Top PDF Genetic Diversity and Population Structure of Theileria annulata in Oman.

Genetic Diversity and Population Structure of Theileria annulata in Oman.

Genetic Diversity and Population Structure of Theileria annulata in Oman.

Mixed genotypes in the bovine host can be considered a pre-requisite for cross-mating and recombination of T. annulata in the vector. Thus, co-uptake of piroplasm/ gametocytes repre- senting distinct genotypes by the feeding tick may result in cross- fertilisation and the forma- tion of heterozygotes following syngamy. Genetic recombination then occurs in the tick gut leading to the generation of novel genotypes [32, 33]. Assuming random pairing of male and female gametes, the frequency of recombinant types equals the probability that these gametes are sampled from different clones carried in a single animal. Thus, the probability of inbreeding can be related to the numbers of genotypes detected per infection, assuming that all blood form parasites are represented in the gametocyte population [34]. Such an approach has been vali- dated in the malaria parasite [34, 35]. Extrapolating this method for multiplicity of T. annulata in Oman provides estimates for effective number of clones (ne) of 3.35 and inbreeding of 0.3 (f = 1/ne) [34, 35]. This provides a measure of a high extent of outcrossing of over 50%, which may have important implications for the success of control measures. In particular, new anti- genic types, distinct form vaccine genotypes, may be formed and recombination of drug resis- tant loci may increase the spread of resistance and the risk that multiple drug resistant genotypes will be produced.
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Genetic diversity and population structure in the iberian endangered Iberochondrostoma lemmingii (Steindachner, 1866)

Genetic diversity and population structure in the iberian endangered Iberochondrostoma lemmingii (Steindachner, 1866)

7 for conservation. Nevertheless, its use has been criticized, in particular, when ESUs are defined solely on neutral molecular markers that ignore adaptive differences (Frankham et al., 2004), meaning that populations with high degree of genetic flow, but with significant adaptive differences, would be treated as a single unit when they might require a separate management. The opposite might also occur: populations with low levels of genetic flow and high genetic differentiation, but with no adaptive differences, would be considered as distinct units when they might benefit from a single management strategy (Moritz, 1994). Another problem with Moritz definition of ESU resides in its dichotomous nature of “ESU or not”. In order to circumvent this, Crandall et al., (2000) proposed a system of discerning populations units based on eight categories of population distinctiveness. Depending on the magnitude of distinctiveness, each population or group of populations is assigned to a particular category that has specific management recommendations based on recent or historical exchangeability. Despite its limitations, in this work, we will use Moritz definition of ESU as it is the most commonly applied and the one that as been used to address conservation studies in Iberian cyprinids.
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Population structure and genetic diversity of the giant anteater( Myrmecophaga tridactyla : Myrmecophagidae, Pilosa) in Brazil

Population structure and genetic diversity of the giant anteater( Myrmecophaga tridactyla : Myrmecophagidae, Pilosa) in Brazil

varied from dry skin (museum), to hair, bone and soft tissues. The original samples were collected from captive individuals of known origin, wild animals captured for eco- logical studies, road-killed individuals, and museum col- lection vouchers. All tissue samples were preserved in 95% ethanol, and stored in -20 ºC. The samples covered the pop- ulations of (i) Minas Gerais state (CEMG, n=21), compris- ing individuals from the National Park of Serra da Canastra and other localities, (ii) Goiás state (CEGO, n=28) com- prising individuals from the National Park Emas, (iii) dif- ferent localities in São Paulo state (CESP, n=7) and (iv) Mato Grosso state (CEMT, n=4), all representative of the biome Cerrado (CE). Additionally, a population from the Atlantic Forest of Paraná state (AF, n=5), from the Pantanal biome (PT, n=5) of Mato Grosso and Mato Grosso do Sul states, and individuals from the Amazon Forest (AM, n=8) were also sampled. Sampling localities are displayed in Figure 1, and details regarding samples are available in Ta- ble S1 from Supplementary Material.
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Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

Due to its offshore position—5 km from Saba Island—and upper-mesophotic reef system (20–50 m deep), Saba Bank coral reefs appear to have suffered relatively little anthropogenic disturbance compared to the fringing reefs of the surrounding islands. This is reflected, for instance, by the relative absence of diseases [4, 5, 9], as well as the presence of large predators (e.g. sharks, groupers and snappers) [8, 10], suggesting Saba Bank could fulfill an essential role in the resilience of nearby reefs as a source of larvae and genetic diversity. Coral reef organisms are strongly dependent on recruitment from surrounding reefs after local disturbances (e.g. hurricanes) [11]. Understanding patterns of connectivity is therefore essential to implement effective reef conservation strategies [12]. If Saba Bank is to serve as a reservoir of diversity for the surrounding reefs, it is important to understand how populations on the bank are posi- tioned in the genetic structure of the wider Caribbean populations and how stress and diseases are currently affecting the populations. The aim of the current study was to examine the genetic connectivity, density, and health status (i.e. presence of diseases or traces of recent bleaching) of populations of two prominent benthic reef species on Saba Bank; the star coral, Montastraea cavernosa (Linnaeus 1767), and the giant barrel sponge, Xestospongia muta (Schmidt 1870). Both species have been recorded on Saba Bank in surveys since the 1970s [3, 5, 9].
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Conservation biology of the caracal (Caracal caracal) in Iran: action plan and conservation genetics

Conservation biology of the caracal (Caracal caracal) in Iran: action plan and conservation genetics

The caracal is the third biggest of the eight felids present in Iran after the leopard and the cheetah. Its habitat is mostly arid areas and it has a key role in the control of rodent populations. The conservation status of caracal populations is not clear across most of the range, but the Asiatic population is threatened and listed in CITES appendix I. The main threats for the caracal are habitat loss and human conflict due to frequent livestock attacks. Lack of knowledge about the caracal and the unknown impacts of the conflict on its population may drive the species to an endangered situation. The main goals of this study are to review the biology, conservation status and conflict with humans of the caracal in Iran, suggest practical measures to reduce such conflict, and conduct a preliminary genetic study. The suggested conservation measures include improving the livestock husbandry system to avoid attacks, predation and thus conflict, education of the local people about carnivores and their importance, and promoting their participation in conservation actions. Genetic diversity and structure in Iran was analyzed based on 24 samples from six provinces. Mitochondrial DNA (mtDNA) and four microsatellite markers were used to assess genetic variation and the results indicated low mtDNA diversity, possibly due to a historical bottleneck of a reflection of the colonization (founder effect and serial bottlenecking) of the Middle East from Africa, or alternatively to the low mutation rate of the genes studied. Forensic genetic analyses of hair and saliva from wounds of livestock carcasses to identify predator species is also recommended to provide insight on the dimension of the conflict. The conservation genetics study initiated here is a starting point for subsequent work with additional samples from across Iran and more microsatellite markers.
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Moraes-Barros, N.a , Miyaki, CY.b and Morgante, JS.a

Moraes-Barros, N.a , Miyaki, CY.b and Morgante, JS.a

In this study we propose the analysis of genetic diversity of the common three-toed sloth, Bradypus variegatus, in an attempt to understand population structure, identify divergent intraspecific units, and contribute to the knowledge of biodiversity in the neotropical forests. We analyzed a 387 bp segment of the mitochondrial DNA control region in 28 individuals distributed in different localities of both Atlantic and Amazon forests. Our results demonstrated that the genetic diversity of B. variegatus is distributed in six management units, MUs. The observed MUs encompass six phylogenetic lineages and represent respectively north and south regions of Atlantic forest, three regions within the Amazon forest, and a transition region between these two biomes. Considering the fact that these MUs are concord- ant with phylogroups and endemism areas already described for other vertebrate species, we can say that the study of B. variegatus, a widely distributed and not endangered species, can help to identify areas for conservation biology purposes in neotropical rain forests.
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Genetic associations in the detection of QTLs for wheat spike‑related traits

Genetic associations in the detection of QTLs for wheat spike‑related traits

Abstract – The objective of this work was to assess the genetic diversity and population structure of wheat genotypes, to detect significant and stable genetic associations, as well as to evaluate the efficiency of statistical models to identify chromosome regions responsible for the expression of spike-related traits. Eight important spike characteristics were measured during five growing seasons in Serbia. A set of 30 microsatellite markers positioned near important agronomic loci was used to evaluate genetic diversity, resulting in a total of 349 alleles. The marker-trait associations were analyzed using the general linear and mixed linear models. The results obtained for number of allelic variants per locus (11.5), average polymorphic information content value (0.68), and average gene diversity (0.722) showed that the exceptional level of polymorphism in the genotypes is the main requirement for association studies. The population structure estimated by model-based clustering distributed the genotypes into six subpopulations according to log probability of data. Significant and stable associations were detected on chromosomes 1B, 2A, 2B, 2D, and 6D, which explained from 4.7 to 40.7% of total phenotypic variations. The general linear model identified a significantly larger number of marker‑trait associations (192) than the mixed linear model (76). The mixed linear model identified nine markers associated to six traits.
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Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola

Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola

Figure 1. Flowchart illustrating the selection of the studied sample of M. tuberculosis clinical isolates and, main results from drug susceptibility testing and genotyping. From the 106 sputum samples positive for acid-fast bacilli, 7 were excluded since they were duplicates from the same patient, 5 were contaminated and another 5 showed no growth, leaving a total of 89 M. tuberculosis clinical isolates. Drug susceptibility testing revealed that 22 isolates were resistant to one or more antibacillary drugs, of which four corresponded to MDR-TB isolates. Genotyping analysis allowed the identification of 13 clustered isolates across five different MIRU-VNTR clusters with one isolate excluded due to mixed strain infection. Spoligotyping analysis revealed a population structure dominated mostly by LAM and T strains.
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Filogeografia global da tartaruga oliva (Lepidochelys olivacea)

Filogeografia global da tartaruga oliva (Lepidochelys olivacea)

The olive ridley is the most abundant species of marine turtle but had a strong history of harvest in the Atlantic Ocean, with some populations being severely depleted. In Brazil egg exploitation was intense before 1982, but population is recovering. However, so far a single study with a very low sample size and exclusively mtDNA investigated the species´ genetic diversity in the region. Here we characterize the olive ridley genetic diversity and population structure in the main nesting areas in the Brazilian coast using 92 mtDNA control region sequences and 67 individuals genotyped for fifteen microsatellite loci. The Brazilian nesting population presented one of the lowest mtDNA diversities known for the species, with only three haplotypes, two previously unknown and very rare. Contrarily, microsatellite data showed relatively high genetic diversity, similar to other few olive ridley nesting populations studied so far, suggesting that the high level of egg harvest in Brazil did not result in a significant genetic bottleneck. MtDNA data indicated an ancient population expansion from a small population, supporting the scenario of colonization of Atlantic Ocean via a founder effect while microsatellite data suggested recent demographic stability. Although we did not detect genetic structure in the Brazilian coast, a marginally significant differentiation between some rookery areas with the microsatellite data in some analyses, together with recent tagging data that indicate high female site fidelity, suggest that genetic differentiation between rookeries promoted by female fidelity may have been constrained by male gene flow.
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GENETIC DIVERSITY AND POPULATION STRUCTURE OF JATOBÁ: A SPECIES WITH ECONOMIC POTENTIAL FOR THE AMAZON REGION

GENETIC DIVERSITY AND POPULATION STRUCTURE OF JATOBÁ: A SPECIES WITH ECONOMIC POTENTIAL FOR THE AMAZON REGION

Jatobá (Hymenaea courbaril L.) is a species that shows ecological importance and occurs in different geographic regions in Brazil. Knowing and evaluating the existence of places with higher genetic variability can help in conservation programs and actions. In this context, the present study aimed to evaluate the genetic diversity and structure in natural populations of Jatobá with occurrence in Mato Grosso Amazon through ISSR markers. Fifty-four individuals were sampled in three populations, being one in the municipality of Marcelândia (MA=24) and two in the municipality of Alta Floresta (Comunidade Central AF=17 and Pista do Cabeça PC=13 individuals). Total genomic DNA was extracted from the leaf tissue by the CTAB method. The 54 individuals were genotyped with 10 ISSR primers. A total of 110 fragments were amplified, being 78.2% polymorphic. The greatest diversity indices were found in the population from MA (H=0.25; I=0.37 and %P=65.45). The genetic distance was higher among the populations of the two municipalities (0.17 between MA and AF; 0.16 between MA and PC). The analysis of molecular variance (AMOVA) indicated that 31.79 % of the total variance is among populations and 68.21 % within populations. There is genetic diversity in native populations of Jatobá in Mato Grosso Amazon. We recommend that individuals from both populations be preserved, in order to ensure the maintenance of genetic variability and the effective conservation of species in Mato Grosso Amazon.
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Development and application of microsatellites in plant breeding

Development and application of microsatellites in plant breeding

ABSTRACT - Molecular markers are powerful tools for analyzing genome diversity within a species, and to evaluate genetic relationships between individuals and populations. Among them, microsatellites (SSRs) are one of the most important polymorphic markers that can be used effectively to distinguish germplasm accessions. These markers present high informative content due to their codominant inheritance, multiallelism, mendelian pattern and good genome coverage. The enrichment methodology for microsatellite development has a superior efficiency in plants, especially when performed using biotin-labeled microsatellite oligoprobes and streptavidin-coated magnetic beads. The development of EST-SSR markers has become a fast and relatively inexpensive way but it is limited to species for which this type of database exists. Given the high polymorphism level of microsatellites when compared to other markers, SSRs have been used to study population structure, for genetic diversity analysis, genetic mapping and marker assisted selection.
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Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its

However, this “reproductive waves” behavior would imply the existence of two populations in the Magdalena River basin. The third population detected by the Bayesian analysis could be a consequence of the repeated restocking programs conducted in this basin. Machado-Schiaffino et al. (2007) provided evidence of significant genetic varia- tion losses in Atlantic salmon stocks (Salmo salar) created for supportive breeding in which the juveniles released in the rivers possessed significantly lower allelic richness than the wild stocks. The cultivated population of Brycon opalinus also presented heterozygosity reduction, indicat- ing a loss of genetic variability in the reproductive supply currently kept in the hatchery (Barroso et al., 2005). A simi- lar trend was reported by Matsumoto and Hilsdorf (2009), in which the broodstock of B. insignis kept at the hatchery has likely maintained the genetic diversity formerly present in some rivers and no longer existing in natural populations. Further studies may clarify whether the broodstock used in stocking programs has influenced the genetic structure and diversity of the P. magdalenae population in the Magda- lena basin.
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GENETIC STRUCTURE OF NATURAL POPULATIONS OF CRYPTOCARYA MOSCHATA NEES (LAURACEAE) FROM SOUTHEASTERN BRAZILIAN ATLANTIC RAIN FOREST

GENETIC STRUCTURE OF NATURAL POPULATIONS OF CRYPTOCARYA MOSCHATA NEES (LAURACEAE) FROM SOUTHEASTERN BRAZILIAN ATLANTIC RAIN FOREST

fˆ = 0.097. These results indicated that individuals within populations must be panmitic, and that the diversity among populations is fairly high, being superior to what would be expected for groups of plants having a full-sib family structure. From estimates of θ ˆ P obtained for populations taken two at a time, the model of isolation by distance was tested; data did not fit the model, showing that ˆ θ P did not increase by the respective increasing of the geographic distance. The estimated gene flow of 0.55 migrants per generation corroborated the pronounced populational differentiation, indicating that drift effects should be more important than the selection ones. The effective population sizes found from the sampled popula- tions showed that there was an adequate genetic representativeness of the samples for those with relatively low values of fˆ . Though, under a metapopulation context, the effective population size was 17.07 individuals, indicating that sampling performed for the species corresponded to 88.44% of the maximum effective size obtained from 11 populations with a θ ˆ P of 0.285, equivalent to only 5.09% individuals for the total sampled. Management and conservation strategies aimed at preserving high intrapopulation genetic variation in C. moschata would imply in the maintenance of populations with great number of individuals. Moreover, for the preservation of the species as a whole, the maintenance of many such populations would be mandatorily recommended, which denotes that the conservation of large areas of Atlantic rain forest should be necessary to hold its evolutionary dynamics.
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Spatial genetic structure in natural populations of Phragmites australis in a mosaic of saline habitats in the Yellow River Delta, China.

Spatial genetic structure in natural populations of Phragmites australis in a mosaic of saline habitats in the Yellow River Delta, China.

a correlation between genetic diversity and environmental heterogeneity in common reed populations [86,87,88,89], but very few studies have explicitly tested the causal environmental factors behind the pattern of genetic variation. This situation is largely due to the fact that environmental heterogeneities were mostly ill-defined in the earlier studies, leading to the uncertainty in selective agent predictions. Spatial analysis of population genetic structure in mosaic environments, from the perspective of landscape genetics, can not only help reveal the potential of dynamic adaptation of organisms to changing environments, but may also contribute to the identification of environmental factors that structure intraspecific genetic diversity, which are of interest for both conservation and ecological restoration. Although such an analysis may just represent the first step in the study of local adaptation, and the results alone are merely correlative, not de facto evidence of adaptive differentiation, it is efficient to identify subtle population structure and concomitant environmental variation representative of a potential selection gradient, to facilitate a further analysis and test of adaptation [90]. In conclusion, our findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.
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Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Results: Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.
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Raoni Gwinner1 , Tesfahun Alemu Setotaw1

Raoni Gwinner1 , Tesfahun Alemu Setotaw1

Abstract: Genetic diversity is an essential factor for the success of any plant breeding program and should be considered to ensure genetic gain through breeding. In Brazil, research on the genetic diversity and population structure of soybean is required since the species is an important commodity of the country. The study addressed the genetic diversity and population structure of 77 soybean genotypes using 35 SSR markers. The estimate of the diversity index showed that the level of genetic diversity in the soybean collection is low. Similarly, the Jac- card coefficient and Bayesian model based on clustering analysis confirmed the low diversity among soybean genotypes, providing evidence for the assumption of a genetic bottleneck effect on Brazilian soybean genotypes. The results also reinforced the importance of finding and incorporating new genetic resources of soybean in the genetic pool of Brazilian soybean to warrant genetic gain in soybean breeding in the future.
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Genetic population structure and connectivity of Azorean limpets

Genetic population structure and connectivity of Azorean limpets

There is growing consensus that anthropogenic activities significantly disrupt the structure and functioning of marine ecosystems. Oceanic islands such as the Azores (NE Atlantic) are unique habitats with fragile communities, which are highly susceptible to degradation and ecosystem disruption. Patellid limpets have traditionally been collected as a food resource and in 1988 the limpet fishery in São Miguel Island collapsed, and after which a one-year ban was implemented allowing the stocks to recover and avoiding catastrophic overexploitation effects. In 1993, legislation was passed to protect this resource, i.e. limpet no-take areas were created, seasonal harvesting restrictions were applied and minimum legal catch sizes were established. However, a recent survey has shown that limpet populations still show clear signs of overexploitation and some populations are virtually extinct in some islands. Here we have developed new multiplexed and described microsatellite markers for the species Patella aspera and P. candei and have examined their genetic diversity, gene flow and population connectivity in the Azores Archipelago. Overall, such information is a fundamental asset to inform conservation strategies and to promote the sustainable exploitation of macaronesian limpets.
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Genetic structure from the oldest Jatropha germplasm bank of Brazil and contribution for the genetic improvement

Genetic structure from the oldest Jatropha germplasm bank of Brazil and contribution for the genetic improvement

Currently, one of the most efficient techniques for the genetic characterization of germplasm collections is the use of molecular markers. Molecular markers can detect genetic differences at the DNA level and in contrast to phenotypic evaluations, they are not affected by environmental factors. Among the molecular markers available, microsatellites or SSRs (simple sequence repeats) and ISSRs (inter simple sequence repeats) are widely used to study the genetic diversity and population structure of many plant species. SSR markers are codominant and multiallelic, whereas ISSR markers are dominant and multilocus (Borém and Caixeta 2009, Faleiro 2007). The combination of two molecular markers can provide a more accurate inference regarding the genetic and genomic composition of a germplasm collection.
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High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae-Perciformes), in the western South Atlantic revealed through multilocus analysis.

High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae-Perciformes), in the western South Atlantic revealed through multilocus analysis.

In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yel- lowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the in- vestigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single ge- netic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscilla- tions at the end of the Pleistocene. In addition, this species is intensively exploited by com- mercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans.
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Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

positively and significantly correlated with geographic distance (r = 0.56, P,0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.
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