Analysis Of Genetic Population Structure Research Articles

Conservation genetics of the endemic species Myricaria laxiflora (Tamaricaceae) in the Three Gorges Reservoir area, Hubei

Allozymic variation of 13 natural populations and one ex situ population of Myricaria laxiflora were analyzed using isoelectric focusing in thin-layer polyacrylamide slab gels. Thirteen loci of five enzyme systems were examined and used for the analysis of population genetic diversity and structure. A high genetic diversity was observed in this species, with mean number of alleles per locus of A=1.8, mean percentage of polymorphic loci P=78.7% and average expected heterozygosity H e=0.317, which were higher than the average value of Chinese endemic plant species. An excess of heterozygous genotypes was found both in natural and ex situ populations, suggesting a slight deviation from the Hardy-Weinberg equilibrium in the populations. The total genetic diversity (H t) is 0.3733 within the species, while the genetic diversity within and among populations (H s vs Dst) were 0.3168 and 0.0565, respectively, indicating that 84.86% of the genetic variation occured within populations and only 15.14% among natural populations. The mean gene flow among populations (Nm) was 1.401 and genetic distances among populations ranges from 0.002 to 0.176. Cluster analysis using UPGMA on Rogers' genetic distance revealed that populations of M. laxiflora growing along riversides in the Three-Gorges Reservior area were separated into upstream and downstream groups at Baishui River, Xietan region in Hubei Province. A level of genetic diversity similar to that of natural populations was observed in the ex situ population at Wuhan Botanical Garden, so the ex situ conservation program was considered to be successful in preserving genetic diversity. Combining analysis of the genetic diversity with available information on breeding system, status of natural habitat, and evolutionary history, the causes for the endangerment of M. laxiflora are discussed. It is likely that the species gradually evolved as a relict species after the Quaternary Glaciation. Based on evaluation of the current ex situ conservation program, we suggest that similar habitats upstream and downstream of the Three-Gorges Reservoir or on nearby tributaries should be selected as ex situ conservation spots for M. laxiflora populations with high genetic diversity before their original habitats are submerged by the Three-Gorges Reservoir.

Egg banks in freshwater zooplankton: evolutionary and ecological archives in the sediment

Many representatives of freshwater zooplankton produce at some stage in their life cycle resting stages. A variable portion of the eggs of the previous growing period will hatch at the next occasion while the remaining ones are added to a persistent egg bank, where they can remain viable for decades or longer. The importance of the study of resting eggs and egg banks in general for such different disciplines as taxonomy, ecological biogeography, paleolimnology, nature conservation, evolutionary ecology and community and population ecology is generally appreciated. The major current and expected future developments in this rapidly expanding field of research are presented here. The structure and dynamics of the egg bank are determined by the life history characteristics of the species (or local population), the hatching phenology of their resting stages, and the characteristics of the habitat. The horizontal distribution of dormant stages is generally patchy, with a greater density in the deeper and/or windward parts of a pond or lake. In sediment cores, most viable (responsive) eggs occur in the upper centimeters, although vertical variation related to the history of fish predation or water quality occurs. The accumulation of resting stages of different species, generations and genotypes with variable regeneration niches results in a mixed egg bank with greater potential biodiversity than the active community sampled at any one moment. Through the benthic–pelagic coupling, this dormant reservoir may have considerable impact on the evolutionary potential of the organisms, the ecological dynamics of the community and the distribution of species. Egg banks can be considered the archive of the local habitat, since the pattern of changes in species assemblage and genotypes from the past up to the present reflect changes due to natural or anthropogenic impact that can be used to reconstruct evolutionary processes or even to restore the local habitat. Overlooking the egg bank as an important component of zooplankton communities may lead to erroneous interpretations in the analysis of community and population genetic structure. This review integrates technical and scientific information needed in the study of the structure and function of egg banks in zooplankton with special focus on the fascinating latest developments in the field.

Population and colony genetic structure of the primitive termite Mastotermes darwiniensis.

The termite Mastotermes darwiniensis is the sole extant member of its family and occupies the basal position in the phylogeny of the eusocial order Isoptera. In this study, we investigated the micro- and macrogeographic genetic structure of M. darwiniensis in its native range in Australia. A total of 1591 workers were sampled from 136 infested trees in 24 locales. Each locale was separated by 2-350 km, and these locales were found within two broader geographic regions approximately 1500 km apart. The multilocus genotypes of all termites were assayed at six polymorphic microsatellite loci. The genetic data indicated that colonies typically fed on multiple trees within locales and extended over linear distances of up to 320 m. Single colonies were frequently headed by multiple reproductives. Workers were highly related (r = 0.40) and substantially inbred (f = 0.10). Thus, M. darwiniensis colonies are characterized by the input of alleles from multiple reproductives, which sometimes engage in consanguineous matings. Our analyses of population genetic structure above the level of the colony indicated that locales and regions were significantly differentiated (theta(locale) = 0.50, theta(region) = 0.37). Moreover, locales showed a pattern of genetic isolation by distance within regions. Thus, M. darwiniensis populations display restricted gene flow over moderate geographic distances. We suggest that the genetic patterns displayed by M. darwiniensis result primarily from selective pressures acting to maintain high relatedness among colonymates while allowing colonies to grow rapidly and dominate local habitats.

Quantitative analysis of genetic parameters in populations of European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer with RAPD markers

A technique for obtaining unbiased estimates of genetic parameters (allelic frequencies of RAPD loci, heterozygosity (H), Wright's F statistic, and Nei's genetic distances) in populations of the European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer is presented. The technique employs jackknifing and multiple comparative analysis based on a modified Holmes's procedure for Bonferroni's test. It was demonstrated that samples from local groups of roe deer in the Trans-Ural region did not differ significantly in allelic frequencies (0.8, 0.81, and 0.78; P > 0.447) or Nei's genetic distances (0.0056, 0.0273, and 0.0218; P = 0.26), but they could be differentiated based on Wright's F statistic (0.0346, 0.0519, and 0.0450; P = 10(-9)). The parameters of intrapopulation heterozygosity (from 0.18 to 0.042) formed a gradient from the east to the west. Calibration estimates of molecular evolution rate in the family Cervidae obtained based on published data and Jukes-Cantor genetic distances estimated in this study demonstrated that the Siberian roe deer has split into two subspecies, C. pygargus pygargus Pall. and C. pygargus tianschanicus Satunin in the interval between 229 and 462.3 thousand years ago. The species formation of the Siberian and European roe deer was dated between 1.375 and 2.75 Myr ago. Based on the results obtained we recommend the approaches used in the study for analysis of population genetic structure and phylogenetic relationships between populations, subspecies, species, and higher taxa.

POPULATION AND COLONY GENETIC STRUCTURE OF THE PRIMITIVE TERMITE MASTOTERMES DARWINIENSIS

The termite Mastotermes darwiniensis is the sole extant member of its family and occupies the basal position in the phylogeny of the eusocial order Isoptera. In this study, we investigated the micro- and macrogeographic genetic structure of M. darwiniensis in its native range in Australia. A total of 1591 workers were sampled from 136 infested trees in 24 locales. Each locale was separated by 2–350 km, and these locales were found within two broader geographic regions approximately 1500 km apart. The multilocus genotypes of all termites were assayed at six polymorphic microsatellite loci. The genetic data indicated that colonies typically fed on multiple trees within locales and extended over linear distances of up to 320 m. Single colonies were frequently headed by multiple reproductives. Workers were highly related (r = 0.40) and substantially inbred (f = 0.10). Thus, M. darwiniensis colonies are characterized by the input of alleles from multiple reproductives, which sometimes engage in consanguineous matings. Our analyses of population genetic structure above the level of the colony indicated that locales and regions were significantly differentiated (θlocale = 0.50, θregion = 0.37). Moreover, locales showed a pattern of genetic isolation by distance within regions. Thus, M. darwiniensis populations display restricted gene flow over moderate geographic distances. We suggest that the genetic patterns displayed by M. darwiniensis result primarily from selective pressures acting to maintain high relatedness among colonymates while allowing colonies to grow rapidly and dominate local habitats.Corresponding Editor: S. Edwards

Data analysis in population genetics.I. analysis of RAPD data with AMOVA

Random Amplified Polymorphic DNA (RAPD) data have been increasingly used in studies on population and conservation genetics. Analysis of molecular variance (AMOVA) has become one of the important methods utilized in analysis of population genetic structure. Currently, WINAMOVA is the most popular software that is used for AMOVA analysis, and often runs together with RAPDistance, a software to calculate genetic distances. However,cautions should be taken when AMOVA analysis is used to process the RAPD data because of the dominant characteristic of RAPD marker and the limitation of RAPDistance. In this paper, we briefly introduce the principle and algorithm of AMOVA analysis and describe a new program, DCFA, that substitutes for RAPDistance. We also illustrate the processes of running the programs DCFA and WINAMOVA. In addition, we analyze eight Oryza rufipogon populations as an example to demonstrate how to process RAPD data with AMOVA, and discuss the results in light of population genetic structure. Finally, based on the comparison of four commonly used distance coefficients, we suggest that the coefficients of Euclidean squared distance and NEI LI rather than JACCARD are suitable for analysis of molecular variance.

Population genetic study in the Balearic endemic plant species Digitalis minor (Scrophulariaceae) using RAPD markers

Digitalis minor (Scrophulariaceae) is a cardenolide-producing plant endemic to the eastern Balearic Islands (Mallorca, Menorca, and Cabrera) that occurs in two morphologically distinct varieties: D. minor var. minor (pubescent) and D. minor var. palaui (glabrous). Levels and patterns of genetic diversity in 162 individuals from 17 D. minor populations across the entire geographic range were assessed using random amplified polymorphic DNA (RAPD) markers. Comigrating RAPD fragments tested were found to be homologous by Southern hybridization in both var. minor and var. palaui. To avoid bias in parameter estimation, analyses of population genetic structure were restricted to those RAPD bands that fulfilled the 3/N criterion (observed frequencies were less than 1 - [3/N] in each population) either among or within each island. Analyses of molecular variance (AMOVAs) with distances among individuals corrected for the dominant nature of RAPD (genotypic analysis) showed low values (1.57-17.55%) of between-population variability, indicating a relatively restricted population differentiation as expected for an outcrossing species such as D. minor. Nested AMOVAs demonstrated, however, a not significant partitioning of genetic diversity among Mallorca, Menorca, and Cabrera islands. Estimates of the Wright, Weir, and Cockerham and the Lynch and Milligan F(ST) from null allele frequencies corroborated AMOVA partitioning and provided evidence for population differentiation in D. minor. Our RAPD data did not show significant differences between pubescent and glabrous populations of D. minor, suggesting a failure to find a correlation between the RAPD loci and this morphological trait.

New polymorphic microsatellite markers for the red squirrel (Sciurus vulgaris) and their applicability to the grey squirrel (S. carolinensis)

AbstractThe geographical range of the red squirrel (Sciurus vulgaris) in Britain has decreased substantially since the introduction of the American grey squirrel (S. carolinensis). We have developed 21 novel, polymorphic microsatellite markers for S. vulgaris to enable analysis of population genetic structure in this species. All 21 markers amplify well, and are generally polymorphic in S. carolinensis, allowing a comparison of population structure of both the introduced and native squirrel species.

Enrichment and Frustration in Fieldwork

********** It was before 7:00 A.M., and already the temperature was in the low nineties. We were at least 50 miles from the nearest settlement, on a deeply rutted dirt road, bound for a remote cactus population to collect data for my master's thesis. We rounded a bend, only to find a roost with dozens of black vultures in bare trees, silhouetted against the early-morning sun. It seemed a portent of events to come. Later that day I found myself extracting spines from my backside after I tangled with a cactus that seemed to hurl its weapons at the closest bystander. We then discovered that our target cactus population was too sparse to measure with our sampling protocol. To make matters worse, a piece of critical equipment we had left in the closed car while we scouted the population had literally melted. Such were the adversities of my first field season as a biogeographer, collecting data for a study of columnar cactus distribution and demography in the northern Sonoran Desert (Figure 1). Despite numerous logistical cha llenges and physical discomfort, that fateful summer twenty-five years ago was the start of my lifelong love of field research. Since that summer I have spent part of nearly every year in the American West or Florida, collecting field data for various studies. Although most projects have focused primarily on biogeographical questions, they have been varied in other respects. The scale of inquiry has ranged from local to regional. Some projects were small, cramped by a shoestring budget and funded with only personal financial resources; others received generous external support and involved multiple principal investigators. Methodologies have included a broad array of procedures and equipment: basic censusing or sampling for distributional and demographic studies of both plants and birds, tree-core extraction for dendroecological and dendroclimatic work, collection of plant-tissue samples to analyze population genetic structure, and soil-profile description and microclimatic monitoring to relate vegetation patterns to environmental parameters. Throughout these approaches, several key themes have proved fundamental to successful field i nvestigation, and these are the focus of this essay. EXPECT THE UNEXPECTED A basic tenet of field research is that unforeseen difficulties will arise during data collection. These seem inevitable, even with thorough reconnaissance; and methodologies often have to be adjusted to accommodate unanticipated field scenarios. I remember well a frantic call to my doctoral adviser from Death Valley, California, one of the intended field sites for my dissertation research, as I fretted about how I would census birds when there was insufficient vegetation at the lowest elevations even to support a resident bird community! In that case, minor site-selection adjustments rescued the project. A less fortunate colleague of mine avoided fieldwork for the majority of his career after methodological problems rendered useless six months of field data collection for his dissertation project. Such surprises need not derail a project or redirect a career. Steps taken can reduce the probability of their occurrence and minimize their impact if they do occur. Thorough reconnaissance of potential study sites before starting data collection helps reduce unexpected problems. Merely seeing an area is not enough, however; potential study sites should be viewed with a specific research project in mind. Often, eyes that observe a landscape in a general context do not discern subtleties that are ideally perceived and registered during reconnaissance. My problems with the low elevations of Death Valley for a study site would have been avoided had I examined potential sites beforehand from the perspective of research on vegetation--bird community relationships. For many projects, and not just in physical geography, reconnaissance includes laying the necessary groundwork with appropriate governmental agencies and private landowners before data collection begins, in order to secure permission to use a study area and to arrange for logistical support. …

Variation in Shell Arching and Sexual Size Dimorphism of River Cooters, Pseudemys concinna, from Two River Systems in Alabama

LYNCH, M. 1991. Analysis of population genetic structure by DNA fingerprinting. In T. Burke, G. Dolf, A. J. Jeffreys, and R. Wolff (eds.), DNA Fingerprinting: Approaches and Applications, pp. 113-126. Birkhauser Verlag, Basel, Switzerland. PARKER, P. G., A. A. SNOW, M. D. SCHUG, G. C. BooTON, AND P. A. FUERST. 1998. What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79:361-382. PFENNIG, D. W. 1997. Kinship and Cannibalism. Bioscience 47:667-675.

DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns.

Genetic isolation among populations can be effectively investigated by multilocus DNA fingerprinting. If populations have diverged, it is expected that the mean proportion of bands shared by individuals from the same population, Bw, exceeds the corresponding mean, Bb, calculated from pairs of individuals from distinct populations. A problem arises in deciding whether any difference between Bw and Bb is statistically significant. In fact, any two band-sharing data (bij), contributing to Bw or Bb, are not independent if they share a common individual (like bij and bjl). This prevents a correct application of parametric tests, such as the Student's t-test. Recently, a modification of this test has been proposed that should avoid the independence problem. Using a large number of samples of fingerprints, simulated from an appropriate 'genetic' model, under a wide range of conditions, we compared the performances of the Student's t-test, the modified t-test and five new permutation tests, where individuals, rather than bij values, are permuted. We found that: (i) the Student's t-test can be very permissive, rejecting too often the null hypothesis when true, but is correct or conservative in certain cases; (ii) the modified t-test is extremely conservative when the null hypothesis is true and very inefficient otherwise; (iii) all five permutation tests are strictly correct, provided that individuals are ordered randomly on gels; and (iv) in this case, the permutation tests are equally efficient, and are not inferior to the Student's t-test when the latter is approximately correct and provides a fair benchmark.

RAPD variation within and among natural populations of outcrossing willow-leaved foxglove (Digitalis obscura L.)

Random amplified polymorphic DNA (RAPD) markers were used to assess levels and patterns of genetic diversity in Digitalis obscura L. (Scrophulariaceae), an outcrossing cardenolide-producing medicinal plant species. A total of 50 plants from six natural populations on the Iberian Peninsula were analysed by six arbitrarily chosen decamer primers resulting in 96 highly reproducible RAPD bands. To avoid bias in parameter estimation, analyses of population genetic structure were restricted to bands (35 of 96) whose observed frequencies were less than 1–3/n in each population. The analysis of molecular variance (AMOVA) with distances among individuals corrected for the dominant nature of RAPDs (genotypic analysis) showed that most of the variation (84.8%) occurred among individuals within populations, which is expected for an outcrossing organism. Of the remaining variance, 9.7% was attributed to differences between regions, and 5.5% for differences among populations within regions. Estimates of the Wright, Weir and Cockerham and Lynch and Milligan FST from null-allele frequencies corroborated AMOVA partitioning and provided significant evidence for population differentiation in D. obscura. A non-parametric test for the homogeneity of molecular variance (HOMOVA) also showed significant differences in the amount of genetic variability present in the six populations. UPGMA cluster analyses, based on Apostol genetic distance, revealed grouping of some geographically proximate populations. Nevertheless, a Mantel test did not give a significant correlation between geographic and genetic distances. This is the first report of the partitioning of genetic variability within and between populations of D. obscura and provides important baseline data for optimising sampling strategies and for conserving the genetic resources of this medicinal species.

Genetics of vegetative incompatibility in cryphonectria parasitica

Vegetative incompatibility in the chestnut blight fungus, Cryphonectria parasitica, in Europe is controlled by six unlinked vic loci, each with two alleles. Four previously identified vic loci (vic1, vic2, vic3, and vic4) were polymorphic in European vegetative compatibility (vc) types. Two new loci, vic6 and vic7, also were identified among European vc types. In one cross, vic genes segregated independently at five loci, and 194 progeny were assigned to 32 vc types; none of these loci were linked. A total of 64 vc types were identified from all crosses. All 64 genotypes possible from six vic loci, each with two alleles (2(6) = 64), were identified and assigned to vc types. Based on our model, vc types v-c 5 and v-c 10, which had been used in previous genetic studies, differ by only five vic genes. Future studies of vc types in C. parasitica can use knowledge of vic genotypes for analysis of population genetic structure based on vic allele frequencies and to determine the effect of each vic gene on virus transmission between vc types.

Microsatellite Variation in Two Populations of Free-Ranging Yellow Baboons ( Papio hamadryas cynocephalus )

We investigated genetic variation at six microsatellite (simple sequence repeat) loci in yellow baboons (Papio hamadryas cynocephalus) at two localities: the Tana River Primate Reserve in eastern Kenya and Mikumi National Park, central Tanzania. The six loci (D1S158, D2S144, D4S243, D5S1466, D16S508, and D17S804) were all originally cloned from and characterized in the human genome. These microsatellites are polymorphic in both baboon populations, with the average heterozygosity across loci equal to 0.731 in the Tana River sample and 0.787 in the Mikumi sample. The genetic differentiation between the two populations is substantial. Kolmogornov–Smirnov tests indicate that five of the six loci are significantly different in allele frequencies in the two populations. The mean F ST across loci is 0.069, and Shriver's measure of genetic distance, which was developed for microsatellite loci (Shriver et al., 1995), is 0.255. This genetic distance is larger than corresponding distances among human populations residing in different continents. We conclude that (a) the arrays of alleles present at these six microsatellite loci in two geographically separated populations of yellow baboons are quite similar, but (b) the two populations exhibit significant differences in allele frequencies. This study illustrates the potential value of human microsatellite loci for analyses of population genetic structure in baboons and suggests that this approach will be useful in studies of other Old World monkeys.

Inheritance of RAPD molecular makers in lake trout Salvelinus namaycush

Inheritance patterns of randomly amplified polymorphic DNA (RAPD) phenotypes were tested in 13 full‐sib families of lake trout Salvelinus namaycush. Single‐pair matings of parents with known phenotypes were made, and up to 20 progeny of each mating were used to test inheritance patterns. Seven RAPD primers amplified 13 polymorphic bands. With the exception of one family, expected segregation ratios for dominant Mendelian genetic traits were observed. Our results support previously reported findings that RAPD markers can be considered Mendelian traits and therefore could be used for analysis of genetic population structure.

Analysis of gene flow and habitat patch network for Chazara briseis (Lepidoptera: Satyridae) in an agricultural landscape

A fine geographic-scale population genetic structure analysis was performed for the endangered butterfly species Chazara briseis in the region of Halle an der Saale, Germany, for the investigation of gene flow and possible effects of habitat fragmentation on genetic variability. Patterns of genetic variance were estimated by allozyme electrophoresis and quantified with F-statistics. Levels of genetic variation were high, expected heterozygosity H e = 0.20, and mean number of alleles per locus, A = 1.93, indicating large population sizes. Butterflies inhabiting the study area probably constituted just one population and the fragmented nature of the habitat patches did not substantially affect gene flow among sites. Sampling sites were isolated by distance due to low median dispersal probabilities. This caused a micro-structure within the population and indicated that habitat patches acted as linked units with no oriented dispersal preferences of C. briseis.

How Does Immigration Influence Local Adaptation? A Reexamination of a Familiar Paradigm

How Does Immigration Influence Local Adaptation? A Reexamination of a Familiar Paradigm

Evaluating loci for use in the genetic analysis of population structure

Loci that show unusually low or high levels of genetic differentiation are often assumed to be subject to natural selection. We propose a method for the identification of loci showing such disparities. The differentiation can be quantified using the statistic F ST . For a range of population structures and demographic histories, the distribution of F ST is strongly related to the heterozygosity at a locus. Outlying values of F ST can be identified in a plot of F ST vs . heterozygosity using a null distribution generated by a simple genetic model. We use published data-sets to illustrate the importance of the relationship with heterozygosity. We investigate a number of models of population structure, and demonstrate that the null distribution is robust to a wide range of conditions. In particular, the distribution is robust to differing mutation rates, and therefore different molecular markers, such as allozymes, restriction fragment length polymorphisms (RFLPS) and single strand conformation polymorphisms (SSCPS) can be compared together. We suggest that genetic variation at a discrepant locus, Identified under these conditions, is likely to have been influenced by natural selection, either acting on the locus itself or at a closely linked locus.

Genetic analysis of population structure of tusk in the North Atlantic

To study the population structure of tusk Brosme brosme in the North Atlantic, samples from six fishing grounds were collected: St Kilda; Storegga; Faroe Islands; Rockall bank; Davis Strait and East Greenland. In addition two samples from the Norwegian coast; Kragerø and Øygarden, were included. Nine enzymes and haemoglobin were analysed by starch gel and agar gel electrophoresis. In addition isoelectric focusing (IEF) was carried out. At least 22 loci were represented. Polymorphisms were shown in eight loci and average heterozygosity was found to be about 0.05. Highest heterozygosity was found in haemoglobin analysed by Smithies buffer pH 8.6. Malate dehydrogenase (MDH‐2) analysed in IEF (pH 3.5‐9.5), and haemoglobin were found as valuable tools for studies of stock structure in tusk. In the Greenland samples only one of the MDH‐2 heterozygotes was found, while in the East Atlantic both the observed heterozygotes were more frequent. The frequencies of the the Hb*b allele were about 0.40 and 0.70 in the samples from east and west Atlantic respectively.

Phytophthora in Australia

Phytophthora spp. are one of Australia's most serious plant pathogens, causing well in excess of $200 million in lost production annually across all of our plant-based industries. Of the more than 50 species of Phytophthora recorded worldwide, over 20 are present in Australia. All species, along with their hosts, distribution and current control measures have been tabulated. Use of molecular markers to analyse population genetic structure has shown that most of these pathogens have been introduced from overseas, and become widely distributed in Australia within relatively short periods of time. The review highlights the general biology of Phytophthora spp. and their impact on agricultural production in Australia, with particular emphasis on the genetics of host/pathogen interactions, population genetic structure and reproduction of Phytophthora populations in Australia. The review highlights the role molecular technologies may play in developing an understanding of host-pathogen recognition and pathogenesis in Phytophthora. Three case histories, involving P. sojae, P. medicaginis and P. cinnamomi, have been developed to provide insights into current levels of understanding, and to identify gaps in our knowledge. Current control measures are summarized and possible new avenues of control discussed.