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PubMed1998

The effective population size of Anopheles gambiae in Kenya: implications for population structure.

We estimated current and long-term effective population size (Ne) of two Anopheles gambiae (savanna cytotype) populations in Kenya. Temporal variation at nine microsatellite loci in each population sampled 7 and 9 years apart and genetic diversity in each sample were analyzed to answer the following questions. (1) Do bottlenecks occur in Kenyan populations of A. gambiae? (2) How variable are different populations with respect to their current and long-term Ne values? (3) What are the implications of these results on population structure and history? The estimates of Ne of Asembo and Jego were 6,359 and 4,258, respectively, and the lower 95% limits were 2,455 and 1,669, respectively. Thus, despite the typical observation of low density at the village level during the dry season, large populations are maintained annually. Large current Ne is consistent with previous studies showing low differentiation across the continent, especially under Wright's isolation-by-distance model. Current Ne in Asembo was 1.5-fold higher than in Jego, but this difference was not significant. Long-term Ne in Asembo (22,667) was 2.9-fold higher than that in Jego (7,855) based on the stepwise mutation model. The difference between populations was significant at both time points regardless of whether long-term Ne values were calculated based on the stepwise mutation model or the infinite-alleles model. Heterozygosity in Jego declined significantly between 1987 (59%) and 1996 (54%), whereas heterozygosity in Asembo was stable (66%-65%). Despite the relatively high and significant differentiation between Asembo and Jego (FST = 0.072-0.10, RST = 0.037-0.038), all alleles in Jego were found in Asembo but not vice versa. All of these findings suggest that lower Ne in Jego magnifies differentiation between the two populations. The long-term Ne was biased downward, because its calculation was based on an upper bound estimate of microsatellite mutation rate. Ne values based on mtDNA and allozymes were an order of magnitude higher. Long-term Ne therefore, is probably measured in hundreds of thousands and hence does not support a recent expansion of this species from a small population.

Animals↗

PubMed2002

The distribution of Wolbachia in fig wasps: correlations with host phylogeny, ecology and population structure.

We surveyed for the presence and identity of Wolbachia in 44 species of chalcid wasps associated with 18 species of Panamanian figs. We used existing detailed knowledge of the population structures of the host wasps, as well as the ecological and evolutionary relationships among them, to explore the relevance of each of these factors to Wolbachia prevalence and mode of transmission. Fifty-nine per cent of these wasp species have Wolbachia infections, the highest proportion reported for any group of insects. Further, neither the presence nor the frequency of Wolbachia within hosts was correlated with the population structure of pollinator hosts. Phylogenetic analyses of wsp sequence data from 70 individuals representing 22 wasp species show that neither the close phylogenetic relationship nor close ecological association among host species is consistently linked to close phylogenetic affinities of the Wolbachia associated with them. Moreover, no genetic variation was detected within any Wolbachia strain from a given host species. Thus, the spread of Wolbachia within host species exceeds the rate of horizontal transmission among species and both exceed the rate of mutation of the wsp gene in Wolbachia. The presence and, in some cases, high frequency of Wolbachia infections within highly inbred species indicate that the Wolbachia either directly increase host fitness or are frequently horizontally transferred within these wasp species. However, the paucity of cospeciation of Wolbachia and their wasp hosts indicates that Wolbachia do not persist within a given host lineage for long time-periods relative to speciation times.

Animals↗

PubMed2006

[Population structure and niche of main scale insects in jujube orchards intercropped with wheat].

To effectively control the scale insects in jujube orchards, a field study was made on the population structure and niche of Pseudococcus comstock Kuwane, Ceroplastes japonicus Green and Quadraspidiotus perniciosus Comstock in the jujube orchards intercropped with wheat in Taigu area of Shanxi Province. The results showed that at the early development stage of jujube trees, these three kinds of scale insects mainly distributed on the southeast direction of the lower and central parts of the tree crown, and P. comstock was the dominant species, with a wider breadth of two-dimensional temporal-spatial niche than the other two scale insects. At the mid-stage of jujube trees development, these scale insects mainly distributed on the northwest direction of the upper part of the tree crown, C. japonicus had a wider breadth of two-dimensional temporal-spatial niche than the other two scale insects, and the niche proportional similarity and interspecific competition of the three kinds of scale insects were not obvious. At the later stage of jujube trees development, there was no significant difference (P > 0.05) in the population structure of the three kinds of scale insects on the different parts and directions of tree crown, but the density of Q. perniciosus was bigger, and C. japonicus had a wider breadth of two-dimensional temporal-spatial niche. The average values of niche proportional similarity and interspecific competition of the three kinds of scale insects were smaller (P < 0.05) at the later development stage of jujube trees. Therefore, P. comstock should be controlled at the early development stage of jujube trees, all the three kinds of scale insects should be controlled selectively at the mid-stage of jujube trees development, and their overwinterings should be decreased by all means at the later development stage of jujube trees.

Agriculture↗

PubMed2003

An RAPD (random amplified polymorphic DNA) analysis of genetic population structure of Balea biplicata (Gastropoda: Clausiliidae) in fragmented floodplain forests of the Elster/Saale riparian system.

Eight German populations of the land snail Balea biplicata (Mollusca: Clausiliidae) were studied using the randomly amplified polymorphic DNA-polymerase chain reaction and morphometrics (principal component and discriminant analysis) to examine population structure and gene flow patterns in a fragmented landscape mosaic along the Elster/Saale riparian system, Germany. A variety of population genetic analyses targeting either more on the geographic scale of gene flow (genetic distances, F statistics, Mantel test) or on local genotypic structure (heterozygosity, linkage disequilibrium, bottleneck probability) showed that (1) the population system in total is governed by high gene flow independent of geographic distance, (2) genetic structure on the narrower sampling scale is mainly determined by stochastic processes due to genetic drift in small isolated and frequently recolonized populations, and (3) the morphometrical variation of the populations was related neither to habitat nor to genetic heterogeneity. The potentials for active and passive dispersal capacity of the snails and possible environmental impacts on their population structure are discussed.

Animals↗

PubMed1995

Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci.

High levels of gene flow have been implicated in producing uniform patterns of allozyme variation among populations of many marine fish species. We have examined whether gene flow is responsible for the limited population structure in the Atlantic cod, Gadus morhua L., by comparing the previously published patterns of variation at 10 allozyme loci to 17 nuclear restriction fragment length polymorphism (RFLP) loci scored by 11 anonymous cDNA clones. Unlike the allozyme loci, highly significant differences were observed among all populations at the DNA markers in a pattern consistent with an isolation-by-distance model of population structure. The magnitude of allele frequency variation at the nuclear RFLP loci significantly exceeded that observed at the protein loci (chi 2 = 24.6, d.f. = 5, P < 0.001). Estimates of gene flow from the private alleles method were similar for the allozymes and nuclear RFLPs. From the infinite island model, however, estimates of gene flow from the DNA markers were fivefold lower than indicated by the proteins. The discrepancy between gene flow estimates, combined with the observation of a large excess of rare RFLP alleles, suggests that the Atlantic cod has undergone a recent expansion in population size and that populations are significantly displaced from equilibrium. Because gene flow is a process that affects all loci equally, the heterogeneity observed among populations at the DNA level eliminates gene flow as the explanation for the homogeneous allozyme patterns. Our results suggest that a recent origin of cod populations has acted to constrain the extent of population differentiation observed at weakly polymorphic loci and implicate a role for selection in affecting the distribution of protein variation among natural populations in this species.

Animals↗

PubMed2026

Whole-Genome Sequencing Reveals Population Structure, Genetic Diversity, and Selection Signatures in Kazakh Dromedary and Bactrian Camels.

Understanding the genomic basis of environmental adaptation is essential for the conservation and genetic improvement of domestic camels. In this study, we investigated the population structure, genetic diversity, and genomic variation potentially associated with environmental adaptation of Kazakh dromedary and Bactrian camels using whole-genome sequencing. Whole-genome sequencing data were generated for Kazakh camels (15 dromedaries and 16 Bactrian camels) and integrated with 131 publicly available genomes representing camel populations from the Arabian Peninsula, Iran, Xinjiang, Inner Mongolia, and Mongolian wild camels. Population structure, genetic diversity, and genome-wide selection were evaluated using principal component analysis, ADMIXTURE, nucleotide diversity, linkage disequilibrium, runs of homozygosity, genomic inbreeding (FROH), and selection scans based on FST, θπ ratio, and XP-EHH. Population genomic analyses revealed clear differentiation between dromedary and Bactrian camels, whereas Kazakh camel populations exhibited higher nucleotide diversity (θπ = 1.307-1.551 × 10-3), and lower genomic inbreeding (median FROH: 0.037-0.056) than Arabian populations. Genome-wide selection analyses identified MC4R as the prominent candidate gene in Kazakh dromedaries and RYR1 as a prominent candidate gene in Kazakh Bactrian camels. Functional enrichment analyses highlighted pathways related to energy metabolism, thermogenesis, calcium signaling, skeletal muscle function, mitochondrial activity, and oxidative stress response. These findings provide new insights into genomic variation potentially associated with environmental adaptation in Kazakh camels and offer valuable genomic resources for future conservation, breeding, and evolutionary studies.

MC4R↗

PubMed1987

Population structure of Sicily: beta-thalassemia and HbS.

The population structure of two alleles with similar characteristics, HbS and beta-thalassemia, was studied in the same area in Sicily. It was observed that beta-thalassemia has uniform frequencies over the island, and that HbS shows a South-North cline. A singularity exists for HbS in the town of Butera, where the frequency of the S gene is six times higher than the island average. It was suggested that HbS entered Sicily from Greece (or directly from North Africa) when the beta-thalassemia allele was already established in the Island.

Alleles↗

PubMed1997

Vaccination and the population structure of antigenically diverse pathogens that exchange genetic material.

Populations of antigenically diverse pathogens undergoing genetic exchange may be categorized into strains on the basis of a set of principal protective antigens. The extent to which polyvalent vaccines based on these protective antigens can alter the population structure of the pathogen is determined by the degree of cross-protection between strains. In the case where there is no cross-protection, vaccinating against a particular strain will have no effect on the others. As cross-protection increases, the strains containing the antigenic variants included in the vaccine will be diminished in prevalence, and those that do not will increase in prevalence. The rise in prevalence of the latter will become more and more exaggerated as cross-protection increases. However, beyond a critical level of cross-protection, in the absence of vaccination, the steady state of the system is asymmetric in that a certain subset of strains (with non-overlapping repertoires of antigenic variants) will dominate over the others in terms of prevalence. Under these circumstances, a vaccine consisting of the most immunogenic combinations of antigenic variants can cause a dramatic increase in frequency of a subset of rare strains.

Alleles↗

PubMed2003

Population structures and the role of genetic exchange in the zoonotic pathogen Cryptosporidium parvum.

Apicomplexan protozoan parasites include some of the most globally important human and animal pathogens, all of which have obligatory sexual cycles in their definitive hosts. Despite their importance and the relevance of understanding the population genetic structure and role of genetic exchange in generating diversity, population genetic analysis has largely been restricted to Plasmodium spp. and Toxoplasma gondii. These species show a considerable diversity of population structure suggesting different strategies for transmission and survival in mammalian hosts. We have undertaken a population genetic analysis of a further apicomplexan species (Cryptosporidium parvum) to extend our understanding of the diversity of genetic structures and test whether it has a clonal population structure. Nothing is known about the population structure of this parasite. We have analyzed 180 parasite isolates from both humans and cattle derived from a single discrete geographical area, using three minisatellite and four microsatellite markers that define 38 multilocus genotypes. Analysis of linkage disequilibria between pairs of loci combined with measures of genetic distance and similarity provides evidence that the sample comprises four genetically isolated populations. One group of human isolates consists primarily of two closely related multilocus genotypes (clonal), while the major subtypes of a second group, common to both humans and animals, show a panmictic population structure. The data provide an important step in understanding the role of genetic exchange in these parasites, which is an essential prerequisite for determining the value of multilocus genotyping for the analysis of sources of human infection as well as future molecular epidemiological studies.

Animals↗

PubMed2000

Quantitative dermatoglyphics and population structure in Northwest India.

The nature and extent of dermatoglyphic variation in northwest India is examined with the help of 28 quantitative variables-20 finger ridge counts and 8 palmar pattern ridge counts-among 12 endogamous populations. These populations represent the entire spectrum of ethnic and socioeconomic variation of the region and are presently distributed in three different states-Rajasthan, Punjab, and Himachal Pradesh. Of a total sample of 1,160 adult males, about 100 from each group were considered. Multiple discriminant analysis and R-matrix analysis were used to derive population relationships and patterns of external gene flow, respectively. Published data on genetic markers were reanalyzed to make the comparative evaluation of the patterns with reference to dermatoglyphs. Both the discriminant analysis and the F(ST) from R-matrix analysis suggest highly significant discrimination among the northwestern groups, whether one uses only 20 finger ridge count variables or all 28 variables, including the 8 palmar pattern ridge counts. The 8 palmar variables add very little to the variation explained by the 20 finger ridge count variables. F(ST) values suggest that the populations of Punjab are most homogeneous and those of Himachal Pradesh most heterogeneous. However, the levels of differentiation are similar for dermatoglyphs and genetic markers. The pattern of external gene flow as inferred through R-matrix analysis is consistent with the breeding and population structure of the groups, although genetic markers portray a relatively more realistic picture. Overall, the patterns of variation observed in dermatoglyphs and genetic markers are consistent with different dimensions of population structure; whereas dermatoglyphs conform more to the geographic pattern and less to ethnic resemblance, the reverse is true in the case of genetic markers. Am. J. Hum. Biol. 12:315-326, 2000. Copyright 2000 Wiley-Liss, Inc.

Journal Article↗

PubMed1988

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA.

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P approximately 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow.

Journal Article↗

PubMed1998

A modified model for projecting age-structured populations in random environments.

A discrete-time age-structured population model with vital rates linked to a stochastic environmental process was developed as a generalization of an existing model by making the explicit link between variability in the vital rates and variability in the environment more flexible. This modified model uses biologically relevant probability distributions for the vital rates, and allows for temporal autocorrelation and an arbitrary covariance structure between vital rates. Through simulations, the properties of the projected population in the short-term were investigated and compared to analytical approximations. The distribution of the total population size did not quickly approach lognormality under all conditions. Furthermore, the sensitivity of the vital rates to the environmental process had a strong effect on the variance and distribution of the projected population size. These results suggest that short-term projections need to be carried out through simulation methods, as the analytical approximations technically apply only to the long-run asymptotic behavior. Techniques for parameter estimation were considered; recommendations depend on the form of the data available. The approach described allows the empirical calculation of the probability distribution for predicted population size, a quantity relevant to the use of formal decision analysis in natural resource management.

Age Factors↗

PubMed1990

Genetic analysis of population structure in marine teleosts around Japan.

Genetic differentiation and genetic variability were estimated from data on electrophoretically detectable isozymic loci in 12 species of marine teleosts belonging to 10 families of six orders, this study permitted conclusions concerning population structures within the species of marine teleosts. As a result the 12 species could be grouped into two classes, one of which showed higher genetic diversity and included the species inhabiting coastal areas; the other showed lower genetic diversity and included the species inhabiting offshore areas and spawning free pelagic eggs. Class I and Class II could be further divided into two groups (I-1 and I-2, and II-1 and II-2) on the basis of the level of average heterozygosity. Based on the above classification and ecological characteristics, the degree of genetic differentiation may be defined mainly by the level of mixing of eggs and by fry migration, and only to a small extent by adult migration between localities. The degree of average heterozygosity should be a measure of effective population size of the breeding units within the species but not of the whole species. Putting together the above facts, six types of population structure have been proposed for marine teleosts as follows: Species in type I-1 have formed some large populations with large breeding units in offshore areas; Type I-2-1, species have formed a large number of breeding populations with relatively large effective sizes of breeding units in the coastal areas or rivers where they were hatched, even though the species may have migrated over a wide pelagic area during their juvenile to adult stages. The species in type I-2-2 would have formed a number of local subpopulations with large to intermediate breeding units in the coastal areas they inhabit. Type I-2-3 species have formed two or more completely isolated local races (or subspecies) with relatively large breeding units, but with a low level of genetic differentiation within each local race. The species in Type II-1 would have formed a single large population consisting of a few breeding units with large effective sizes in offshore areas around Japan. Type II-2 species would have formed one large population consisting of a large number of breeding units with small effective sizes in wide offshore areas around Japan.

Alleles↗

PubMed2004

A global invader at home: population structure of the green crab, Carcinus maenas, in Europe.

The European green crab, Carcinus maenas, has a native distribution that extends from Norway to Mauritania. It has attracted attention because of its recent invasions of Australia, Tasmania, South Africa, Japan and both coasts of North America. To examine the population structure of this global invader in its native range, we analysed a 502-base-pair fragment of the mitochondrial cytochrome c oxidase I (COI) gene from 217 crabs collected in the North Atlantic and 13 specimens from the Mediterranean. A clear genetic break (11% sequence divergence) occurs between the Mediterranean and Atlantic, supporting the species-level status of these two forms. Populations in the Faeroe Islands and Iceland were genetically distinct from continental populations (F(ST) = 0.264-0.678), with Iceland represented by a single lineage also found in the Faeroes. This break is consistent with a deep-water barrier to dispersal in green crabs. Although there are relatively high levels of gene flow along the Atlantic coast of Europe, slight population structure was found between the central North Sea and populations to the south. Analysis of variance, multidimensional scaling, and the distribution of private haplotypes support this break, located between Bremerhaven, Germany, and Hoek van Holland. Similar biogeographical and genetic associations for other species, such as benthic algae and freshwater eels, suggest that the marine fauna of Europe may be generally subdivided into the areas of Mediterranean, western Europe and northern Europe.

Analysis of Variance↗

PubMed2002

Fine-scale population structure and dispersal in Biomphalaria glabrata, the intermediate snail host of Schistosoma mansoni, in Venezuela.

Biomphalaria glabrata is the main intermediate host of Schistosoma mansoni in America and one of the most intensely studied species of freshwater snails, yet very little is known about its population biology. Here, we used seven highly polymorphic microsatellite loci to analyse genetic diversity in the Valencia lake basin, which represents the core of the endemic area for schistosomiasis in Venezuela. Populations were sampled at short spatial scale (a few kilometres), both inside the lake and in ponds or rivers near the lake. Our results indicate that B. glabrata essentially cross-fertilizes, with little variation in selfing rates among populations. Our markers detected considerable genetic variation, with an average heterozygosity of 0.60. More diversity per population was found within than outside the lake, suggesting an influence of connectivity among populations on the levels of genetic diversity. A marked population structure was detected and lake populations were less structured than other populations. Most individuals were assigned to their population of origin using an assignment test. No strong demographic signal (e.g. bottleneck) was detected, though lake populations are likely to experience bottlenecks more frequently than the other populations analysed. Differences in gene flow therefore seem to play an important role in population differentiation and in the restoring of genetic diversity in demographically unstable populations.

Animals↗

PubMed1994

Population structure of goat biting louse Bovicola caprae (Phthiraptera: Ischnocera).

The population structure of Bovicola caprae on goats has been recorded by examining 57 goatskins (45 by brushing cum searching and 12 by dissolving method). Population composition, sex ratio, adult nymph ratio has been recorded at different levels of infestation. The female dominated over the male population and male: female has been found to be 1:2 by brushing cum searching and 1:1.7 by dissolving method. Likewise, A:N was found to be 1:1.2 by brushing cum searching and 1:17 by dissolving method. The number of males and females follow similar pattern throughout population and were found to exhibit a high degree of correlation.

Animals↗

PubMed2005

Vocal dialects, sex-biased dispersal, and microsatellite population structure in the parrot Amazona auropalliata.

Geographic variation in microsatellite allele frequencies was assessed at nine sites in two regional vocal dialects of the parrot Amazona auropalliata (yellow-naped amazon) to test for correspondence between dialects and population structure. There was no relationship between the genetic distances between individuals and their dialect membership. High rates of gene flow were estimated between vocal dialects based on genetic differentiation. In addition, 5.5% of pairs of individuals compared across the dialect boundary were estimated to be related at the level of half siblings, indicating that dispersal is ongoing. The number of effective migrants per generation between dialects estimated with the microsatellite data was roughly one-seventh the number estimated with mitochondrial control region sequence data from the same individuals, suggesting that gene flow may be female-biased. Together, these results suggest that the observed mosaic pattern of geographic variation in vocalizations is maintained by learning of local call types by immigrant birds after dispersal. We found no evidence that ongoing habitat fragmentation has contributed to cryptic population structure.

Animals↗

PubMed2005

Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model.

Structure of Wheat streak mosaic virus (WSMV) populations derived from a common founding event and subjected to serial passage at high multiplicity of infection (MOI) was evaluated. The founding population was generated by limiting dilution inoculation. Lineages of known pedigree were sampled at passage 9 (two populations) and at passage 15, with (three populations) or without mixing (four populations) of lineages at passage 10. Polymorphism within each population was assessed by sequencing 17-21 clones containing a 1371 nt region (WSMV-Sidney 81 nts 8001-9371) encompassing the entire coat protein cistron and flanking regions. Mutation frequency averaged approximately 5.0 x 10(-4)/nt across all populations and ranged from 2.4 to 11.6 x 10(-4)/nt within populations, but did not consistently increase or decrease with the number of passages removed from the founding population. Shared substitutions (19 nonsynonymous, 10 synonymous, and 3 noncoding) occurred at 32 sites among 44 haplotypes. Only four substitutions became fixed (frequency = 100%) within a population and nearly one third (10/32) never achieved a frequency of 10% or greater in any sampled population. Shared substitutions were randomly distributed with respect to genome position, with transitions outnumbering transversions 5.4:1 and a clear bias for A to G and U to C substitutions. Haplotype composition of each population was unique with complexity of each population varying unpredictably, in that the number and frequency of haplotypes within a lineage were not correlated with number of passages removed from the founding population or whether the population was derived from a single or mixed lineage. The simplest explanation is that plant virus lineages, even those propagated at high MOI, are subject to frequent, narrow genetic bottlenecks during systemic movement that result in low effective population size and stochastic changes in population structure upon serial passage.

Base Sequence↗