Examine Population Structure Research Articles

Is multiple mating beneficial or unavoidable? Low multiple paternity and genetic diversity in the shortspine spurdog Squalus mitsukurii

Proposed benefits of multiple paternity include increased reproductive output, elevated fitness of progeny, and maintenance of population genetic diversity. However, another consideration is whether multiple paternity is simply an unavoidable byproduct of sexual conflict, with males seek- ing to maximize mating encounters while females seek to minimize the stress of copulation. Here we examined the polyandrous mating system in sharks, with a focus on the reproductive genetics of the shortspine spurdog Squalus mitsukurii. Members of the genus Squalus are long-lived, slow-growing, and employ among the longest gestation periods of any vertebrate. To evaluate multiple paternity and genetic diversity in S. mitsukurii, we genotyped 27 litters plus 96 individuals with 8 microsatel- lite loci. Further, 670 bp of the mtDNA control region were sequenced in 112 individuals to examine population structure. S. mitsukurii in Hawaii showed low genetic diversity relative to other sharks (π = 0.0010 ± 0.0008) and no significant population structure in the Hawaiian Archipelago. Direct allele counts and Bayesian approximations returned concordant estimates of 11% multiple paternity, the lowest observed in sharks to date. Considering the protracted reproductive interval of S. mitsu- kurii, sexual conflict that results from differential male and female reproductive strategies may favor the development of female mating avoidance behavior to minimize trauma. In S. mitsukurii this behavior includes segregation of sexes and an asynchronous reproductive cycle.

Population Structure and Relatedness among Female Northern Pintails in Three California Wintering Regions

Abstract. Female Northern Pintails (Anas acuta) were sampled in California's three main Central Valley wintering regions (Sacramento Valley, Suisun Marsh, San Joaquin Valley) during September–October before most regional movements occur and microsatellite and mitochondrial DNA were analyzed to examine population structure and relatedness. Despite reportedly high rates of early-fall pairing and regional fidelity, both sets of markers indicated that there was little overall genetic structuring by region. Pintails from Suisun Marsh did exhibit higher relatedness among individuals and capture groups than in the Sacramento or San Joaquin Valleys, likely reflecting a sample comprised of a greater proportion of local breeders. The lack of genetic structuring among regions indicates that a high degree of movement and interchange occurs among pintails wintering in the Central Valley. Thus, although maintaining the existing distribution of pintails among Central Valley regions is important for other reasons, it doe...

Effects of secondary tuber harvest on populations of devil’s claw (Harpagophytum procumbens) in the Kalahari savannas of South Africa

AbstractDevil’s claw (Harpagophytum procumbens) is an internationally traded species that is harvested for its secondary tubers. Root extracts are used to treat arthritis and other inflammatory diseases. This study examined population structure, density, growth, mortality, and seed and fruit production in harvested and unharvested populations in the Kalahari savannas of South Africa over 4 years. Plant density and population structure differed significantly between overgrazed and grass‐dominated areas, suggesting that the differences may be due to competition for water and nutrients. Experimental removal of secondary tubers (harvest) was not a significant factor for mortality in any of the harvested size classes. Harvest also did not affect growth, although plants in the 3–4 cm size class grew more in both the harvested and unharvested populations. Fruit production was variable; fruits matured only after sufficient rains. Under the conditions of this study, the species appears to be resilient to harvest, with both harvested and unharvested plants surviving. After harvest, both groups recovered and grew (on average) at the same rate. Because of the spatially variable habitat and the plasticity of the plants themselves, a large number of plants over a wide area are required to better understand the species’ life history.

Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx

Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. All the alleles of different loci exhibited good peak resolutions and hence were clearly identified. Moreover, none of the stutter peaks impaired the recognition or differentiation between homozygote and heterozygote. Our findings suggest that correct identification of alleles in the presence of co-amplified nonspecific fragments is important for reliable interpretation of microsatellite data.

Restricted dispersal in a continuously distributed marine species: common bottlenose dolphinsTursiops truncatusin coastal waters of the western North Atlantic

The marine environment provides an opportunity to examine population structure in species with high dispersal capabilities and often no obvious barriers to genetic exchange. In coastal waters of the western North Atlantic, common bottlenose dolphins, Tursiops truncatus, are a highly mobile species with a continuous distribution from New York to Florida. We examine if the highly mobile nature coupled with no obvious geographic barriers to movement in this region result in a large panmictic population. Mitochondrial control region sequences and 18 microsatellite loci indicate dolphins are partitioning the habitat both latitudinally and longitudinally. A minimum of five genetically differentiated populations were identified among 404 samples collected in the range of New Jersey to northern Florida using both genetic marker types, some inhabiting nearshore coastal waters and others utilizing inshore estuarine waters. The genetic results reject the hypothesis of a single stock of coastal bottlenose dolphins put forth after the 1987-1988 epizootic that caused a large-scale die-off of dolphins and suggest instead the disease vector was transferred from one population to the next as a result of seasonal migratory movements of some populations. These coastal Atlantic populations also differ significantly from bottlenose dolphin samples collected in coastal waters of the northern Gulf of Mexico, implying a long-term barrier to movement between the two basins.

Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newtCalotriton asper(Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA

Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt (Calotriton asper) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F(ST) values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper. The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.

Isolation and characterization of microsatellite loci in the Indian false vampire bat Megaderma lyra

We isolated and characterized eight microsatellite markers for Indian false vampire bat Megaderma lyra. These loci were tested on 60 individuals representing four populations, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.1 (range from 5 to 24). Observed heterozygosity values range from 0.876 to 0.982, and expected heterozygosity value were ranged from 0.986 to 1.0. Out of eight loci, only two loci deviated significantly from Hardy-Weinberg equilibrium, and no pairs of loci were in linkage disequilibrium. These polymorphic markers will be useful to examine population structure, mating and dispersal behaviour, including monitoring the effect of habitat fragmentation and parental analysis.

Fine‐scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul, which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure (F(ST) = 0.051-0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes (N(e) = 7-30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B. exsul's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy-Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

Isolation and characterization of microsatellite loci in the western long‐fingered bat, Miniopterus magnater

We isolated and characterized 10 microsatellite loci in the western long‐fingered bat, Miniopterus magnater. These loci were tested on 48 individuals from Anhui Province of China, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.6 (range from six to 27). Observed and expected heterozygosity values ranged from 0.364 to 0.957, and from 0.676 to 0.951, respectively. After Bonferroni correction, four loci deviated significantly from Hardy–Weinberg equilibrium. No pairs of loci were in linkage disequilibrium. These polymorphic markers will be used to examine population structure and genetic diversity in this species.

POPULATION STRUCTURE OF MOUNTAIN PLOVER AS DETERMINED USING NUCLEAR MICROSATELLITES

Abstract Mountain Plover (Charadrius montanus) is a species of conservation concern that has experienced significant habitat loss and population decline. This, coupled with previous observations that the species exhibits strong fidelity to breeding grounds, suggests that breeding populations may be genetically differentiated and possibly suffer from reduced genetic variation associated with relatively small population sizes. A previous genetic study comparing mitochondrial DNA sequences of plovers in Montana and Colorado found high levels of genetic variability and very little genetic differentiation among breeding locales. Because mitochondrial DNA can track only female movements and is sampled from only one locus, we used 14 nuclear microsatellite loci to further examine population structure, thereby both documenting male movements and providing a more comprehensive view of genetic structure. We found no significant differences among breeding populations. The most likely number of unique genetic cluster...

Diversity, relative abundance, new locality records and population structure of Antarctic demersal fishes from the northern Scotia Arc islands and Bouvetøya

A primary objective of the ICEFISH 2004 cruise was to collect and study notothenioid fishes from remote localities in the Atlantic sector of the Southern Ocean. Nearly 1 month was devoted to bottom trawling for fishes on the shelf and upper slope (to 1,000 m) areas around Shag Rocks, South Georgia, South Sandwich Islands and Bouvetoya. The focus was on the latter two locations, because their faunas are more poorly known. Eight species were collected at Shag Rocks with Patagonotothen guntheri most abundant; 17 at South Georgia with Lepidonotothen nudifrons, L. larseni and Gobionotothen gibberifrons most abundant; 13 at the South Sandwich Islands with L. larseni, L. nudifrons and G. gibberifrons most abundant; and 11 at Bouvetoya with L. larseni, Macrourus holotrachys and L. squamifrons most abundant. Ten new locality records were established: Shag Rocks (1), South Georgia (1), South Sandwich Islands (5), South Sandwich Trench at 5,350 m (1) and Bouvetoya (2). Total known demersal fish diversity on the shelf and upper slope at Shag Rocks/South Georgia, South Sandwich Islands and Bouvetoya is 42, 31 and 17 species, respectively. To examine population structure in the four most abundant notothenioids at Bouvetoya (L. larseni, L. squamifrons, Notothenia coriiceps and Chaenocephalus aceratus), we examined the ND2 portion of mitochondrial DNA. Chaenocephalus aceratus, N. coriiceps and L. larseni exhibited no significant genetic differentiation in comparison with samples from localities in the Scotia Sea and the Antarctic Peninsula. However, L. squamifrons showed significant genetic differentiation between the South Shetlands and Bouvetoya populations (F ST = 0.189, P = 0.015). Thus, these data combined with previous studies of two other notothenioids suggest that five of the six notothenioid species at Bouvetoya are not genetically differentiated from other localities in the Atlantic sector of the Southern Ocean. The location of Bouvetoya within the Antarctic Circumpolar Current and the long (1–2 years) pelagic stages of the notothenioids at Bouvetoya may be at least partly responsible for this genetic homogeneity.

Isolation and characterization of 30 polymorphic microsatellite loci from the mycophagous fly Drosophila innubila

Drosophila innubila is a mushroom-feeding member of the quinaria group, found in the woodlands and forests of the 'sky islands' in Arizona and New Mexico and extending south into central Mexico. Here, we describe and characterize 30 polymorphic microsatellite loci from D. innubila collected in the Chiricahua Mountains in Arizona. The number of alleles ranged from three to 21, and observed heterozygosity ranged from 0.0513 to 0.9737. Six loci were putatively X-linked, six departed from Hardy-Weinberg equilibrium, seven had evidence of null alleles, and six showed evidence of linkage disequilibrium. These markers will be useful for examining population structure of D. innubila and its association with male-killing Wolbachia.

Isolation and characterization of microsatellite loci in the long‐fingered bat Miniopterus fuliginosus

We isolated and characterized 10 microsatellite loci in the long-fingered bat Miniopterus fuliginosus. These loci were tested on 48 individuals from Anhui Province of China, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.6 (range from six to 27). Observed and expected heterozygosity values ranged from 0.364 to 0.957, and from 0.676 to 0.951, respectively. After Bonferroni correction, four loci deviated significantly from Hardy-Weinberg equilibrium. No pairs of loci were in linkage disequilibrium. These polymorphic markers will be used to examine population structure and genetic diversity in this species.

Population structure of ice‐breeding seals

The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

Tracing the Geographic Origins of Major Avocado Cultivars

It has been difficult to infer the genetic history of avocado breeding, owing to the role of hybridization in the origin of contemporary avocado cultivars. To address this difficulty, we used the model-based clustering program, STRUCTURE, and nucleotide polymorphism in 5960 bp of sequence from 4 nuclear loci to examine population structure in 21 wild avocado accessions. The origins of 33 cultivars were inferred relative to the wild sample. Nucleotide sequence diversity in domesticated avocados ranged between 80% and 90% of that observed for the same loci in wild avocado, depending on the diversity statistic used for comparison. Substantial genetic differentiation among 3 geographic groups of wild germplasm corresponded to the classically defined horticultural races of avocado. Previously undetected genetic differentiation was revealed in wild populations from Central Mexico, where 2 subpopulations were distinguished based on elevation and latitude.

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

BackgroundAnalyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus.ResultsTwo thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.ConclusionThe whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Population genetic structure across dissolved oxygen regimes in an African cichlid fish

Ecological isolation is a process whereby gene flow between selective environments is reduced due to selection against maladapted dispersers, migrant alleles, or hybrids. Although ecological isolation has been documented in several systems, gene flow can often be high among selective regimes, and more studies are thus needed to better understand the conditions under which ecological gradients or divergent selective regimes should influence population structure. We test for ecological isolation in a system in which high plasticity occurs with respect to traits that are adaptive in alternate forms under different environmental conditions. Pseudocrenilabrus multicolor victoriae is a widespread haplochromine cichlid fish in East Africa that exploits both normoxic (normal oxygen) rivers/lakes and hypoxic (low oxygen) swamps. Here, we examine population structure, using mitochondrial DNA and microsatellites, to determine if genetic divergence is significantly increased between dissolved oxygen regimes relative to within them, while controlling for geographical structure. Our results indicate that geographical separation influences population structure, while no effects of divergent selection with respect to oxygen regimes were detected. Specifically, we document (i) genetic clustering according to geographical region, but no clustering according to oxygen regime; (ii) higher genetic variation among than within regions, but no effect of oxygen regime on genetic variation; (iii) isolation by distance within one region; and (iv) decreasing genetic variability with increasing geographical distance from Lake Victoria. We speculate that plasticity may be facilitating gene flow between oxygen regimes in this system.

Genetic Diversity, Population Structure, and Demographic History of The Rio Grande Sucker, Catostomus (Pantosteus) Plebeius, in New Mexico

Abstract We used 991 bp of mtDNA (D-loop/ND4L/ND4) and eight microsatellite loci to examine population structure and genetic diversity of Catostomus plebeius from nine localities across the northern part of its range in New Mexico. Two phylogeographic regions (Mimbres and Rio Grande) were defined by phylogenetically distinct collections of mtDNA haplotypes. Mismatch distribution analysis and relatively deep coalescence of haplotypes within the upper Rio Grande suggested rapid population expansion of Rio Grande populations following putative colonization from the ancestral Cabeza de Vaca lake system during the Miocene. Mitochondrial haplotypes indicated that individuals from Palomas Creek (near present-day Elephant Butte Reservoir) shared most recent common ancestry with the Rio Grande phylogeographic region. Microsatellite diversity and allele identity supported the hypothesis of native status of C. plebeius from Sapillo Creek in the Gila River drainage. Analysis of molecular variance within and among sam...

Natural variability in δ18O values of otoliths of young Pacific sardine captured in Mexican waters indicates subpopulation mixing within the first year of life

Abstract Valle, S. R., and Herzka, S. Z. 2008. Natural variability in δ18O values of otoliths of young Pacific sardine captured in Mexican waters indicates subpopulation mixing within the first year of life. – ICES Journal of Marine Science, 65: 174–190. Oxygen stable isotopes were measured in whole sagittae of young Pacific sardine (δ18Ooto) collected throughout their range in the Mexican Pacific to quantify natural variability, to reconstruct temperature histories, and to infer whether fish mix at a population or subpopulation level. Isotopic values and derived temperature estimates (Toto) of sardine captured simultaneously showed high variability (up to 2.0‰ and 10°C at a given location). Given limited variations in salinity, this implies differences in thermal history and the prevalence of subpopulation-level mixing processes. We tested the null hypothesis of local residence by comparing δ18Ooto values with predicted isotopic values on a location-specific basis, and age- and location-specific average sea surface temperatures (SSTs) with derived Toto. Some fish exhibited values outside the local range of predicted oxygen isotope values and SSTs, suggesting that they were not permanent residents. Using an otolith growth model, we show that otolith growth and age differences cannot fully account for the variability in δ18Ooto values. The absence of significant differences in δ18Ooto values between the Pacific and Gulf indicates that oxygen isotope ratios cannot be used to examine population structure or migration among these regions. However, they can be used to infer mixing within and among subpopulations.