Amount Of Genetic Differentiation Research Articles

High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California

Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment efforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, salt marsh bird’s-beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration efforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the range of this subspecies in southern California, and three additional occurrences from Baja California, Mexico. We used flow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found five distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These findings can bolster management and restoration efforts by identifying potentially isolated occurrences and areas that are the richest sources of allelic diversity, and by providing insight into the amount of genetic differentiation across the taxon’s range.

Genome-wide population structure and genetic diversity of Japanese whiting (Sillago japonica) inferred from genotyping-by-sequencing (GBS): Implications for fisheries management

Japanese whiting (Sillago japonica) is a relatively common marine fish inhabiting in the coastal shallow waters and the target species in an important commercial and recreational fishery. In this study, eighty-three specimens in five sites were collected along coasts of China and Japan, and genotyping-by-sequencing (GBS) technology was carried out to investigate the genetic structure and difference among them. Consistent with prior research conclusions, a relatively high genetic diversity was detected in S. japonica, and an increasing tendency of genetic variation level was detected as the latitude decreased in Chinese populations. Although estimated value of pairwise population differentiation (FST) was low, the genetic heterogeneity analysis demonstrated a certain amount of genetic differentiation among local populations of S. japonica. Samples from Rushan were differentiated from other Chinese populations, but closely correlate with Ise Bay (IB) and Tokoy Bay (TB) populations, indicating gene flow between Rushan population (RS) and Japanese populations to a certain extent. Isolation by distance (IBD) analysis showed that genetic differentiation was significantly affected by geographical isolation. While, the results of isolation by environment (IBE) test showed that genetic distance was correlated with seawater salinity, which might be a selective pressure promoting genetic variation in S. japonica. Given the complex pattern of genetic differentiation of Japanese whiting among Chinese and Japanese populations, we suggested treating them as different management units in utilization of offshore fisheries resources.

Molecular evidence on evolutionary switching from particle-feeding to sophisticated carnivory in the calanoid copepod family Heterorhabdidae: drastic and rapid changes in functions of homologues

ABSTRACTThe oceanic calanoid copepod family Heterorhabdidae is unique in that it comprises both particle-feeding and carnivorous genera with some intermediate taxa. Both morphological and molecular (nuclear 18S and 28S rRNA) phylogenetic analyses of the family suggest that an evolutionary switch in feeding strategy, from transitions of typical particle-feeding through some intermediate modes to sophisticated carnivory, might have occurred with the development of a specially designed ‘poison’ injection system. In view of the small amount of genetic differentiation among genera in this family, the switching of feeding modes and re-colonization from deep to shallow waters might have occurred over a short geological period since the Middle to Late Miocene.

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of F(ST).

Loci responsible for local adaptation are likely to have more genetic differentiation among populations than neutral loci. However, neutral loci can vary widely in their amount of genetic differentiation, even over the same geographic range. Unfortunately, the distribution of differentiation--as measured by an index such as F(ST)--depends on the details of the demographic history of the populations in question, even without spatially heterogeneous selection. Many methods designed to detect F(ST) outliers assume a specific model of demographic history, which can result in extremely high false positive rates for detecting loci under selection. We develop a new method that infers the distribution of F(ST) for loci unlikely to be strongly affected by spatially diversifying selection, using data on a large set of loci with unknown selective properties. Compared to previous methods, this approach, called OutFLANK, has much lower false positive rates and comparable power, as shown by simulation.

Impact of Geographical Isolation on Genetic Differentiation In An Insular Population of the Carpet ShellRuditapes decussatusin the Mediterranean Basin

ABSTRACT Genetic variation was investigated using allozymes, cytochrome c oxidase subunit I, internal transcribed spacer region 1, and microsatellite markers in mainland and insular populations of the carpet shell Ruditapes decussatus from the western and eastern Mediterranean Basin. Five morphometric parameters and weight of valves were also used to study the distribution of variation within and among populations. The species is characterized by a relatively high inter- and intrapopulation morphological and genetic variability. The highest values of percent polymorphism and heterozygosity (allozyme and microsatellite data) were found in the sample from Kerkennah Island. The occurrence of higher levels of genetic variability in insular population is probably because this population inhabit marginal environment characterized by temporal-ecological instability. The genetic heterogeneity analysis demonstrates a certain amount of genetic differentiation among local populations of R. decussatus with a relative...

Influence of stocking history on the population genetic structure of anadromous alewife (Alosa pseudoharengus) in Maine rivers

Stocking programs have been used extensively to mitigate declines in anadromous fishes, but these programs can have long-term unintended genetic consequences. Stocking can homogenize population structure, impede local adaptation, and hinder the use of genetic stock identification as a fishery management tool. Using 12 microsatellite loci, we evaluate the spatiotemporal genetic structure of 16 anadromous alewife (Alosa pseudoharengus) populations in Maine, USA, to determine whether inter-basin stocking practices have influenced population structure and the genetic diversity of the species in this region. Although, no pre-supplementation samples exist, comparative analyses of stocked and non-stocked populations show that stock transfers have influenced alewife population genetic structure. Genetic isolation by distance (IBD) was non-significant among stocked populations, but significant among non-stocked populations. However, two populations, Dresden Mills and Sewell Pond, appear to have resisted genetic homogenization despite stocking. Non-significant genic and genetic differentiations were broadly distributed among alewife populations. Hierarchical AMOVA indicated highly significant differentiation among temporal replicates within populations, and Bayesian clustering analysis revealed weak population structure. A significant correlation was observed between stocking (time and events) and pairwise \({\text{F}}_{\text{ST}}^{{\prime }}\) among alewife collections, and an analysis of IBD residuals showed a significant decline in the amount of genetic differentiation among populations as the extent of stocking activity increased. These findings call for an increased awareness of evolutionary processes and genetic consequences of restoration activities such as inter-basin stock transfers by fisheries management and conservation practitioners.

Population genetics of the endangered Wattled Curassow (Crax globulosa, Cracidae, Aves) of the Colombian–Peruvian Amazon using DNA microsatellites and ND2 mitochondrial sequences

The Wattled Curassow (Crax globulosa, Cracidae, Aves) is a large bird living in the Western Amazon basin and a critically endangered species in the Colombian and in the Peruvian Amazon. We carried out the first population genetics analysis of this species employing six nuclear microsatellite markers and sequences of the mtND2 gene. The main results are as follows. (1) The levels of gene diversity were high for the overall population as well as for each of the three islands for both microsatellites and mtDNA. (2) A small amount of genetic differentiation among populations was found with both types of markers (FST = 0.027 for microsatellites and NST = 0.17 for mitochondrial sequences). (3) Using microsatellites, the Geneclass 2.0 software detected a low correct assignment of individuals to their respective populations. The Structure software only detected one gene pool for the entire area studied. These results are relevant for conservation efforts of this critically endangered species.

Local population structure of Hymenoscyphus fraxineus surveyed by an enlarged set of microsatellite markers

SummaryThe population structure of Hymenoscyphus fraxineus, the causal agent of ash dieback, was assessed at four closely located sites in the Czech Republic. To analyse the genetic variation, one Swiss and one Norwegian population with known population structures were selected as reference points. The analysis was performed using 16 previously published and five newly developed microsatellite markers. The quality of the new markers was assessed by sequencing the flanking region, identifying the type of the mutation and analysing the inheritance and linkage between all pairs of loci. In addition, markers were tested on 45 Japanese strains to confirm their usability on native H. fraxineus populations in Asia. One of the new markers was monomorphic in all European populations and one marker exhibited a high percentage of null alleles in the Japanese samples. Twenty markers in the four Czech populations showed lower average gene diversity than in the other two European populations. One Czech population significantly differed from all the others, with a pairwise GST of approximately 0.2, the lowest allelic richness and very low average gene diversity, likely resulting from a founder effect. The amount of genetic differentiation between the four neighbouring Czech populations exceeds the expected value from previous Europe‐wide population studies and suggests that local population dynamics can affect the population structure of H. fraxineus.

Evolution of introduced Chinook salmon (Oncorhynchus tshawytscha) in Lake Huron: emergence of population genetic structure in less than 10 generations

Abstract – Population genetic structure was detected in Chinook salmon Oncorhynchus tshawytscha in their non‐native range of Lake Huron using microsatellite DNA. All Chinook salmon in this system descend from Green River, Washington cohorts, originally transplanted to Michigan hatcheries in the late 1960s. We tested for population genetic differentiation of age 0 fish collected from 13 rivers and two hatcheries in 2007. The amount of genetic differentiation among collection sites was low but statistically significant, with FST values ranging from 0.036 to 0.133 and RST values ranging from 0.008 to 0.157 for specific loci. Based on pairwise FST and RST values and Bayesian cluster analysis, the Maitland River population in the Main Basin of Lake Huron was genetically distinct from the remaining collection sites. Based on analysis of bycatch data from commercial gill net fisheries, Chinook salmon likely colonised the Main Basin by 1975 (10 generations ago) and the North Channel and southern Georgian Bay regions by 1980 (eight generations ago). Thus, population genetic structure has emerged in Lake Huron Chinook salmon in <10 generations.

Multilocus haplotypes reveal variable levels of diversity and population structure of Plasmodium falciparum in Papua New Guinea, a region of intense perennial transmission

BackgroundThe South West Pacific nation of Papua New Guinea has intense year round transmission of Plasmodium falciparum on the coast and in the low-lying inland areas. Local heterogeneity in the epidemiology of malaria suggests that parasites from multiple locations will need to be surveyed to define the population biology of P. falciparum in the region. This study describes the population genetics of P. falciparum in thirteen villages spread over four distinct catchment areas of Papua New Guinea.MethodsTen microsatellite loci were genotyped in 318 P. falciparum isolates from the parasite populations of two inland catchment areas, namely Wosera (number of villages (n) = 7) and Utu (n = 1) and; and two coastal catchments, Malala (n = 3) and Mugil (n = 3). Analysis of the resultant multilocus haplotypes was done at different spatial scales (2-336 km) to define the genetic diversity (allelic richness and expected heterozygosity), linkage disequilibrium and population structure throughout the study area.ResultsAlthough genetic diversity was high in all parasite populations, it was also variable with a lower allelic richness and expected heterozygosity for inland populations compared to those from the more accessible coast. This variability was not correlated with two proxy measures of transmission intensity, the infection prevalence and the proportion multiple infections. Random associations among the microsatellite loci were observed in all four catchments showing that a substantial degree of out-crossing occurs in the region. Moderate to very high levels of population structure were found but the amount of genetic differentiation (FST) did not correlate with geographic distance suggesting that parasite populations are fragmented. Population structure was also identified between villages within the Malala area, with the haplotypes of one parasite population clustering with the neighbouring catchment of Mugil.ConclusionThe observed population genetics of P. falciparum in this region is likely to be a consequence of the high transmission intensity combined with the isolation of human and vector populations, especially those located inland and migration of parasites via human movement into coastal populations. The variable genetic diversity and population structure of P. falciparum has important implications for malaria control strategies and warrants further fine scale sampling throughout Papua New Guinea.

Genetic diversity in two Lilium (Liliaceae) species from different regions of Greece based on a Random Amplified Polymorphic DNA (RAPD) analysis.

Distribution of genetic variation between populations of Lilium albanicum and Lilium chalcedonicum was investigated using RAPD (random amplified polymorphic DNA) profiles. Plants for the analysis were collected from four different populations, containing 33 individuals. Eleven primers yielded 88 polymorphic bands. UPGMA clustering and principle coordinate analysis indicated a clear separation between the populations of the two species and all the analyzed individuals clustered in three groups, one comprising L. chalcedonicum and the other two groups encompassing three populations of L. albanicum. The analysis of molecular variance (AMOVA) indicated that 33% of the total variance is between species. The highest amount of genetic differentiation, 51% of the total variance, is found within the individual populations.

Next generation population genetics and phylogeography

Next generation population genetics and phylogeography

Y chromosome diversity, human expansion, drift, and cultural evolution

The relative importance of the roles of adaptation and chance in determining genetic diversity and evolution has received attention in the last 50 years, but our understanding is still incomplete. All statements about the relative effects of evolutionary factors, especially drift, need confirmation by strong demographic observations, some of which are easier to obtain in a species like ours. Earlier quantitative studies on a variety of data have shown that the amount of genetic differentiation in living human populations indicates that the role of positive (or directional) selection is modest. We observe geographic peculiarities with some Y chromosome mutants, most probably due to a drift-related phenomenon called the surfing effect. We also compare the overall genetic diversity in Y chromosome DNA data with that of other chromosomes and their expectations under drift and natural selection, as well as the rate of fall of diversity within populations known as the serial founder effect during the recent "Out of Africa" expansion of modern humans to the whole world. All these observations are difficult to explain without accepting a major relative role for drift in the course of human expansions. The increasing role of human creativity and the fast diffusion of inventions seem to have favored cultural solutions for many of the problems encountered in the expansion. We suggest that cultural evolution has been subrogating biologic evolution in providing natural selection advantages and reducing our dependence on genetic mutations, especially in the last phase of transition from food collection to food production.

Population Genetic Structure ofAphis glycines

The soybean aphid (Aphis glycines Matsumura) is an invasive pest of cultivated soybean (Glycine max L.) in North America. After the initial invasion in 2000, the aphid has quickly spread across most of the United States and Canada, suggesting large-scale dispersal and rapid adaptation to new environments. Using microsatellite markers from closely related species, we compared the genetic diversity and the amount of genetic differentiation within and among 2 South Korean and 10 North American populations. Overall allelic polymorphism was low, never exceeding four alleles per locus. However, differences in genetic diversity were seen among South Korean and North American populations in terms of heterozygote excesses and genotypic richness. Within North America, two populations (Michigan and Ontario), had lower genetic diversities and exhibited high genetic differentiation compared with the remaining eight populations. The earlier collection time of Michigan and Ontario samples explained the genetic differences better than geographic subdivisions. These data indicate a pattern of small colonizing populations on soybeans, followed by rapid clonal amplification and subsequent large-scale dispersal across North America.

Biochemical systematics of the Savi's bat (Hypsugo savii) (Chiroptera: Vespertilionidae)

In order to assess the controversial systematic position of the Savi's bat (Hypsugo savii), 43 ves-pertilionid bats belonging to 10 species were analyzed by mean of isozyme electrophoresis. The results were interpreted in two ways: first, we found that the amount of genetic differentiation between Hypsugo and the true Pipistrellus (D # 0.719) is of the same magnitude as the mean distance which separates the other pipistrelloid genera (D = 0.738). Secondly, the cladogram based on these biochemical results confirms the splitting of these “pipistrelles”, as Hypsugo is more closely related to Vespertilio than to any other palearctic genus. The other species analyzed in this study group themselves in a different clade, including Pipistrellus, Eptesicus and Nyctalus. This phylogenetic interpretation presents a testable hypothesis, which could be confirmed by an analysis of other loci or other allied species.

Population structure of the Atlantic sand fiddler crab Uca pugilator along the eastern coast of US revealed by molecular data

Abstract The Atlantic sand fiddler crab Uca pugilator is an extremely abundant crab found along the eastern coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30 - 90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However, a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U. pugilator and to determine whether these differences may have a genetic basis. The population structure of the fiddler crab was analyzed using 472 individuals collected from 12 sites along the eastern coast. PCR-based single stand conformation polymorphism (SSCP) was used to investigate between-site variation in the mitochondrial 16S rRNA gene of these individuals. Analysis of genetic variation indicated frequent gene flow between nearby localities' but much reduced levels between populations separated by larger geographic distances. Thus, despite the potential for high dispersal by planktonic larvae, population differentiation and isolation by distance is evident between northern and southern populations of U. pugilator. A high amount of genetic differentiation (FST = 0.3468) was found between northern and southern regions suggesting that the morphological and behavioral differences between these two regions have a genetic basis and may represent subspecies.

Reproductive Compatibility of Prairie and Montane Populations of <I>Dermacentor andersoni</I>

Genetic analysis of prairie and montane populations of Dermacentor andersoni (Stiles) originating from Alberta (AB) and British Columbia (BC), Canada, respectively, indicated limited gene flow (Nm <1) and a large amount of genetic differentiation (Fst = 0.49) between the populations. The prairie population also had a greater level of genetic diversity. Mating experiments indicated that females of geographically heterogeneous crosses had similar engorgement and oviposition failure as homogenous crosses in the parental generation but that egg mass sterility was greatest for the ABfemale x BCmale cross, intermediate for the homogenous crosses, and lowest for the BCfemale x ABmale cross. The progeny of all crosses produced fertile eggs, and the only significant effect in the progeny generation was increased oviposition failure of the pure AB cross. Covariate analysis indicated that egg mass sterility was associated with BC males in the parental generation and that oviposition failure was associated with AB males and AB females in the progeny generation. The hazard of cumulative reproductive failure was increased with AB females in both generations, reduced for AB males in the parental generation, and increased with AB males in the progeny generation. Overall, heterogenous crosses had the greatest and least reproductive failure in the parental generation, but they were intermediate to the homogenous crosses in the progeny generation. The limited gene flow between the populations seems to have been sufficient to maintain reproductive compatibility.

Genetic differentiation among European whitefish ecotypes based on microsatellite data

The amount of genetic differentiation at DNA microsatellite loci in European whitefish (Coregonus lavaretus) was assessed among ecotypes, populations and run-timing types. The magnitude of genetic changes potentially caused by hatchery broodstock rearing were also compared with those observed in corresponding natural populations. A total of 35 populations were studied, including 33 Coregonus lavaretus populations and two samples of Coregonus peled. Five of the six whitefish ecotypes in Finland were represented within C. lavaretus populations. Genetic diversity among C. lavaretus populations proved to be high compared to two C. peled populations. The genetic D(A) distance between these two species was as high as 0.86. The genetic differentiation among ecotypes was generally low and thus gives support for the hypothesis of one native European whitefish species in Scandinavia. Among the ecotypes the northern, large sparsely-rakered, bottom-dwelling whitefish was most unique. Thus, observed genetic differences in quantitative traits have either developed independently of phylogenetic lineages, or have mixed and later changed according to environments and selection pressures. Overall genetic distances between the anadromous whitefish populations along the Finnish coast, especially in the Bothnian Bay area, were small. Populations of this area have been heavily influenced by human activities, and they also have the highest probability of mixing by natural means. In two cases, the Rivers Iijoki and Tornionjoki, statistically significant genetic differences could be observed between summer- and autumn-run spawning-time types. Wild populations had slightly higher allelic diversity than hatchery-reared populations of corresponding rivers. Although some reduction in genetic diversity during hatchery rearing is possible, it is an important aid in maintaining endangered populations.

The distribution of genetic variation in Norway spruce (Picea abies Karst.) populations in the western Alps

AbstractAim In order to look for a possible centre of survival for the Norway spruce (Picea abies Karst.) in the south‐western Alps, six natural populations of this area were investigated by means of genetic markers in order to assess the degree and the distribution of genetic diversity within the species.Location Western and South‐western Alps.Methods Populations were genotyped using seven simple sequence repeat (SSR) markers. Basic population genetics parameters were estimated and the amount of genetic differentiation calculated.Results A large amount of variability was found (0.59 &lt; He &lt; 0.67); genetic differentiation as measured by FST was 0.05, close to other similar studies; no isolation by distance was detected by a Mantel test. Analysis of molecular variance confirmed a high degree of variability within populations and a low degree of variability among populations. Finally, the number of populations from which those observed could have arisen was estimated by Bayesian analysis.Main conclusions The results presented here suggest that the present populations derive their genetic make‐up from three inferred clusters. The possible existence in this area of a relict/refuge population during the last glaciation is discussed.

Species-Specific Population Structure in Rock-Specialized Sympatric Cichlid Species in Lake Tanganyika, East Africa

Species richness and geographical phenotypic variation in East African lacustrine cichlids are often correlated with ecological specializations and limited dispersal. This study compares mitochondrial and microsatellite genetic diversity and structure among three sympatric rock-dwelling cichlids of Lake Tanganyika, Eretmodus cyanostictus, Tropheus moorii, and Ophthalmotilapia ventralis. The species represent three endemic, phylogenetically distinct tribes (Eretmodini, Tropheini, and Ectodini), and display divergent ecomorphological and behavioral specialization. Sample locations span both continuous, rocky shoreline and a potential dispersal barrier in the form of a muddy bay. High genetic diversity and population differentiation were detected in T. moorii and E. cyanostictus, whereas much lower variation and structure were found in O. ventralis. In particular, while a 7-km-wide muddy bay curtails dispersal in all three species to a similar extent, gene flow along mostly continuous habitat appeared to be controlled by distance in E. cyanostictus, further restricted by site philopatry and/or minor habitat discontinuities in T. moorii, and unrestrained in O. ventralis. In contrast to the general pattern of high gene flow along continuous shorelines in rock-dwelling cichlids of Lake Malawi, our study identifies differences in population structure among stenotopic Lake Tanganyika species. The amount of genetic differentiation among populations was not related to the degree of geographical variation of body color, especially since more phenotypic variation is observed in O. ventralis than in the genetically highly structured E. cyanostictus.