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PubMed1981

Population structure of multilocus associations.

A method of analysis is presented whereby the structure of multilocus associations among and within several populations can be partitioned into its components. The components are measured by their contributions to the variance in the number of heterozygous loci in two randomly chosen gametes. The singlelocus components are the average and the variation among populations in gene diversity and the variance among populations in allele frequency. The two-locus components include the mean and variance of disequilibria, the covariance of allele frequencies over populations, and various interactions. When applied to allozyme data from populations of wild (Hordeum spontaneum) and cultivated barley (H. vulgare), the analysis highlighted the repetitive pattern of the multilocus associations in the composite crosses whereas it emphasized the regionally localized and geographically variable pattern present in the natural populations of the wild species. The analysis is flexible and applicable to multilocus gametic data from any set of populations, without regard to the number of alleles per locus or the reproductive method of the organism.

Journal Article↗
PubMed2000

Molecular systematics, biogeography and population structure of neotropical freshwater needlefishes of the genus Potamorrhaphis.

Phylogenetic relationships of populations and species within Potamorrhaphis, a genus of freshwater South American needlefishes, were assessed using mitochondrial cytochrome b sequences. Samples were obtained from eight widely distributed localities in the Amazon and Orinoco rivers, and represented all three currently recognized species of Potamorrhaphis. The phylogeny of haplotypes corresponded imperfectly to current morphological species identities: haplotypes from P. guianensis, the most widespread species, did not make up a monophyletic clade. Geography played a strong role in structuring genetic variation: no haplotypes were shared between any localities, indicating restricted gene flow. Possible causes of this pattern include limited dispersal and the effects of current and past geographical barriers. The haplotype phylogeny also showed a complex relationship between fishes from different river basins. Based on the geographical distribution of clades, we hypothesize a connection between the middle Orinoco and Amazon via rivers of the Guianas. More ancient divergence events may have resulted from Miocene alterations of river drainage patterns. We also present limited data for two other Neotropical freshwater needlefish genera: Belonion and Pseudotylosurus. Pseudotylosurus showed evidence of substantial gene flow between distant localities, indicating ecological differences from Potamorrhaphis.

Animals↗
PubMed1990

Population structure of the Jirels: patterns of mate choice.

The influence of mating practices on genetic structure has been an area of great interest for anthropologists. In this paper, the techniques of potential mates analysis are employed to explore the mating patterns observed among the Jirels, a tribal population of eastern Nepal. Genealogical, anthropometric, dermatoglyphic, and demographic data for members of seven Jirel villages are used. Potential mate pools for a sample of 268 females are enumerated by village. Age structure and the Jirel restriction against clan endogamy are found to severely limit the number of males who are potential mates for a given female. The mating structure of the population is illuminated by statistical analysis of the characteristics of 160 actual mate pairs and all corresponding potential mate pairs. Using this approach several general mate choice practices were verified: 1) biological kin tend to be avoided as mates, 2) members of the same clan are excluded as potential mates, 3) mate exchange between clans is nonrandom, 4) individuals similar in age tend to be selected as mates, and 5) mates are drawn from the natal village more often than random expectation. A multivariate phenotypic distance measure between individuals did not reveal any evidence for assortative mating for either anthropometric or dermatoglyphic characters.

Age Factors↗
PubMed2005

A model for pathogen population structure with cross-protection depending on the extent of overlap in antigenic variant repertoires.

The persistence of discrete antigenic types among pathogens with multiple immunogenic loci can be explained by the action of immune-mediated competition. It has previously been shown that pathogen populations will self-organize into non-overlapping subsets of antigenic variants if cross-protection between pathogen types sharing any variants is high. Here, we examine the critical question of whether such strain structure will emerge if the degree of immune-mediated competition is dependent on the number of variants shared between pathogen types, rather than in an all-or-nothing manner. Our analysis uncovers a progression from no strain structure through to discrete stable strain structure through intermediate partially structured states. This suggests that the number of loci or epitope regions required to detect linkage disequilibrium (as a manifestation of stable discrete strain structure) in pathogen populations correlates inversely with the strength of immune selection.

Antigenic Variation↗
PubMed2005

[Population structure and community characteristics of Pseudotaxus chienii in Fengyangshan National Natural Reserve].

Pseudotaxus chienii, an endemic plant in China, is one of the second grade state protection wild plants, and distributes in Fengyangshan Natural Reserve as one of its concentrative dwelling places. A survey in the region was carried out on 10 communities, which were dominated by P. chienii. The analysis on its size structure, spatial distribution pattern and community characteristics showed that the populations of P. chienii could grow in the communities dominated by Rhododendron simiarum, Fokienia hodginsii-R. simiarum, and evergreen broad-leaved forests. In R. simiarum communities, the size structure, survival curve, and overwhelming community distribution pattern of P. chienii showed a sustaining development, while in communities dominated by F. hodginsii-R. simiarum, though the size structure was declining, the survival curve was Deevy- III type. Plenty of plantlets were still existed, and the populations kept steady. Two types were considered to be the most suitable ones for P. chienii populations. The important value of P. chienii reached 5% - 10%. In evergreen broad-leaved forests, the populations of P. chienii showed to be a declining type, and the survival curve was Deevy- II type. The distribution pattern was random, indicating that P. chienii populations could not fit for survive in this kind of communities. Correlation analysis showed that P. chienii populations had a positive correlation with R. simiarum and F. hodginsii, but a negative correlation with Cyclobalanopsis stewardiana and Schima superba. P. chienii could associate to the habits with the community canopy density of about 0.6 - 0.8. From the results mentioned above, the populations of P. chienii could be able to sustain and develop, and the existing habitat in Fengyangshan should be protected effectively. The protection of P. chienii requires more basic work to establish efficient measures to protect its habitat.

China↗
PubMed1999

Variations in cell and structure populations along the length of murine small intestine.

Previous workers have reported a range of structural variations occurring along the length of small intestine. These studies have concentrated on the major intestinal components with little information available on the intersite variation of other members of a highly heterogeneous population. Using resin histology, the current study has collected data per circumference for all definable structural features within the murine intestinal wall, along with measurements for epithelial, muscle, nerve and connective tissue areas, and villous height and cryptal depth. Seven different sites along the length of the small intestine were examined. Following statistical comparisons a number of features exhibited no intersite variation; these were numbers of villi, submucosal vessels, myenteric nerve plexus profiles, inner muscle nuclei and apoptotic bodies as well as measurements for tissue areas and cryptal depth. Variations were seen between sites for crypts, enterocytes, villous and cryptal stromal cells, cryptal goblet cells, cryptal non-secretory epithelial cells, Paneth cells, endocrine cells, intra-epithelial lymphocytes, submucosal nerve plexus profiles, outer muscle nuclei and mitotic figures. A reduced villous height was observed caudally. Certain correlations between villous height/crypt number and constituent parameters have been noted. The results provide a complete description of how each definable structural feature within the gut wall varies at regular intervals along the length of the small intestine in C57 BL mice. A number of previously unreported variations have been described. The work provides a comprehensive data bank for future intestinal investigations.

Analysis of Variance↗
PubMed1997

Genetic population structure of the Greater Bilby Macrotis lagotis, a marsupial in decline.

The Greater Bilby has shown a rapid decline in range during this century and now occupies only a small isolated area in south-western Queensland (QLD) and a larger, but mostly low-density area in the north-western deserts of the Northern Territory (NT) and Western Australia (WA). We have examined variation in the control region of mitochondrial DNA (mtDNA) and at nine microsatellite loci in order to investigate the extent of current and historical subdivision across the species range, and to provide a preliminary assessment of genetic structuring and mating system on a finer scale within the QLD population. Both mtDNA and microsatellite loci had substantial variation within and among populations, with mtDNA divergence being greater between QLD and NT than between NT and WA. The QLD population had two unique and divergent mtDNA lineages, but there was no evidence for strong phylogeographical structure across the range. The available evidence suggests that the bilby should be considered as a single Evolutionarily Significant Unit consisting of multiple Management Units. Augmentation of the remnant QLD population from the NT does not appear necessary at this stage, at least not on genetic grounds. Finer-scale analysis of microsatellite variation for two QLD colonies revealed a deficiency of heterozygotes and significantly greater relatedness within than between colonies. However, structuring was observed only for males; relatedness values for females did not depart from those expected under panmixia. Parentage exclusion analysis for one colony allowed the construction of a partial pedigree which indicated strong polygyny, with one male fathering all but one of the eight offspring assigned. The extent to which fine-scale genetic structuring and differences between sexes is due to sex-biased dispersal vs. effects of mating system remain to be determined.

Animals↗
PubMed1999

Population structure and dispersal of the saltmarsh mosquito Aedes vigilax in Queensland, Australia.

Population genetics of the mosquito Aedes vigilax (Skuse) (Diptera: Culicidae), a major vector of arboviruses (e.g. Barmah Forest, Ross River), were investigated to obtain an indirect estimate of mosquito dispersal characteristics in typical habitats of Aedes vigilax in south-east Queensland: on the off-shore islands of Moreton Bay and on the mainland where disjunct breeding populations of Ae. vigilax are distributed along intertidal marsh. Six allozyme loci were assessed for genetic differentiation between samples from 11 localities. Significant larval variation between some breeding sites was attributed to site-specific selection. Nonsignificant genetic differentiation was found among collections of adult mosquitoes caught in light traps throughout the study area (exceeding 60x27 km), indicating widespread dispersal. As distances of < or = 9 km over water did not appear to act as effective barriers to Ae. vigilax dispersal, localized control activities applied to Ae. vigilax breeding sites are unlikely to be effective against the vagile adult population. Therefore, the contiguous shires programme of broad acre control is endorsed to prevent the spread of arboviruses carried by Ae. vigilax

Aedes↗
PubMed1993

Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting.

Animals↗
PubMed2002

Great bustard population structure in central Spain: concordant results from genetic analysis and dispersal study.

We found significant sex differences in the mtDNA genetic structure and dispersal patterns of great bustards in a population of 11 breeding groups, "leks", in central Spain. The analysis of genetic distances showed that the female population was divided into three groups of leks separated by ca. 50 km, whereas male haplotypes were randomly distributed among leks. Genetic distances among pairs of leks were positively correlated with geographical distances in females but not in males. While female haplotype distributions were homogeneous among leks at close distances, differences in male genetic structure were highly variable even between two close leks. These results from genetic analyses were concordant with those from a radiotracking study on natal dispersal. Natal dispersal distances were higher in males than in females. Also, the frequency of movement of a female between two leks was positively correlated with their genetic affinity and geographical proximity. In males, the frequency of movement was correlated with geographical proximity but not with genetic affinity. Males dispersed among genetically unrelated leks, contributing to keep nuclear genetic diversity in the population, whereas females tended to be philopatric. These results suggest that isolation-by-distance influences the distribution of maternal lineages at a regional level.

Animal Migration↗
PubMed2004

Patterns of population structure in maize landraces from the Central Valleys of Oaxaca in Mexico.

Assessing the impact of farmer management of maize landraces in the Central Valleys of Oaxaca, Mexico is crucial to an understanding of maize evolution, as it was first domesticated there. In this paper, we report on the impact of traditional farmer management of maize populations in this region in structuring molecular diversity and on the population dynamics of maize landraces. These populations, from a sample of local landraces cultivated by farmers in six villages, show little among-population differentiation (Fst=0.011). Most surprisingly, there is no isolation by distance and small among-village differentiation (Fst=0.003). For an outbreeding plant such as maize, one would expect populations to fit Hardy-Weinberg equilibrium, but significant homozygote excess (Fis=0.13) was found. This homozygote excess shows remarkable interpopulation and interlocus differences. We show that this pattern is related to variation in the mean anthesis-silking interval as well as to the flowering range or heterogeneity in flowering of a given population. A short anthesis-silking interval and high level of heterogeneity in flowering precocity will favor assortative mating. This leads to a locus-dependent population substructure giving an unusual case of Wahlund effect and inbreeding while high levels of seed exchange among farmers prevent population differentiation at both village and regional levels.

Agriculture↗
PubMed2004

Estimating sex-specific dispersal rates with autosomal markers in hierarchically structured populations.

A recent study suggests that sex-specific dispersal rates can be quantitatively estimated on the basis of sex- and state-specific (pre- vs. postdispersal) F-statistics. In the present paper, we extend this approach to account for the hierarchical structure of natural populations, and we validate it through individual-based simulations. The model is applied to an empirical data set consisting of 536 individuals (males, females, and predispersal juveniles) of greater white-toothed shrews (Crocidura russula), sampled according to a hierarchical design and typed for seven autosomal microsatellite loci. From this dataset, dispersal is significantly female biased at the local scale (breeding-group level), but not at the larger scale (among local populations). We argue that selective pressures on dispersal are likely to depend on the spatial scale considered, and that short-distance dispersal should mainly respond to kin interactions (inbreeding or kin competition avoidance), which exert differential pressure on males and females.

Animals↗
PubMed2001

Effects of rumen fluid collection site on microbial population structure during in vitro fermentation of the different substrates quantified by 16S rRNA hybridisation.

Rumen fluid samples from a cow were withdrawn manually from the feed mat (solid phase) or the liquid phase below this mat and incubated in vitro with wheat straw, sorghum hay and a concentrate mixture. From the inoculum and several samples collected during in vitro incubation RNA was extracted to assess microbial population size and structure. RNA content recovered from the solid phase rumen fluid was significantly higher than from the liquid phase. The composition of the microbial population in the solid phase material was characterised by a high proportion of Ruminococci. Neither the proportion of other cell wall degrading organisms (Fibrobacter and Chytridiomycetes) nor the Eukarya and Archaea populations differed between the two sampling sites. Gas production was higher when substrates were incubated with solid phase than with liquid phase rumen fluid regardless of sampling time. However, the higher level of gas production was not accompanied by a corresponding increase in true digestibility. The RNA probes showed that during in vitro incubation with liquid phase rumen fluid, the eukaryotic population was inactive no matter which substrate was used and the activity of methanogens (Archaea) was lower than with solid phase rumen fluid. The population pattern of the cell wall degrading organisms was influenced mainly by the substrate fermented, and to a smaller extent by the inoculum used for in vitro fermentation.

Animals↗
PubMed2006

Experimental habitat fragmentation increases linkage disequilibrium but does not affect genetic diversity or population structure in the Amazonian liverwort Radula flaccida.

Habitat fragmentation increases the migration distances among remnant populations, and is predicted to play a significant role in altering both demographic and genetic processes. Nevertheless, few studies have evaluated the genetic consequences of habitat fragmentation in light of information about population dynamics in the same set of organisms. In a 10,000-km(2) experimentally fragmented landscape of rainforest reserves in central Amazonia, we examine patterns of genetic variation (amplified fragment length polymorphisms, AFLPs) in the epiphyllous (e.g. leaf-inhabiting) liverwort Radula flaccida Gott. Previous demographic work indicates that colonization rates in this species are significantly reduced in small forest reserves. We scored 113 polymorphic loci in 86 individuals representing five fragmented and five experimentally unmanipulated populations. Most of the variation (82%) in all populations was harboured at the smallest (400 m(2)) sampling unit. The mean ((+/-) SD) within-population genetic diversity (Nei's), of forest remnants (0.412 +/- 0.2) was indistinguishable from continuous (0.413 +/- 0.2) forests. Similarly, F(ST) was identical among small (1- and 10-ha) and large (> or = 100-ha) reserves (0.19 and 0.18, respectively), but linkage disequilibrium between pairs of loci was significantly elevated in fragmented populations relative to those in continuous forests. These results illustrate that inferences regarding the long-term viability of fragmented populations based on neutral marker data alone must be viewed with caution, and underscore the importance of jointly evaluating information on both genetic structure and demography. Second, multilocus analyses may be more sensitive to the effects of fragmentation in the short term, although the effects of increasing linkage disequilibrium on population viability remain uncertain.

Environment↗
PubMed1974

Population structure in relation to cost of selection.

The opposing requirements in an evolving population for a rapid rate of multiple gene substitution and for the maintenance of normal population size can be reconciled in a variety of ways. The ways out of the impasse suggested here invoke deviations from the usual assumption of a large continuous population with constant numbers. In a colonial population system there may be significant random fluctuations in the accidental mortality rate between different colonies; and those colonies with reduced numbers of accidental deaths could tolerate the larger number of selective deaths that go hand in hand with rapid evolution. In new daughter colonies founded by one or a few colonizing individuals from a large polymorphic ancestral population, some genes may reach complete fixation in one or a few generations, without the usual concomitant selective cost. Or, in the same setup, the favored alleles may change by chance from rare to moderately common, but not to complete fixation, during the founding of some daughter colonies; and this raises the allele frequencies above the low range, where the cost of selection is greatest, so that the cost of further selective changes is bearable.

Alleles↗
PubMed2005

Population structure attributable to reproductive time: isolation by time and adaptation by time.

Many populations are composed of a mixture of individuals that reproduce at different times, and these times are often heritable. Under these conditions, gene flow should be limited between early and late reproducers, even within populations having a unimodal temporal distribution of reproductive activity. This temporal restriction on gene flow might be called "isolation by time" (IBT) to acknowledge its analogy with isolation by distance (IBD). IBD and IBT are not exactly equivalent, however, owing to differences between dispersal in space and dispersal in time. We review empirical studies of natural populations that provide evidence for IBT based on heritabilities of reproductive time and on molecular genetic differences associated with reproductive time. When IBT is present, variation in selection through the reproductive season may lead to adaptive temporal variation in phenotypic traits [adaptation by time (ABT)]. We introduce a novel theoretical model that shows how ABT increases as (i) selection on the trait increases; (ii) environmental influences on reproductive time decrease; (iii) the heritability of reproductive time increases; and (iv) the temporal distribution of reproductive activity becomes increasingly uniform. We then review empirical studies of natural populations that provide evidence for ABT by documenting adaptive temporal clines in phenotypic traits. The best evidence for IBT and ABT currently comes from salmonid fishes and flowering plants, but we expect that future work will show these processes are more widespread.

Adaptation, Physiological↗
PubMedDate not supplied

[Analysis of the population structure of the South German coldblood in Bavaria, Germany].

Gene contributions of foreign populations as well as coefficients of inbreeding and relationship were calculated in 1918 South German Coldblood horses registered in Bavaria in 2003. Based on nearly complete 8-generation-pedigrees (index of pedigree completeness: 76%) the mean coefficient of inbreeding was 23%. After considering missing pedigree data, the mean coefficient of inbreeding was 3%. The rates of inbreeding per generation in the current population amount to about 0.43% over the last eight generations and to about 0.15% in the forthcoming generation. In the total current population, the mean degree of relationship was 6%. The proportion of purebred South German Coldblood horses in the current population is about 43%. As the Noric horse is of same origin as the South German Coldblood, these two breeds can be considered as an entity and thus the proportion of purebred genes in the current Bavarian South German Coldblood population reaches more than 93%. The Suffolk Punch and Thoroughbred Horse were the most important contributors to the current South German Coldblood population, whereas the Rhenish-German and Black Forest Draught Horse as well as the Percheron had neglectable influences. The effective population size in the current Bavarian South German Coldblood population is Ne = 332.

Animals↗