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At least 757 records · Page 42Linked to original sources
PubMed1999

Estimating population structure in diploids with multilocus dominant DNA markers.

Multilocus DNA markers [random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphism (AFLPs)] are important for population studies because they reveal many polymorphic loci distributed over the genome. The markers are dominant, that is two phenotypes are distinguished at each locus, with a band and with no band. The latter one represents null-homozygotes with unamplified, recessive null-alleles. The frequency of a null-allele can be estimated by taking the square root of the fraction of individuals with no band. Lynch and Milligan (1994) have suggested a modified procedure that reduces bias introduced by the square-root transform. However, the procedure recommends to ignore those samples in which fewer than four null-homozygotes are observed. This may lead to significant bias in estimates of genetic diversity. In this study, I introduce a Bayesian approach to estimation of null-allele frequencies for dominant DNA markers. It follows from computer simulations and data on two conifer species that the Bayesian method gives nearly unbiased estimates of heterozygosity, genetic distances and F-statistics. The influence of a prior distribution and departure from Hardy-Weinberg proportions on the estimates is also considered.

Alleles↗
PubMed2002

The influence of mating system, demography, parasites and colonization on the population structure of Biomphalaria pfeifferi in Madagascar.

Current evolutionary forces and historical processes interact to shape the distribution of neutral genetic variability within and among populations. Focusing on the genetics of recently introduced organisms offers a good opportunity to understand the relative importance of these factors. This study concerns variation at 8 polymorphic microsatellite loci in 30 populations of Biomphalaria pfeifferi. The sampling area spans most of the species' range in Madagascar where it was probably introduced recently. Extremely low variation was found within all populations studied, which may partly result from high selfing rates. However, this cannot account for the variance of variation across populations, which is better explained by habitat openness (that reflects environmental stochasticity), the prevalence of the parasitic trematode Schistosoma mansoni and historical demography (colonization and subsequent bottlenecks). Large global differentiation was also observed, suggesting that current gene flow among populations is limited to small distances, within watersheds and to few individuals. Our data set also allowed us to test several hypotheses regarding colonization, based on bottleneck and admixture tests. The observed pattern requires at least two independent introductions from slightly differentiated genetic sources in the western part of Madagascar. Another introduction, from a very different genetic origin, should also be postulated to explain the genetic composition of eastern populations. That this introduction occurred recently suggests that the colonization of Madagascar by B. pfeifferi is an ongoing process.

Animals↗
PubMed2000

Population structure and history in East Asia.

Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.

China↗
PubMed2003

Population structure of Argas arboreus (Acari: Argasidae) ticks associated with seasonally abandoned mixed heronries, dominated by cattle egrets (Bubulcus ibis), in South Africa.

During winter populations of Argas arboreus from heronries of the cattle egret, Bubulcus ibis, in South Africa are composed of adults, with some predominance of males, and II-IV instar nymphs, in a state of diapause. The period of tick activity, including reproduction and development of eggs, larvae and N1 nymphs, is synchronized with the nesting and breeding season of their avian hosts. It begins during spring with the return of birds to the heronry, and ceases in autumn through induction of reproductive diapause in engorged females, and behavioural diapause in unfed nymphs and adult ticks. Many ticks showed morphological anomalies and malformations, the study of which could possibly be used for monitoring of environmental pollution.

Animals↗
PubMed1967

Population structure in the Culex pipiens complex of mosquitos.

Mosquitos of the Culex pipiens complex offer unique opportunities for study of the mechanisms that separate populations and of the possible advantages of the blood-feeding habit. C. pipiens is a polytypic species in which there are at least three major adaptations to environment. The tropical quinquefasciatus (fatigans) is a generalized blood-feeder dependent on the year-round availability of a variety of hosts. The obligate blood-feeding pipiens form of the temperate zone appears to be adapted to feeding upon nesting birds. The autogenous molestus form is essentially non-blood-feeding. Additional variants are present in different parts of the world.The variety of devices that serve to separate these different populations pose difficult problems for the taxonomist.

Animals↗
PubMed1980

[Population structure of forest Nentsee. II. Results of a geneologic study].

Inbreeding and its effect on fertility have been investigated in small (N approximately 1500) population of fisherman, hunters and reindeer breeders living in Northwestern Siberia. Average coefficient of inbreeding in total population was found to be 0.012, ranging from 0.003 to 0.016 between six subisolates. 8% of the total number of matings were matings between close relatives of uncle-niece, first cousins and double first cousins type. Nine polygamic matings were observed among presently living males belonging to elder generation. Comparative analysis of fertility in women whose reproduction had been completed was performed for 64 consanguineous and 120 non-consangineous matings. Insignificant decrease of average number of live births and surviving children was observed in matings of uncle-niece type and could be attributed to the greater number of sterile couples than in control matings. No differences have been observed when consanguineous matings of first cousins type were compared with control families with almost the same proportion of sterile couples. It can be concluded that if inbreeding has any distinct effect on fertility in families in the Forest Nentsee, this happens mainly as a result of increased proportion of sterile matings in inbred part of the population.

Consanguinity↗
PubMed1995

Population structure of Algonquian speakers.

Speakers of Algonquian languages are widely dispersed geographically but are homogeneous linguistically. We examine anthropometric differentiation among Algonquian-speaking populations distributed from New Brunswick to Montana. Head and face measurements and body measurements were analyzed separately in an attempt to address the effect of phenotypic plasticity on relationships. The head and face and body dimensions yield somewhat different pictures of relationships. From the head and face data an east to west geographic pattern can be discerned. The principal feature of the body measurements is the distinctiveness of the Ojibwa located northwest of Lake Superior. The formal correlation between the two sets of measurements is low and not significant. Only the head and face dimensions correlate significantly with geographic distances. Language distances do not correlate with anthropometric distances. The set of populations is also more strongly differentiated with respect to body measurements than to head and face measurements. We interpret this as reflecting phenotypic plasticity and possibly greater interobserver variation.

Anthropometry↗
PubMed1994

Plasmodium falciparum: the population structure of mature gametocyte cultures has little effect on their innate fertility.

In vitro cultured Plasmodium falciparum gametocytes were fed to Anopheles gambiae (G3) mosquitoes to identify parasite population characteristics useful for predicting successful mosquito infections. Parameters were collected from an initial study of 90 infections over a two year period and a second study of 55 infections over 12 weeks. Parasite isolate/clone was identified as the most reliable predictor of gametocyte infectiousness. Parameters such as gametocyte age structure (stage IV:V ratio), exflagellation rate and macrogametocyte maturity were not reliable for predicting infectiousness but were useful for monitoring overall culture maturity. Other variables such as gametocyte density, chronological age of the culture at the time of feed, gametocyte sex ratio, asexual parasitemia, and mixing cultures before mosquito feeding were not predictive. Thus, if a reliable parasite isolate or clone is used, there is no need to measure other characteristics of in vitro gametocyte populations because these will not significantly improve one's ability to predict oocyst infection rates.

Animals↗
PubMedDate not supplied

Efficiency of population structures for mapping of Mendelian and imprinted quantitative trait loci in outbred pigs using variance component methods.

In a simulation study different designs for a pure line pig population were compared for efficiency of mapping QTL using the variance component method. Phenotypes affected by a Mendelian QTL, a paternally expressed QTL, a maternally expressed QTL or by a QTL without an effect were simulated. In all alternative designs 960 progeny were phenotyped. Given the limited number of animals there is an optimum between the number of families and the family size. Estimation of Mendelian and parentally expressed QTL is more efficient in a design with large family sizes. Too small a number of sires should be avoided to minimize chances of sires to be non-segregating. When a large number of families is used, the number of haplotypes increases which reduces the accuracy of estimating the QTL effect and thereby reduces the power to show a significant QTL and to correctly position the QTL. Dense maps allow for smaller family size due to exploitation of LD-information. Given the different possible modes of inheritance of the QTL using 8 to 16 boars, two litters per dam was optimal with respect to determining significance and correct location of the QTL for a data set consisting of 960 progeny. The variance component method combining linkage disequilibrium and linkage analysis seems to be an appropriate choice to analyze data sets which vary in marker density and which contain complex family structures.

Analysis of Variance↗
PubMed2004

Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences.

The genetic relationships among northern South China Sea populations of the six bar wrasse (Thallasoma hardwicki) were investigated. Fish collected from the Solomon Islands were used for geographic comparison. In 1998 and 1999, a total of 100 fish were sampled from 6 localities of the northern South China Sea and 3 localities of the Solomon Islands. Genetic variations in DNA sequences were examined from the first hypervariable region (HVR-1) of the mitochondrial control region, as amplified by polymerase chain reaction. High levels of haplotypic diversity (h = 0.944 +/- 0.0016, pi = 0.0224 +/- 0.01171) in the HVR-1 region of the mitochondrial control region of T. hardwicki were detected. This yielded 94 haplotypes that exhibited a minimum spanning tree with a starburst structure, suggestive of a very recent origin for most haplotypes. Neutrality tests indicated that the pattern of genetic variability in T. hardwicki is consistent either with genetic hitchhiking by an advantageous mutation or with population expansion. Partitioning populations into coherent geographic groups divided the northern South China Sea samples (Phi(CT) = 0.0313, P < 0.001) into 3 major groups: a north-central group composed of northwestern Taiwan and northern Vietnam; a southwestern group containing southern Vietnam; and a southern group including the central Philippines. These results are in concordance with mesoscale boundaries proposed by allozyme markers, thus highlighting the importance of identifying transboundary units for the conservation and management of fisheries in the South China Sea.

Analysis of Variance↗
PubMed1997

Molecular advances in understanding social insect population structure.

Social insects present many phenomena seen in all organisms but in more extreme forms and with larger sample sizes than those observable in most natural populations of vertebrates. Microsatellites are proving very much more informative than allozymes for the analysis of population biological problems, and prolifically polymorphic markers are fairly readily developed. In addition, the male-haploid genetic system of many social insects facilitates genetic analysis. The ability to amplify DNA from sperm stored in a female's sperm storage device enables the determination of mating types long after the death of the short-lived males, in addition to information on the degree of mixing of sperm from different males. Mitochondrial (mt) DNA sequences are also proving important, not only in phylogenetic studies but also in molecular population genetics, as a tracer of female movements. Mitochondrial markers have definitively shown the movement of females between colonies, challenging models giving exclusive primacy to kin selection as the explanation for multiqueen colonies, in Australian meat ants, Iridomyrmex purpureus, and the aridzone queenless ant Rhytidoponera sp. 12. Microsatellite and mtDNA variation are being studied in Camponotus consobrinus sugar ants, showing an unexpected diversity of complexity in colony structure, and microsatellites have shown that transfer of ants between nests of the weaver ant Polyrhachis doddi must be slight, despite an apparent lack of hostility.

Animals↗
PubMed2026

Mitogenomic Insights Into the Population Structure and Demographic History of Tree Shrews (Tupaia belangeri) in China.

The northern tree shrew (Tupaia belangeri) exhibits significant morphological and geographical variations, but its evolutionary history and subspecies boundaries remain controversial. Here, we analyzed the complete mitochondrial genomes of 63 individuals, representing 12 populations in China to study phylogenetic relationships, genetic diversity, and population history. Phylogenetic analysis consistently restored four mitochondrial branches with strong geographic structures and significant differences. The three lineages correspond to geographically restricted subspecies (T. b. tonquinia, T. b. modesta, and T. b. gaoligongensis), while individuals assigned to several traditional subspecies cluster in a broad mainland lineage (T. b. chinensis, T. b. yunalis, and T. b. yaoshanensis). The divergence time estimate places the origin of the main lineage in the Miocene, consistent with major tectonic and geomorphological events. Demographic analysis revealed different population histories, including varying degrees of expansion in recent continental and island lineages, as well as the long-term stability of T. b. gaoligongensis. Genetic diversity varied markedly among lineages, with the highest diversity observed in the T. b. gaoligongensis and the lowest diversity observed in the T. b. modesta. These findings demonstrate that landscape complexity and demographic history are key drivers of evolutionary diversification in T. belangeri, challenging classical morphology-based subspecies classifications and underscoring the need for comprehensive sampling across both domestic and international ranges.

Tupaia belangeri↗
PubMed1985

Comparison of distance matrices in studies of population structure and genetic microdifferentiation: quadratic assignment.

Questions concerning the relative effects of various evolutionary forces in molding the genetic variability exhibited by groups of human populations have typically been investigated by comparing a variety of genetic and cultural/historical "distance" matrices. A major methodological difficulty has been the lack of formal testing procedures with which to assess the degree of confirmation or disconfirmation of an estimated measure of relationship between such matrices. In this paper, we examine a very flexible matrix combinatorial procedure which generates statistical significance levels for correlational measures of pattern similarity between distance matrices. A recent generalization of the basic procedure to the three-matrix case allows questions concerning which of two matrices best fits a third matrix to be formally tested. Applications of these hypothesis testing and inference procedures to two separate sets of genetic, geographic, and cultural distance matrices illustrates their potential for finally solving a long-standing problem in anthropological genetics.

Anthropometry↗