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PubMed1996

Phylogeography and population structure of the Atlantic and Mediterranean green turtle Chelonia mydas: a mitochondrial DNA control region sequence assessment.

Mitochondrial (mt) DNA sequences were analysed to resolve the phylogeography and population genetic structure of Atlantic and Mediterranean populations of green turtles (Chelonia mydas). Analysis of sequence variation over 487 base pairs of the control (D-loop) region identified 18 haplotypes among 147 individuals from nine nesting populations. Pairwise comparisons of haplotype frequencies distinguished most nesting colonies, indicating significant genetic differentiation among rookeries and a strong propensity for natal homing behaviour by nesting females. Comparison of control region sequence data to earlier restriction fragment length polymorphism (RFLP) data for the same individuals demonstrates approximately a sixfold higher substitution rate in the 5' end of the control region. The sequence data provide higher resolution both in terms of the number of mtDNA genotype variants and the phylogeographic relationships detected within the Atlantic region, and reveal a gene genealogy that distinguishes two groups of haplotypes corresponding to (i) the western Caribbean and Mediterranean, and (ii) eastern Caribbean, South Atlantic and West Africa. The data suggest that phylogeographic patterns in the Atlantic Ocean may be interpreted in terms of female nest site fidelity and episodic dispersal events. The distribution of mtDNA haplotypes within the region is thus explained by the geological and climatic alternations (glacial and interglacial) over the last million years.

Animals↗
PubMed2001

Comparative allozyme and microsatellite population structure in a narrow endemic plant species, Centaurea corymbosa Pourret (Asteraceae).

Centaurea corymbosa Pourret (Asteraceae) is a narrow endemic species known only from six populations located in a 3-km2 area in the south of France. Earlier field experiments have suggested that pollen and seed dispersal were highly restricted within and among populations. Consistent with the field results, populations were highly differentiated for five allozyme loci and among-population variation fitted an isolation-by-distance model. In the present study, we investigated the genetic structure of C. corymbosa using six microsatellite loci. As with allozymes, microsatellites revealed no within-population structure and a large differentiation among populations. However, allozyme loci were less powerful than microsatellites in detecting the extent of gene flow assessed by assignment tests. The patterns of structuration greatly varied among loci for both types of marker; we suggest that differences in single-locus pattern could mainly be an effect of stochastic variation for allozymes and an effect of variation in mutation rate for microsatellites. In contrast to the multilocus results, the two most polymorphic microsatellite loci did not show any isolation-by-distance pattern. Our results suggest that highly variable loci might not always be the best suited markers to quantify levels of gene flow among populations.

Asteraceae↗
PubMed1994

Anthropometric variation and population structure of the island of Pag, Croatia.

Anthropometric variation in the population of the island of Pag (eastern Adriatic, Croatia) was investigated by using data on 14 head and 24 body dimensions. The data were related to past and present migration patterns, geography, and linguistics. The analyses revealed heterogeneity among three population groups inhabiting geographically defined regions of the island and heterogeneity among the village populations. The congruence between anthropometric variation, migration history, geographic distances, and current linguistic features says much for the strength of the isolating factors on this ecologically uniform island, which have effected the genetic structure of the population.

Adult↗
PubMed1999

The effects of host heterogeneity on pathogen population structure.

We have shown that among pathogens, populations may self-organize into strains with non-overlapping repertoires of antigenic variants as a consequence of strong immune selection operating on polymorphic antigens. Recently, we have also demonstrated that over a wide range of intermediate levels of immune selection, pathogens may still be structured into discrete strains, but different sets of non-overlapping pathogen types will replace each other in a cyclical or chaotic manner. These models assume that the ranking of antigens in terms of the strength of the induced immune response is the same for every host. However, host immune responses may be restricted by the genotype of the individual. To explore this issue, a mathematical model was constructed under the assumption that a proportion of the host population responds principally to a variable antigen while the remainder of the population responds principally to a conserved antigen. The results of this analysis indicate that discrete strain structure (DSS) will be maintained even with a high frequency of hosts that do not respond in a variant-specific manner. Furthermore, the range of the immune selection pressure over which DSS prevails is increased (and the region of cyclical or chaotic behaviour reduced) by the inclusion of hosts that respond in a cross-reactive rather than a variant-specific manner.

Animals↗
PubMed1999

Population structure and gene flow of the brazilian shrub helicteres brevispira

Helicteres brevispira is a pioneer species of the tropical riparian forest whose populations appear to cycle through episodes of extinction and recolonization. Therefore, genetic consequences of founding events may strongly affect the genetic structure of its populations. An analysis of F-statistics showed that the studied population of H. brevispira is genetically substructured with the highest values of FST found in areas of high plant densities. Spatial autocorrelation analysis showed that genetic patches have diameters of 3-6 m. Although pollinator movements are usually between plants which are 3-6 m apart, longer flights occur and the neighbourhood area is estimated to have a diameter of 15 m. This suggests that genetic patches are smaller than the neighbourhood area. Seed dispersal is limited, mostly less than 2 m from the mother plants. Thus, short seed dispersal, seed dormancy and founder effects in the seed bank may be the most important determinants of genetic structure in populations of H. brevispira. Factors such as drift and inbreeding may also increase the level of substructure in this population, but the equilibrium model of isolation by distance does not fit our data.

Journal Article↗
PubMed2006

The Bacillus cereus group: novel aspects of population structure and genome dynamics.

AIMS: To provide new insights into the population and genomic structure of the Bacillus cereus group of bacteria. METHODS AND RESULTS: The genetic relatedness among B. cereus group strains was assessed by multilocus sequence typing (MLST) using an optimized scheme based on seven chromosomal housekeeping genes. A set of 48 strains from different clinical sources was included, and six clonal complexes containing several genetically similar isolates from unrelated patients were identified. Interestingly, several clonal groups contained strains that were isolated from similar human sources. Furthermore, comparative whole genome sequence analysis of 16 strains led to the discovery of novel ubiquitous genome features of the B. cereus group, such as atypical group II introns, IStrons, and hitherto uncharacterized repeated elements. CONCLUSIONS: The B. cereus group constitutes a coherent population unified by the presence of ubiquitous and specific genetic elements which do not show any pattern, either in their sequences or genomic locations, which allows to differentiate between the member species of the group. Nevertheless, the population is very dynamic, as particular lineages of clinical origin can evolve to form clonal complexes. At the genome level, the dynamic behaviour is indicated by the presence of numerous mobile and repeated elements. SIGNIFICANCE AND IMPACT OF THE STUDY: The B. cereus group of bacteria comprises species that are of medical and economic importance. The MLST data, along with the primers and protocols used, will be available in a public, web-accessible database (http://mlstoslo.uio.no).

Bacillus cereus↗
PubMed2004

Competitive exclusion and coexistence for a quasilinear size-structured population model.

We present a quasilinear size-structured model which describes the dynamics of a population with n competing ecotypes. We assume that the vital rates of each subpopulation depend on the total population due to competition. We provide conditions on the individual rates which guarantee competitive exclusion in the case of closed reproduction (offspring always belongs to the same ecotype as the parent). In particular, our results suggest that the ratio of the reproduction and mortality rates is a good measure to determine the winning ecotype. Meanwhile, we show that in the case of open reproduction all ecotypes coexist.

Animals↗
PubMed2003

Pathogen frequency in an age-structured population of Plantago lanceolata.

Life-history traits can play important roles in determining the course of ecological species interactions. We explored the consequences of host age on a host-pathogen interaction by quantifying pathogen frequency in an age-structured host population. Our project was motivated by an interest in whether the demographic structure of a host population has consequences for species interactions. In 2 successive years, we planted large cohorts of the perennial herb Plantago lanceolata in its natural environment and observed infection by Fusarium moniliforme, a non-lethal floral fungal pathogen, over 3 years. We documented substantial variation of pathogen frequency across years and between cohorts. Logistic regression revealed that pathogen frequency increased with the number of inflorescences produced and with evidence of prior pathogen presence, whereas it decreased with increasing plant longevity. In addition, interannual variation and an age-year interaction contributed to the observed pathogen frequencies. There was a significant positive effect of age on pathogen frequency overall, but this was not consistent over all ages. Pathogen frequency was higher in 2-year-old plants than in 1-year-olds, suggesting that age-structure can influence the host-pathogen interaction. This pattern did not continue into 3-year-old plants. A possible explanation for this is that selective mortality allows only generally robust plants, and consequently the most resistant plants, to survive to the oldest ages.

Ecology↗
PubMed2000

Error, population structure and the origin of diverse sign systems.

Evolutionary models of communication are used to shed some light on the selective pressures involved in the evolution of simple referential signals, and the constraints hindering the emergence of signs. Error-prone communication results from errors in transmission (in which individuals learn the wrong associations) and communication (in which signs are mistaken for one another). We demonstrate how both classes of errors are required to generate diversity and subsequently impose limits on the sign repertoire within a population. We then explore the influence of geographic structuring of a population on the evolution of a shared sign system and the importance of such structure for the maintenance of sign diversity. Deceit tends to erode conventional signs systems thereby reducing signal diversity, we demonstrate that population structure can act as a hedge against deceit, thereby ensuring the persistence of sign systems.

Animals↗
PubMed2006

Population structure between environmentally transmitted vibrios and bobtail squids using nested clade analysis.

Squids from the genus Euprymna (Cephalopoda: Sepiolidae) and their symbiotic bacteria Vibrio fischeri form a mutualism in which vibrios inhabit a complex light organ within the squid host. A host-mediated daily expulsion event seeds surrounding seawater with symbiotically capable V. fischeri that environmentally colonize newly hatched axenic Euprymna juveniles. Competition experiments using native and non-native Vibrio have shown that this expulsion/re-colonization phenomenon has led to cospeciation in this system in the Pacific Ocean; however, the genetic architecture of these symbiotic populations has not been determined. Using genetic diversity and nested clade analyses we have examined the variation and history of three allopatric Euprymna squid species (E. scolopes of Hawaii, E. hyllebergi of Thailand, and E. tasmanica from Australia) and their respective Vibrio symbionts. Euprymna populations appear to be very genetically distinct from each other, exhibiting little or no migration over large geographical distances. In contrast, Vibrio symbiont populations contain more diverse haplotypes, suggesting both host presence and unidentified factors facilitating long-distance migration structure in Pacific Vibrio populations. Findings from this study highlight the importance of how interactions between symbiotic organisms can unexpectedly shape population structure in phylogeographical studies.

Animals↗
PubMed2004

Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru).

The dispersal abilities and the population genetic structure of nematodes living in the soil are poorly known. In the present study, we have pursued these issues in the potato cyst nematode Globodera pallida, which parasitizes potato roots and is indigenous to South America. A hierarchical sampling regime was conducted in Peru to investigate gene flow on regional, field and plant scales. Multilocus genotypes of single individuals were obtained using eight polymorphic microsatellites markers. Large heterozygote deficiencies were observed at most loci. The limited active dispersal of larvae from their cyst, which favours mating between (half) siblings, could be responsible for this pattern. Within fields, as well as among fields within regions (even 35 km apart), low F(ST) values suggest extensive gene flow. Among fields within regions, only 1.5-4.4% genetic variability was observed. Passive dispersal of cysts by natural means (wind, running water, or wild animals) or by anthropogenic means (tillage, movement of infected seed tubers) is probably responsible for the results observed. Among regions, high F(ST) values were observed. Thus long-range dispersal (more than 320 km apart) is probably limited by major biogeographical barriers such as the mountains found in the Andean Cordillera. These results provide useful information for the management of resistant varieties, to slow down the emergence and spread of resistance-breaking pathotypes.

Analysis of Variance↗
PubMed2006

A multilevel approach to predict toxicity in copepod populations: assessment of growth, genetics, and population structure.

One of the goals of environmental risk assessment (ERA) is to understand effects of toxicant exposure on individual organisms and populations. We hypothesized that toxicant exposure can reduce genetic diversity and alter genotype composition, which may ultimately lead to a reduction in the average fitness of the exposed population. To test this hypothesis, we exposed a copepod, Nitocra psammophila, to a toxic reference compound and assayed resulting alterations in genetic structure, i.e. expected heterozygosity and percent polymorphic loci, as well as other population- and fitness-related measures, i.e. population abundance, demographic structure and juvenile growth. The copepods were exposed to 0.11-1.1 microg of the pentabromo-substituted diphenyl ether (BDE-47) mg(-1) freeze-dried algae for 24 days (i.e. >1 generation). There was no significant decline in total population abundance. However, there were significant alterations in population structure, manifested as diminished proportion of nauplii and increased proportion of copepodites. In addition, individual RNA content in copepodites decreased significantly in exposed individuals, indicating declined growth. Finally, in the exposed populations, heterozygosity was lower and genotype composition was altered compared to the controls. These results therefore confirm the hypothesized reduction in overall genetic variability resulting from toxicant exposure. Multilevel approaches, such as the one used in the present study, may help unravel subtle effects on the population level, thus increasing the predictive capacity of future ERA.

Animals↗
PubMedDate not supplied

Genetic structure and population history of Ireland: a comparison of blood group and anthropometric analyses.

Population structure and history may be studied on a local or a regional level. This paper examines the regional population structure of the Republic of Ireland and Northern Ireland with respect to population history and demographic processes. Blood-group and anthropometric data obtained from the literature are analysed. The blood-group data consist of ABO and Rhesus gene frequencies for 32 counties and the Aran Islands. Anthropometric data consist of summary statistics for 15 variables collected from 19 regions. The degree and pattern of population differentiation is assessed using new methods of population-structure analysis. Both blood group and anthropometric analyses show a west-east division of populations corresponding to the known history of inhabitation of Ireland, where successive waves of immigrants pushed earlier populations further west. In both analyses there were two deviations to this basic pattern: the Aran Islands and the midlands. In both cases, alternative historical explanations are examined. The genetic relationship of the Aran Islands to the rest of Ireland and England appears to be due to English admixture following the garrisoning of soldiers several centuries ago. The genetic position of the midlands is more complex, but suggests the effects of early Viking inhabitation. These findings are related to studies of the local, rather than regional, population structure of Ireland.

Anthropometry↗
PubMed2005

Population structure and stock identification of Eulachon (Thaleichthys pacificus), an anadromous smelt, in the pacific northwest.

The genetic structure of eulachon (Thaleichthys pacificus) populations was examined in an analysis of variation of 14 microsatellite loci representing approximately 1900 fish from 9 sites between the Columbia River and Cook Inlet, Alaska. Significant genetic differentiation occurred among the putative populations. The mean F(ST) for all loci was 0.0046, and there was a significant correlation between population genetic differentiation (F(ST)) and geographic distance. Simulated mixed-stock samples comprising populations from different regions suggested that variation at microsatellite loci provided reasonably accurate estimates of stock composition for potential fishery samples. Marine sampling indicated that immature eulachons from different rivers, during the 2 to 3 years of prespawning life in offshore marine waters, do not mix thoroughly. For eulachons captured incidentally in offshore trawl fisheries, there was a clear geographic cline in relative abundance of eulachons from different geographic areas. The sample from northern British Columbia was dominated by northern and central coastal populations of British Columbia, the sample from central British Columbia was composed of eulachons from all regions, and the sample from southern British Columbia was dominated by Columbia River and Fraser River populations. These results have implications for the management of trawl fisheries and conservation of spawning populations in some rivers where abundance is at historically low levels.

Alaska↗
PubMed2001

Genetic relationships and population structure of the endangered Steamboat buckwheat, Eriogonum ovalifolium var. williamsiae (Polygonaceae).

Eriogonum ovalifolium var. williamsiae (Steamboat buckwheat) is a narrow endemic subshrub, known from a single locality in Washoe County, Nevada. We examined genetic structure of the only known population by analyzing patterns of allozyme variation. Our results suggest that Steamboat buckwheat has high genetic variability, with levels of variation similar to that typical of a widespread species rather than a narrow endemic. Genotype frequencies suggest that mating is random. We detected no genetic subdivision of the population. Several clones spanning up to 67 cm were found, but we do not know if such clones are common. We used allozyme data to assess the genetic similarity of var. williamsiae to five other varieties of E. ovalifolium. All six varieties are very similar allozymically with var. williamsiae being the most similar to the widespread var. ovalifolium. Although var. williamsiae and var. ovalifolium are morphologically distinct, their genetic similarity warrants further study to determine whether or not they should be treated as separate taxa. Evidence of male sterility in var. williamsiae plus other data leads us to hypothesize that this taxon might be either a hybrid or undergoing cytoplasmic introgression. Information gathered from this study, in concert with ongoing work on the breeding system of Steamboat buckwheat, should be helpful in forming management strategies for this plant.

Journal Article↗
PubMed2006

History vs. current demography: explaining the genetic population structure of the common frog (Rana temporaria).

The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.

Alleles↗
PubMed2000

Comparative genetic diversity of parasites and their hosts: population structure of an urban cockroach and its haplo-diploid parasite (oxyuroid nematode).

Few studies have investigated the genetic structure of both host and parasite populations at a level of populations and at a level of individuals. We investigated the genetic structure of the urban cockroach Blattella germanica and its oxyuroid parasite Blatticola blattae. Random amplified polymorphic DNA (RAPD) markers were used to quantify genetic diversity between and within four populations (from two cities in France) of the host and its parasite. Diversity based on phenotypic frequencies was calculated for each RAPD marker using Shannon-Wiener's index. We used multivariate analyses to test the significance of genetic differentiation between host and parasite populations. Analysis of molecular variance was also used. Both methods gave similar results. Diversity between pairs of individuals was estimated by Nei & Li's index. Genetic diversity was higher within host or parasite populations (80% and 82%, respectively, of explained diversity) than between host or parasite populations (20% and 18%, respectively, explained diversity). The genetic distances between pairs of parasite populations (or individuals) were not correlated with the genetic distances between the corresponding pairs of host populations (or individuals).

Animals↗