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PubMed2005

Genetic structure and environmental heterogeneity in the European hake (Merluccius merluccius).

This study aimed at assessing the genetic structure and the state of the stocks of the European hake (Merluccius merluccius). To this end, 15 samples were taken from the whole range of the species and analysed using allozymes. Since 11 samples were taken from the poorly studied Mediterranean Sea, the results obtained provided a complete picture of the hake's genetic structure and an initial insight into its relationships with environmental features. Atlantic and Mediterranean hake populations are separated by the Almeria-Oran front. This area has been proved to be the boundary between Atlantic and Mediterranean stocks of many marine organisms, but some doubt exists concerning the efficaciousness of the local gyres as barriers to the gene flow. Our data have evidenced a latitudinal cline at loci Gapdh and Gpi-2 within the Mediterranean Sea, with a further steep change across the Almeria-Oran front. The genetic pattern showed a strong correlation with the values of the salinity both at the surface and at -320 m and of the salinity + temperature at the surface, suggesting a role for these parameters in maintaining the genetic differentiation among the two population groups through selective processes. Finally, the levels of genetic variability were found to be slightly lower in the depleted Atlantic stock than in the Mediterranean one.

Animals↗
PubMed1980

Genetic structure of Pileolaria pseudomilitaris (Polychaeta: Spirorbidae).

The genetic structure of Pileolaria pseudomilitaris was studied by means of gene-diversity analysis of allozyme frequencies. At an esterase locus, most of the gene diversity was due to subdivision of the population into colonies and subpopulations separated by less than 100 meters. Gene frequencies at a phosphoglucose isomerase locus were similar over many kilometers, but differed between two habitat types. Differences between colonies are attributed to drift and founder effect; similarities over greater distances are attributed to similar selection pressures. A mathematical appendix details the method of gene diversity analysis for a multi-leveled, hierarchically subdivided population.

Animals↗
PubMedDate not supplied

Genetic structure of Balearic honeybee populations based on microsatellite polymorphism.

The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

Animals↗
PubMed1998

The population genetic structure of the facultatively sexual parasitic nematode Strongyloides ratti in wild rats.

We have investigated the population genetic structure of the parasitic nematode Strongyloides ratti in wild rats. In the UK, S. ratti reproduces predominantly by mitotic parthenogenesis, with sexual forms present at a rate of less than 1%. S. ratti was found to be a prevalent parasite and substantial genetic diversity was detected. Most rats were infected with a genotypic mixture of parasites. A hierarchical analysis of the genetic variation found in S. ratti sampled across Britain and Germany showed that 73.3% was explained by variation between parasites within individual hosts and 25.3% by variation between rats within sample sites. Only a small proportion (1.4%) of the total genetic variation was attributable to genetic subdivision between sample sites, suggesting that there is substantial gene flow between these sites. Most parasites sampled were found to exist in Hardy-Weinberg equilibrium and this population genetic structure is discussed in view of the virtual absence of sexual reproduction.

Animals↗
PubMed2003

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes.

We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as theta, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities.

Alleles↗
PubMed2006

Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

Alleles↗
PubMed1995

Host movement and the genetic structure of populations of parasitic nematodes.

Mitochondrial DNA (mtDNA) sequence data were used to compare the population genetic structures of five species of parasitic nematodes from three different hosts: Ostertagia ostertagi and Haemonchus placei from cattle, H. contortus and Teladorsagia circumcincta from sheep, and Mazamastrongylus odocoilei from white-tailed deer. The parasites of sheep and cattle showed a pattern consistent with high gene flow among populations. The parasite of deer showed a pattern of substantial population subdivision and isolation by distance. It appears that host movement is an important determinant of population genetic structure in these nematodes. High gene flow in the parasites of livestock also indicates great opportunity for the spread of rare alleles that confer resistance to anthelmintic drugs. All species, including the parasite of deer, had unusually high within-population diversities (averages of 0.019-0.027 substitutions per site between pairs of individuals from the same population). Large effective population sizes (Ne), perhaps in combination with rapid mtDNA evolution, appear to be the most likely explanation for these high within-population diversities.

Alleles↗
PubMed2000

Spatial genetic structure in a Neolitsea sericea population (Lauraceae).

Neolitsea sericea (Bl.) Koidz. (Lauraceae) is a dioecious, insect-pollinated, and broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, F-statistics, and spatial autocorrelation statistics (Moran's I ) to examine the changes in genetic structure among five age classes within a study population (60 m x 100 m area) in southern Korea. No significant differences in expected heterozygosity were found among the age classes. The mean F-values averaged over loci were similar among age classes and showed overall conformance of heterozygosities with Hardy-Weinberg proportions. Differences in allelic frequencies among age classes were small (mean G(ST)=0.012), and statistically significant only for one locus (Pgd-2). The mean Moran's I-values for each of five age classes indicated essentially random spatial distribution. The homogeneity of genetic structure and genetic diversity among the five age classes may reflect the occurrence of similar reproductive events, year after year. The results may reflect the attractive red drupes of N. sericea in that they cause various frugivorous birds to disperse the seed long distances and independently, which in turn may help N. sericea maintain higher levels of genetic diversity within populations.

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↗
PubMed1996

Genetic structure and parasite compatibility of Bulinus globosus (Gastropoda: Planorbidae) from two areas of different endemicity of Schistosoma haematobium in Zimbabwe.

A comparative study of the genetic structure of 8 populations of B.globosus from 2 areas of different endemicity of Schistosoma haematobium was done. Five populations were from Chiweshe (high endemicity) and three were from Plumtree (low endemicity). Genetic structure, as determined by allozyme genetics, revealed high levels of genetic variability in Chiweshe populations (Ho = 0.12-0.26) and low levels in Plumtree (Ho = 0.06-0.12). Populations from Chiweshe were genetically heterogeneous whereas in Plumtree the populations were uniform. There were significant deviations from Hardy-Weinberg proportions at different loci in Chiweshe populations. The observed excess of homozygotes was probably caused by partial selfing. The compatibility studies showed variation between allopatric and sympatric combinations of snails and parasites, and the Plumtree parasite had a significant influence on the compatibility parameters. This strain had a positive correlation (P < 0.01) of its infection rate with allele frequency of Est-2(100) and a negative correlation (P < 0.05) with allele Idh100.

Animals↗
PubMed1995

Microevolution and the genetic structure of parasite populations.

The development of polymerase chain reaction-based methods for assessing the genotypes of small individual organisms will promote groundbreaking investigations of the genetic architecture of parasite populations. Both quantitative genetic models and general knowledge of parasite natural history are useful for making general predictions about the distribution of genetic variation over geographic space. However, designing experimental studies to assess relationships between specific life history variables and patterns of genetic structure in natural populations will be challenging. Traditional biochemical-genetic methods have already been used to study a limited number of parasite populations, and inferred patterns of genetic structure are distinctly different between certain species. Some of these differences in genetic architecture may be explained by parasite or host factors that either promote or retard the dissemination of life cycle stages over geographic space. Many additional empirical studies are needed to characterize basic features of parasite populations, including the spatial distribution and group size of random mating populations and levels of gene flow among parasite subpopulations.

Animals↗
PubMed2006

Genetic structure of the star sea squirt, Botryllus schlosseri, introduced in southern European harbours.

The introduction of new genetic variants or species is often caused by maritime transport between harbours. Botryllus schlosseri is a cosmopolitan ascidian species that is found in both harbours and open shore habitats. In order to determine the influence of ship traffic on the genetic structure and phylogeography of B. schlosseri in southern Europe, we analyzed the variability of a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). We sampled seven Atlanto-Mediterranean harbour populations and three open-shore populations. In addition, we sequenced some colonies from the US-Atlantic coast and from other Mediterranean localities to perform phylogenetic analyses. Although the number of polymorphic sites recorded (25.8%) was within the range observed in other population studies based on ascidian COI sequences, the haplotypic diversity (16 haplotypes out of 181 sequences) was much lower. Moreover, a lack of intermediate haplotypes was observed. This pattern of high nucleotide diversity and low haplotype diversity was consistent with introduction events of a few divergent haplotypes. We found a strong genetic structure in the study populations. Gene flow was only appreciable between some harbour populations. Harbour- and open-shore populations were well differentiated, although there was no evidence for isolation by distance. A nested clade analysis pointed to long-distance colonization, possibly coupled with subsequent fragmentation, as the underlying process. Our results suggest that B. schlosseri entered the study area via harbour-hopping, possibly through recurrent introduction events. The haplotypes from North America and most of the European ones were grouped in the same phylogenetic clade. This suggests occasional gene flow between both continents, probably through ship transport.

Animals↗
PubMed2004

The population genetic structure of Littorina littorea (Mollusca: Gastropoda) along a pollution gradient in the Scheldt estuary (The Netherlands) using RAPD analysis.

The population genetic structure of the periwinkle Littorina littorea was analysed using random amplified polymorphic DNA (RAPD). Three primers, coding for six putative polymorphic loci were surveyed to infer the genetic structure of seven populations located along the heavily polluted Western (i.e. in order of decreasing pollution load W1, W2, W3 and R1) and the relatively clean Eastern Scheldt (E1, E2 and E3) estuary (The Netherlands). A genetic distance based UPGMA (Unweighted pair group method with arithmetic mean) dendrogram revealed an estuary-related structuring, as Eastern and Western Scheldt sites formed two separate clusters. The Western Scheldt cluster was, however, much more heterogeneous, with three RAPD loci revealing a significant genetic heterogeneity compared to none when the Eastern Scheldt sites were compared. Overall mean heterozygosity levels were high, but did not reveal a difference between the estuaries. The current data (1) confirm the patterns of variation previously observed with electrophoretic analyses of esterases and (2) strongly support that these patterns of variation have a genetic basis, in the presence of intense gene flow. In addition, it is suggested that selection, rather than bottleneck effects, induced by the less favourable living conditions at W1, W2 and W3 are responsible for the genetic patterning.

Animals↗
PubMed1999

Patterns of gene flow and population genetic structure in the canyon treefrog, Hyla arenicolor (Cope).

Patterns of gene flow and genetic structuring were examined in the canyon treefrog, Hyla arenicolor (Cope). Hierarchical analysis of genetic variation was performed on mitochondrial cytochrome b haplotypes from 323 individuals, representing 32 populations from previously described phylogeographic regions. Results from AMOVA revealed that 60.4-78.9% of the recovered genetic variation was the result of differences in the appointment of genetic variation between subdivisions of the primary phylogeographic regions. In contrast, populations only contained between 13.9 and 30.1% of the observed haplotypic variation. Gene flow estimates based on calculations of phi ST revealed moderate levels of gene flow within phylogeographic regions, but there was no evidence of gene flow between these regions, suggesting that geographical boundaries were probably important in the formation of phylogeographic structure in H. arenicolor. Phylogeographic regions exhibited very different patterns of gene flow. One region showed evidence of recent colonization. Another region exhibited very limited gene flow. Moderate to high estimates of gene flow were obtained for populations from two distinct phylogeographic regions characterized by mesic and xeric environments. Isolation by distance was observed in both regions suggesting that these regions are in genetic equilibrium. Because gene flow is extremely unlikely between the populations in the xeric region, this result is interpreted as historical gene flow. These results indicate that isolation-by-distance effects may still be observed even when population genetic structure and gene flow are the result of historical association.

Algorithms↗
PubMed2002

Historical vicariance and postglacial colonization effects on the evolution of genetic structure in Lophocereus, a Sonoran Desert columnar cactus.

Distinguishing the historical effects of gene migration and vicariance on contemporary genetic structure is problematic without testable biogeographic hypotheses based on preexisting geological and environmental evidence. The availability of such hypotheses for North America's Sonoran Desert has contributed to our understanding of the effect of historical vicariance and dispersal events on the diversification of this region's vertebrate biota but have not yet been applied to its flora. In this paper we describe a detailed allozyme analysis of the population genetic structure and phylogeography of the Sonoran Desert columnar cactus, Lophocereus schottii (senita). Inferred phylogroup distributions reflect two historical vicariance events: (1) a middle Pliocene northward transgression of the Sea of Cortéz that is reflected in well-supported Baja California peninsular and continental phylogroups but not in current taxonomic treatments of the species; and (2) a late Pliocene transpeninsular seaway across southern Baja that is reflected in tentative support for peninsular and southern Cape Region phylogroups corresponding to taxonomic varieties L. schottii var. schottii and L. schottii var. australis, respectively. A middle Pleistocene midpeninsular seaway hypothesized to explain congruent phylogroup distributions in several vertebrate taxa is not reflected in L. s. var. schottii, nor is the distinction of a third variety, L. s. var. tenuis, from continental populations of L. s. var. schottii. Linear regression of pairwise estimates of interpopulation differentiation (M and F(ST)/[1 - F(ST)]) on interpopulation geographic distance revealed significant evidence of isolation by distance within peninsular and continental phylogroups but not between them, consistent with historical vicariance between but not within these regions. We also found significant evidence of isolation by distance between putative L. s. var. schottii and L. s. var. australis phylogroups, suggesting that reproductive isolation between peninsular and Cape Region forms is incomplete. Within peninsular, but not continental, phylogroups, northward range expansion from southern Pleistocene refugia is reflected in significant declines in genetic variation with increasing latitude and in an area phenogram in which populations are progressively nested from south (ancestral) to north (descendant) along the Baja peninsula. Although the geographic concordance of phylogenetic topologies suggests that ancient vicariance events, and not dispersal, have primarily influenced the biogeographic distributions of Baja's vertebrate biota, the phylogeographic structure of L. schottii suggests that Sonoran Desert plant species may exhibit genetic signatures of postglacial range expansion and gene flow as well as vicariance.

Arizona↗
PubMed2002

Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayana.

Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self-compatible and have limited seed dispersal. However, long-lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species, Grevillea macleayana (Proteaceae), that occurs in many small populations, is self-compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long-lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found that G. macleayana may have relatively low within-population diversity (3.2-4.2 alleles/locus; Hexp = 0.420-0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation-drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire-shaped distribution, may have restricted long-distance gene flow in the past.

Alleles↗
PubMed2004

Genetic structure of desert ground squirrels over a 20-degree-latitude transect from Oregon through the Baja California peninsula.

The genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500-km transect, from 43 to 22 degrees north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome b gene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.

Animals↗
PubMed2005

Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms.

Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.

Animals↗