean Basin as one the world's most biologically diverse regions provides an interesting area for the study of plant evolution and spatial structure in plant populations. The dioecious moss Pleurochaete squarrosa is a widespread and common bryophyte in the Mediterranean Basin. Thirty populations were sampled for a study on molecular diversity and genetic structure, covering most major islands and mainland populations from Europe and Africa. A significant decline in nuclear and chloroplast sequence and allozyme variation within populations from west to east was observed. While DNA sequence data showed patterns of isolation by distance, allozyme markers did not. Instead, their considerable interpopulation genetic differentiation appeared to be unrelated to geographic distance. Similar high values for coefficients of gene diversity (GST) in all data sets provided evidence of geographic isolation and limited gene flow among populations (i) within islands, (ii) within mainland areas, and (iii) between islands and mainland. Notably, populations in continental Spain are strongly genetically isolated from all other investigated areas. Surprisingly, there was no difference in gene diversity and GST between islands and mainland areas. Thus, we conclude that large Mediterranean islands may function as ,mainland' for bryophytes. This hypothesis and its implication for conservation biology of cryptogamic plants warrant further investigation. While sexually reproducing populations were found all over the Mediterranean Basin, high levels of multilocus linkage disequilibrium provide evidence of mainly vegetative propagation even in populations where sexual reproduction was observed. [source]

    Dispersal and genetic structure in the American marten, Martes americana

    MOLECULAR ECOLOGY, Issue 6 2006
    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]

    Patterns of vegetative growth and gene flow in Rhizopogon vinicolor and R. vesiculosus (Boletales, Basidiomycota)

    MOLECULAR ECOLOGY, Issue 8 2005
    Abstract We have collected sporocarps and tuberculate ectomycorrhizae of both Rhizopogon vinicolor and Rhizopogon vesiculosus from three 50 × 100 m plots located at Mary's Peak in the Oregon Coast Range (USA); linear map distances between plots ranged from c. 1 km to c. 5.5 km. Six and seven previously developed microsatellite markers were used to map the approximate size and distribution of R. vinicolor and R. vesiculosus genets, respectively. Genetic structure within plots was analysed using spatial autocorrelation analyses. No significant clustering of similar genotypes was detected in either species when redundant samples from the same genets were culled from the data sets. In contrast, strong clustering was detected in R. vesiculosus when all samples were analysed, but not in R. vinicolor. These results demonstrate that isolation by distance does not occur in either species at the intraplot sampling scale and that clonal propagation (vegetative growth) is significantly more prevalent in R. vesiculosus than in R. vinicolor. Significant genetic differentiation was detected between some of the plots and appeared greater in the more clonal species R. vesiculosus with ,ST values ranging from 0.010 to 0.078*** than in R. vinicolor with ,ST values ranging from ,0.002 to 0.022** (*P < 0.05, **P < 0.01, ***P < 0.001). When tested against the null hypothesis of no relationship between individuals, parentage analysis detected seven likely parent/offspring pairs in R. vinicolor and four in R. vesiculosus (, = 0.001). Of these 11 possible parent/offspring pairs, only two R. vinicolor pairs were still supported as parent/offspring when tested against the alternative hypothesis of being full siblings (, = 0.05). In the latter two cases, parent and offspring were located at approximately 45 m and 28 m from each other. Challenges to parentage analysis in ectomycorrhizal fungi are discussed. [source]

    Heterogeneous genetic structure in a Fagus crenata population in an old-growth beech forest revealed by microsatellite markers

    MOLECULAR ECOLOGY, Issue 5 2004
    Y. Asuka
    Abstract The within-population genetic structure of Fagus crenata in a 4-ha plot (200 × 200 m) of an old-growth beech forest was analysed using microsatellite markers. To assess the genetic structure, Moran's I spatial autocorrelation coefficient was calculated. Correlograms of Moran's I showed significant positive values less than 0.100 for short-distance classes, indicating weak genetic structure. The genetic structure within the population is created by limited seed dispersal, and is probably weakened by overlapping seed shadow, secondary seed dispersal, extensive pollen flow and the thinning process. Genetic structure was detected in a western subplot of 50 × 200 m with immature soils and almost no dwarf bamboos (Sasa spp.), where small and intermediate-sized individuals were distributed in aggregations with high density because of successful regeneration. By contrast, genetic structure was not found in an eastern subplot of the same size with mature soils and Sasa cover, where successful regeneration was prevented, and the density of the small and intermediate-sized individuals was low. Moreover, genetic structure of individuals in a small-size class (diameter at breast height < 12 cm) was more obvious than in a large-size class (diameter at breast height , 12 cm). The apparent genetic structure detected in the 4-ha plot was therefore probably the result of the structure in the western portion of the plot and in small and intermediate-sized individuals that successfully regenerated under the favourable environment. The heterogeneity in genetic structure presumably reflects variation in the density that should be affected by differences in regeneration dynamics associated with heterogeneity in environmental conditions. [source]