Determine Population Genetic Structure Research Articles

Random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) PCR of Vibrio cholerae from a foodborne outbreak in Limbang, Sarawak

Toxigenic and non-toxigenic V. cholerae strains can be monitored for changes in clones or serogroups, linkages between clinical and environmental isolates, genesis and clonal selection of epidemic strains, and population structure. Also, determining genetic relatedness among V. cholerae strains is critical for determining population genetic structure and evolutionary trends. In collaboration with the Sarawak Government Hospital, the present work was carried out on a total of 16 V. cholerae isolates in order to determine the genetic relatedness or heterogeneity of V. cholerae isolates from a foodborne outbreak among guests who attended a wedding ceremony in Limbang, Sarawak, Malaysia. The random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) were conducted to compare and determine strains and trace disease-causing microorganism. The RAPD fingerprinting was conducted using a total of 10-mer oligos 100 nmole random primers (OPAE1 - OPAE20). The primers OPAE7, OPAE10, OPAE14, and OPAE17 were selected because they were the most stable and discriminatory for V. cholerae. The PCR fingerprinting of ERIC-PCR was carried out using primer set of ERIC, ERIC1R (5’- ATGTAAGCTCCTGGGGATTCAC-3’), and ERIC2F (5’- AAGTAAGTGACTGGGGTGAGCG-3’). As a result, the 1 confirmed V. cholerae O1 samples were successfully fingerprinted. Based on the profiling results, the genetic fingerprint of some of the isolates from the clinical and environmental samples had 100% similarity, as indicated by the dendrogram. This indicated that the strains shared the same genetic profile. The smaller the genetic distance, the more homogeneous the strains are. The clinical and environmental strains shared some genetic characteristics. As indicated by the dendrogram, some strains were found to be closely linked to one another, while others were heterogeneous. Therefore, RAPD-PCR and ERIC-PCR produced the highest discrimination index. By combining these typing methods, evaluation of isolates' genetic diversity may be improved. The findings of the present work demonstrated the need for continued surveillance of V. cholera in Sarawak, Malaysia.

Polymorphism study of novel microsatellite markers to determine population genetic structure of Coptotermes gestroi (Blattodea: Rhinotermitidae) from infested urban buildings

Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) is a common economic termite pest widely distributed in Peninsular Malaysia. Nevertheless, research on C. gestroi is frequently employed in phylogeographic investigations using mitochondrial gene sequences that ceased to discuss further the population dynamics and colonization pattern. In this sense, the application of another highly variable molecular tool, such as microsatellite markers is suitable to effectively assess the population genetic structure of this invasive species. This study aims to identify and characterize seven microsatellite markers for the population structure analysis of C. gestroi. The seven microsatellite markers exhibited significant polymorphic characteristics with PIC values ranging from 0.7696 to 0.9609 (mean equal to 0.9009). A high homozygotes level has been found on Tm-Di08, Tm-Tr06, TmTe-07, TmTe08, and Tm-Pe9 markers, which leads to a higher estimation of null alleles and deviation from Hardy-Weinberg Equilibrium. All seven microsatellite markers were unlinked and distinct from one another and hence eligible for usage in this study. The population genetic study found significant inbreeding (FIT = 0.386, FIS = 0.281) within the C. gestroi individuals. The five C. gestroi populations were moderately genetically differentiated (FST = 0.141) but also relatively connected due to the moderate value of the relatedness coefficient (r = 0.204). Furthermore, the moderate degree of genetic variance (16 %) found among the populations in the AMOVA study supported the findings. A genetic structure study with PCoA and STRUCTURE revealed three genetic clusters. Pop1, Pop2, and Pop3 were separated into three different genetic clusters, while Pop4 and Pop5 have undistinguishable levels of groups for three genetic clusters respectively. In conclusion, the microsatellite markers were demonstrated as informative primers with polymorphic characteristics and can be utilized to study the genetic structure of C. gestroi population.

Genetic and ecological drivers of molt in a migratory bird

The ability of animals to sync the timing and location of molting (the replacement of hair, skin, exoskeletons or feathers) with peaks in resource availability has important implications for their ecology and evolution. In migratory birds, the timing and location of pre-migratory feather molting, a period when feathers are shed and replaced with newer, more aerodynamic feathers, can vary within and between species. While hypotheses to explain the evolution of intraspecific variation in the timing and location of molt have been proposed, little is known about the genetic basis of this trait or the specific environmental drivers that may result in natural selection for distinct molting phenotypes. Here we take advantage of intraspecific variation in the timing and location of molt in the iconic songbird, the Painted Bunting (Passerina ciris) to investigate the genetic and ecological drivers of distinct molting phenotypes. Specifically, we use genome-wide genetic sequencing in combination with stable isotope analysis to determine population genetic structure and molting phenotype across thirteen breeding sites. We then use genome-wide association analysis (GWAS) to identify a suite of genes associated with molting and pair this with gene-environment association analysis (GEA) to investigate potential environmental drivers of genetic variation in this trait. Associations between genetic variation in molt-linked genes and the environment are further tested via targeted SNP genotyping in 25 additional breeding populations across the range. Together, our integrative analysis suggests that molting is in part regulated by genes linked to feather development and structure (GLI2 and CSPG4) and that genetic variation in these genes is associated with seasonal variation in precipitation and aridity. Overall, this work provides important insights into the genetic basis and potential selective forces behind phenotypic variation in what is arguably one of the most important fitness-linked traits in a migratory bird.

Comparison of genotyping by sequencing procedures to determine population genetic structure.

Advancements in technology over the past few decades have resulted in the development of genome sequencing at lower costs. Protocols, costs, and the amount of data produced by different sequencing technologies are highly variable. Ion Torrent and Illumina sequencing instruments are two sequencing technologies which use very similar library preparation procedures. Enzymatic combinations can be changed in genotyping by sequencing (GbS) library protocols without significant adjustments. To compare the outputs from two different GbS procedures, we sequenced samples of two sister species of yellow-nosed albatross collected at multiple geographic locations. The data sets involving different sequencing instruments and enzymatic combinations were analysed using the Stacks pipeline and aligned to the same reference genome. Both procedures identified the same genetic clusters separating Atlantic and Indian yellow-nosed albatross and substructure within Indian yellow-nosed albatross.

Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers.

Assessing genetic differentiation among natural populations can aid understanding of dispersal patterns and connectivity among habitats. Several molecular markers have become increasingly popular in determining population genetic structure for this purpose. Here, we compared the resolution of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear single nucleotide polymorphism (SNP) markers for detecting population structure among stream insects at small spatial scales. Individuals of three endemic taxa-Coloburiscus humeralis (Ephemeroptera), Zelandobius confusus (Plecoptera), and Hydropsyche fimbriata (Trichoptera)-were collected from forested streams that flow across open pasture in the North Island of New Zealand. Both COI and SNP data indicated limited population structure across the study area, and small differences observed among these species were likely related to their putative dispersal abilities. For example, fine-scale genetic differentiation between and among neighbouring stream populations for H. fimbriata suggests that gene flow, and hence dispersal, may be more limited for this species relative to the others. Based on the generally similar results provided by both types of markers, we suggest that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.

Reevaluating Genetic Diversity and Structure of Helianthus verticillatus (Asteraceae) after the Discovery of New Populations

Determining population genetic structure of isolated or fragmented species is of critical importance when planning a conservation strategy. Knowledge of the genetic composition and differentiation among populations of a rare or threatened species can aid conservation managers in understanding how, and which, populations to protect. The whorled sunflower, Helianthus verticillatus (Asteraceae), is a federally endangered sunflower species endemic to the southeastern United States. The distribution of the species comprises four known populations within three states: Alabama, Tennessee, and Georgia. Recently, new populations were discovered in Marshall County, Mississippi, and Franklin County, Virginia. Here, we carry out a population genetic study of these new populations using nuclear microsatellite markers and compare our results to those from previously known populations of H. verticillatus. Our results show that both newly discovered populations contain novel genetic variation, with Mississippi containing the most private alleles out of all populations tested. The Virginia population is genetically similar to the previously known populations but is under the most conservation concern given the recovery of only two unique genetic individuals found in this population. These results indicate these new populations are worthy of protection and conservation efforts given the unique genetic variation they harbor.

Population genetic structure in a rapidly expanding mesocarnivore: golden jackals in the Dinaric-Pannonian region

Species range expansions and (re)colonization of landscapes variously dominated by humans occur on a global scale. Understanding such range enlargements and subsequent changes in the composition of ecological communities is important for conservation management, and the golden jackal (Canis aureus) can be considered a model species for regional and continental range expansion. Although this mesopredator has been known from the Adriatic Coast of southeastern Europe for over 500 years, the species is a recent arrival further north, including in Slovenia where jackals were first confirmed in the 1950s. Research from eastern Italy found jackals with ancestry from the Dalmatian region on the Adriatic Coast and the Pannonian region further east. We predicted similar ancestry for Slovenian jackals, and examined samples from Croatia, including Dalmatia and interior regions, Serbia, Hungary, and Slovenia with 25 microsatellite markers to determine population genetic structure. We detected two distinct genetic clusters, representing the Dalmatian and Balkan-Pannonian (Pannonian) jackal populations (FST = 0.157, 95% CI: 0.112–0.209). Contrary to expectations, only few individuals in Slovenia exhibited signs of Dalmatian ancestry, and none appeared to be direct immigrants. Some results suggested a third cluster centered in northern Hungary. These divergent profiles might indicate immigration from outside the study area, and samples from regions further east are required for additional resolution. Based on our results, we hypothesize that Dalmatia has not been a substantial source for recent range expansion of the species, which has likely occurred from the east. Further investigation can help resolve the ancestry and current distribution of the Dalmatian and Pannonian populations, and the ecological relationships resulting from progressively overlapping distributions of canid species. Finally, genomic research could illuminate whether genetic variants from eastern areas might have facilitated jackal expansion into regions characterized by a colder climate, the presence of snow, and extensive forest cover; habitats seemingly avoided by the jackals occupying the Adriatic Coast and surrounding areas in southeastern Europe.

Landscape Genetics: Understanding the factors that determine population genetic structure using landscape ecological methods

Landscape Genetics: Understanding the factors that determine population genetic structure using landscape ecological methods

Demographic responses of forest-utilizing bats to past climate change in South Africa

AbstractHistorical forest contractions may have restricted the distributions of forest-utilizing fauna while providing opportunities for range expansions for open-habitat species. We aimed to test if habitat associations have played an important role in determining population genetic structure and demographic responses of six bats to oscillations in forest extent since the Last Glacial Maximum (LGM). We hypothesized that forest-associated species would display high levels of population structure and past population contractions as their distribution is dependent on fragmented forests. By contrast, habitat generalists would demonstrate low geographical structuring and historical population stability as suitable habitats are widely available. We used mitochondrial DNA to generate genetic diversity and population structure metrics of three forest-associated species and three habitat generalists in South Africa. Neutrality tests and Bayesian skyline plots were used to investigate demographic histories. A forest habitat association did not inform the population genetics of the study species. Rather, species-specific traits of roosting requirements, philopatry to the natal range and dispersal ability informed the observed structure. All species demonstrated population expansions during the Pleistocene, with no apparent decline during the LGM. It appears that the lower climate change footprint and refuge-status of eastern South Africa prevented population declines of insectivorous bats during the LGM.

Strong population structure and limited gene flow between Yellow-billed Ducks and Mallards in southern Africa

AbstractSecondary contact and hybridization between recently diverged taxa have been increasing due to anthropogenic changes to the environment. Determining whether secondary contact leads to gene flow between species is important for understanding both the evolutionary consequences of such events (i.e. genetic swamping, speciation reversal, hybrid speciation) and for establishing proper conservation measures. Mallards (Anas platyrhynchos), which natively have a Holarctic distribution, have been introduced nearly worldwide due to game-farm and domestic pet releases. Their expanding range has resulted in secondary contact and increased incidences of hybridization with many closely related Mallard-like ducks that comprise the Mallard complex. Here, we assay molecular diversity for 19 nuclear introns and the mitochondrial DNA for wild Mallards (n = 50) across their Holarctic range and Yellow-billed Ducks (n = 30–75; Anas undulata) from southern Africa to determine population genetic structure and test for evidence of Mallard introgression into Yellow-billed Ducks. While we found limited support for contemporary gene flow across nuclear markers, we provide evidence from mitochondrial DNA that best supports ancient gene flow between Yellow-billed Ducks and Mallards. Yellow-billed Ducks best fit a single population at nuclear markers but show some location-specific mtDNA structure that suggests recent founder or bottleneck events. Although we find that introgression from Mallards into Yellow-billed Duck is limited, Yellow-billed Duck populations should be monitored to determine if expanding feral Mallard populations in southern Africa are increasing introgression.

Population genetic structure of the whorl-leaf watermilfoil Myriophyllum verticillatum shaped by topography and geographic distance

Interpopulation gene flow plays an important role in determining population genetic structure. In this study, we sampled 24 populations of the whorl-leaf watermilfoil Myriophyllum verticillatum from three disjunct regions in China (Northwest China, Northeast China, and the Qinghai-Tibet Plateau (QTP) plus Southwest China) with different topographies and examined its population genetic structure using 17 microsatellite loci. Deserts, plains, and mountains are the main geomorphological features of Northwest China, Northeast China, and the QTP plus Southwest China, respectively. High genetic differentiation and genetic isolation by geographic distance were observed at the overall scale and in all three regions. When compared among the three regions, the lowest level of genetic differentiation and weakest correlation between genetic and geographic distances were presented in Northeast China. Two genetic clusters corresponding to Northwest China and the other two regions were identified, suggesting unequal gene flow among the three disjunct regions. Our findings emphasize the role of topography and geographic distance in shaping population genetic structure in aquatic plants.

Genetically distinct populations of the pygmy rabbit (Brachylagus idahoensis) in the Mono Basin of California

We examined patterns of genetic variation and diversity of extant pygmy rabbit (Brachylagus idahoensis) populations across the species' current range in Nevada and California. Our aims were to determine population genetic structure and levels of diversity across the southern portion of the species' range. We genotyped 13 microsatellite loci from 194 fecal samples collected across 14 localities. Our Bayesian cluster analyses found 2 genetically distinct groups: 1 in the Mono Basin of California and the other encompassing all remaining Nevada Great Basin populations. Considering only the Nevada Great Basin group, we found 4 minimally divergent groups that overlap spatially with many individuals maintaining composite genomes with representation from multiple genetic groups. On average, the Mono Basin populations maintain lower levels of genetic diversity than the Nevada Great Basin populations as measured by both heterozygosity and numbers of alleles. The Mono Basin contains the only populations of pygmy rabbits remaining in California. Given their geographic isolation from other known populations and their genetic distinction, these remnant, peripheral populations warrant special attention to ensure maintenance of genetic variation and continued viability.

Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers.

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B824; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

Kinship structures create persistent channels for language transmission

Languages are transmitted through channels created by kinship systems. Given sufficient time, these kinship channels can change the genetic and linguistic structure of populations. In traditional societies of eastern Indonesia, finely resolved cophylogenies of languages and genes reveal persistent movements between stable speech communities facilitated by kinship rules. When multiple languages are present in a region and postmarital residence rules encourage sustained directional movement between speech communities, then languages should be channeled along uniparental lines. We find strong evidence for this pattern in 982 individuals from 25 villages on two adjacent islands, where different kinship rules have been followed. Core groups of close relatives have stayed together for generations, while remaining in contact with, and marrying into, surrounding groups. Over time, these kinship systems shaped their gene and language phylogenies: Consistently following a postmarital residence rule turned social communities into speech communities.

Population genetics of the diamondback terrapin, Malaclemys terrapin, in Louisiana

Previous population genetic studies of diamondback terrapins (Malaclemys terrapin) have typically focused on either the entire range or relatively small spatial scales. The Louisiana coastline contains vast salt marshes suitable for terrapins; however, two major freshwater inputs (Atchafalaya River and Mississippi River Deltas) break up the seemingly contiguous habitat and may isolate populations of terrapins. To determine population genetic structure and connectivity of terrapins occupying Louisiana marshes, we collected 573 individuals from 26 study sites across the Louisiana coastline. Twelve microsatellite loci were used to evaluate population structure using standard genetic and spatially explicit approaches. Patterns of gene flow were examined via model testing, including those to determine if freshwater inputs serve as barriers to movement. We also assessed levels of genetic diversity, inferred the historical demography and estimated effective population sizes across our sampling. While we did not detect significant population structure, we found that terrapins are not panmictic, and demonstrated a pattern of isolation by distance along the Louisiana coastline. Genetic diversity in this study was comparable to the Atlantic coast, but was higher than other sites within the Gulf of Mexico. Though terrapins in eastern Louisiana were historically harvested and apparently experienced a genetic bottleneck, this is not reflected in estimates of effective population sizes. Although, there was no strong genetic structuring across Louisiana, historical differences and patterns of habitat loss suggest that it may be necessary to develop separate management strategies for the western and eastern portions of the state.

Fitness differences and persistent founder effects determine the clonal composition during population build‐up in Daphnia

During the initial stages of population build‐up in new habitats, the time at which immigrants arrive may influence their contribution to the population and thus determine population genetic structure. While the numerical advantage associated with founder effects may promote dominance of the offspring of early colonizers, fitness differences associated with ecological differences among genotypes may potentially overwhelm these founder effects. We conducted an outdoor mesocosm experiment to test whether the sequence of arrival determines the relative contribution of genetic lineages (clones) to populations of the water flea Daphnia. A set of D. galeata clones was inoculated pairwise in different time sequences and clonal abundances were monitored over time. In general, we found that, after six weeks (four generations), clones with an initial time advantage of five or fifteen days (1/3 of a generation or one generation) had higher relative abundances than in the treatments with simultaneous inoculations. These differences were in some cases maintained over a longer period (nine months). However, in cases where abundances of genetic lineages varied strongly when inoculated simultaneously, reflecting strong differences in fitness among clones in our experimental containers, initial numerical advantages could be overwhelmed and the competitively strongest clone became dominant after nine months independently of inoculation sequence. Our results highlight the importance of two different processes that determine the fate of clonal lineages and ultimately determine population genetic structure. First, the sequence of arrival is crucial, with an advantage of five days being already sufficient to dominate the population in specific cases. Second, if fitness differences among clones are sufficiently strong, then they may overrule founder effects.

Genetic structure in native and non-native populations of the direct-developing gastropod Crepidula convexa

In many marine invertebrate species, larval development plays an important role in population connectivity and gene flow: species with direct benthic development generally show more genetic structure than those with planktonic development. We used nuclear markers (microsatellites) to determine population genetic structure of the direct-developing snail Crepidula convexa (Gastropoda: Calyptraeidae) in seven populations with 15–85 individuals each within its native range of the northwest Atlantic and compared it to Crepidula fornicata, a congener with planktonic development. Our results are consistent with general expectations and previous work in these species with other markers: C. convexa had greater population structure and even at a regional scale shows significant isolation-by-distance, in contrast to C. fornicata. We also genotyped a single population of C. convexa introduced to the northeastern Pacific to investigate the prediction of reduced genetic diversity following introduction (founder effect). We did not find a reduction in genetic diversity, suggesting that this non-native population may be characterized by multiple introductions. This pattern is consistent with many other introduced populations of marine invertebrates, including C. fornicata.

English

Afzelia xylocarpa is listed as an endangered species on the IUCN World list of Threatened Trees, due to over exploitation for its valuable timber and habitat loss, have resulted in a rapid decline of populations size and local population extinction. Understanding of the processes that determine population genetic structure, gene flow and mating systems is important to conserve and manage the existing populations for this endangered tree species. This study describes the level of genetic diversity and differentiation of fifteen populations of A. xylocarpa in Thailand. Genetic variations at seven nuclear microsatellite loci were examined. The seven nuclear microsatellite loci employed detected a total of 53 alleles (n=432). The nSSRs data indicate that a high level of genetic diversity (HS = 0.575) and low level of genetic differentiation among the 15 examined A. xylocarpa populations. The observed level of genetic differentiation among the 15 populations was low, as revealed by FST = 0.074 and GST = 0.078. The results for the nSSRs suggested that all of the populations in North Eastern, Central Thailand and the Klong Lan populations harbored the high genetic diversity and less divergent from the other populations. Therefore, these populations should be assigned the highest priority for conservation of this species.   Key words: Afzelia xylocarpa, genetic diversity, endangered species, tropical tree, conservation.

Verticillium dahliae Populations from Mint and Potato Are Genetically Divergent with Predominant Haplotypes

In total, 286 Verticillium dahliae isolates from mint, potato, and other hosts and substrates were characterized for mating type, vegetative compatibility group (VCG), and multilocus microsatellite haplotype to determine population genetic structure among populations infecting mint and potato. Populations from mint and potato fit a clonal reproductive model, with all isolates a single mating type (MAT1-2) and multiple occurrences of the same haplotypes. Haplotype H02 represented 88% of mint isolates and was primarily VCG2B, while haplotype H04 represented 70% of potato isolates and was primarily VCG4A. Haplotypes H02 and H04 typically caused severe disease on mint and potato, respectively, in greenhouse assays regardless of host origin. Principal coordinate analysis and analysis of molecular variance indicated that mint and potato populations were significantly genetically diverged (P = 0.02), and identification of private alleles and estimation of migration rates suggested restricted gene flow. Migration was detected between infected potato plants and seed tubers, infested tare soil, and field soils. Genetic differentiation of V. dahliae from mint and potato may be due to the occurrence of a single mating type and differences in VCG. Populations of V. dahliae in potato and mint were characterized by the presence of aggressive, clonally reproducing haplotypes which are widely distributed in commercial mint and potato production.

Mating System of Brassica napus and Its Relationship with Morphological and Ecological Parameters in Northwestern Spain

Mating systems play a central role in determining population genetic structure and the methods to be used to develop new cultivars and preserve the variability of a crop. A Brassica napus crop called nabicol is grown in northwestern Spain. Knowledge on its mating system is needed in order to manage the germplasm correctly and design breeding strategies. The aims of this work were to study the mating system of nabicol under field conditions and the relationship of different traits with the mating system. We analyzed 2 populations with microsatellites using a multilocus approach, finding that both had a mixed mating system with an outcrossing rate of 30%. This system would allow application of breeding methods for both autogamous and allogamous species in order to improve nabicol populations. Nabicol populations should be multiplied in isolation conditions in the same way as allogamous species in order to avoid contamination and preserve genetic integrity. The relationship of outcrossing rate, phenological, ecological, and morphological traits was studied, but the model explained only a small percentage of the variability. None of the traits studied could be used as indirect selection criteria for a type of mating system under the conditions of northwestern Spain. This is the first work that studies in depth the possible causes of the mixed mating system of B. napus, finding that, surprisingly, it is not related to the most obvious factors.