Ocean circulation model predicts high genetic structure observed in a long‐lived pelagic developer

Understanding the movement of genes and individuals across marine seascapes is a long‐standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time‐integrated processes and may not capture present‐day connectivity between populations. Here, we use a high‐resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well‐studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6–10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20–50 km of their parents, suggesting a necessity for close‐knit design of Marine Protected Area networks.     

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae)

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.     

Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns

Subalpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.) represent two closely related species with contrasting abundance and distribution patterns in Western North America. Genetic diversity at seven informative microsatellite loci was determined for 19 populations of subalpine larch and nine populations of western larch. Contrasting genetic diversity and patterns of population differentiation were observed between the two species. The overall within-population genetic diversity parameters were lower in subalpine larch (A = 3.2; A(P) = 3.6; H(E) = 0.418) than in western larch (A(P) = 5.51; H(E) = 0.580), a pattern that is likely related to historical or demographic factors. No evidence of interspecific hybridization was observed. Significantly more population differentiation (theta = 0.15; R(ST) = 0.07), consistent with more restricted gene flow, was observed for subalpine larch as compared to western larch (theta = 0.05; R(ST) = 0.04). Under the assumption of an infinite allele mutation model, 12 of the 19 subalpine larch populations showed signs of deviation from the mutation-drift equilibrium, which suggests Holocene population bottlenecks and fluctuations in effective population size for this species. None of the western larch populations deviated significantly from the mutation-drift equilibrium. For both species, Mantel's test revealed a significant positive relationship between geographical and genetic distances indicative of isolation by distance. A similar geographical structure was detected in both species, suggesting at least two genetically distinct glacial populations in each species. The various implications for gene conservation are discussed.     

Spatio-genetic population structure in mustached tamarins, Saguinus mystax

Dispersal and philopatry influence gene flow and thus the spatio-genetic structure within and between populations. In callitrichids the flexible social and mating system corresponds with a variable migration pattern where both sexes might be philopatric or might disperse. We investigated the relationship between the spatio-genetic structure and migration patterns in a population of mustached tamarins, Saguinus mystax. Using the rapidly evolving hypervariable region I (HVI) of the mitochondrial control region and 11 microsatellite markers we detected a high variation (HVI: 16 haplotypes in 69 individuals; microsatellites: H(O) = 0.75, average: 7.45 alleles/locus), with mating partners usually not sharing the same haplotype, indicating that matings are generally between partners that are not closely related. Similar high variance of haplotype differences for male-male and female-female pairs, along with a slightly higher number of haplotype differences in males show that both sexes habitually migrate. Spatial analyses suggest that females usually migrate longer distances, corresponding to very limited breeding positions for females in a polyandrous social mating system.     

Inference of sex‐specific expansion patterns in human populations from Y‐chromosome polymorphism

Studying the current distribution of genetic diversity in humans has important implications for our understanding of the history of our species. We analyzed a set of linked STR and SNP loci from the paternally inherited Y chromosome to infer the past demography of 55 African and Eurasian populations, using both the parametric and nonparametric coalescent‐based methods implemented in the BEAST application. We inferred expansion events in most sedentary farmer populations, while we found constant effective population sizes for both nomadic hunter‐gatherers and seminomadic herders. Our results differed, on several aspects, from previous results on mtDNA and autosomal markers. First, we found more recent expansion patterns in Eurasia than in Africa. This discrepancy, substantially stronger than the ones found with the other kind of markers, may result from a lower effective population size for men, which might have made male‐transmitted markers more sensitive to the out‐of‐Africa bottleneck. Second, we found expansion signals only for sedentary farmers but not for nomadic herders in Central Asia, while these signals were found for both kind of populations in this area when using mtDNA or autosomal markers. Expansion signals in this area may result from spatial expansion processes and may have been erased for the Y chromosome among the herders because of restricted male gene flow. Am J Phys Anthropol 157:217–225, 2015. © 2015 Wiley Periodicals, Inc.     

Genotypic characteristics in populations of Sclerotinia sclerotiorum from New York State,USA

White mould, caused by the fungus Sclerotinia sclerotiorum, is one of the most destructive diseases of beans globally. In New York State, USA, white mould causes substantial losses in soybean, snap, dry and succulent baby lima beans, which are grown successively in intensive crop rotations. Management strategies for white mould in these crops are reliant upon the prophylactic use of fungicides. No complementary information on the genetic structure of the populations of S. sclerotiorum in New York State, USA is available. Twenty isolates of S. sclerotiorum were collected from symptomatic bean plants within each of 10 fields across New York State, USA in 2014. Eight microsatellite (SSR) markers were used to characterise the genotypic diversity of the hyphal‐tipped isolates. Twenty‐four multilocus genotypes (MLGs) were detected within the population but one MLG was most prevalent. Although STRUCTURE analysis identified two subpopulations, these subpopulations were not associated with geographic location, suggesting no spatial structure to the population. In addition, the pathogen populations were predominantly clonal, with some evidence of infrequent outcrossing. These findings may assist in understanding the durability of management strategies for white mould and support the selection of representative isolates for host resistance screening for pathogen populations in the sampling area.     

Gene flow between insular, coastal and interior populations of brown bears in Alaska

The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2–4 km and 7km in width, respectively.     

Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites

To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides , 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F _ST, global amova , and genetic admixture analysis identified three clusters — the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations — indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals ( P _SAxy) analyses between the Sea of Japan and the other samples, P _SAxy was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P _SAxy data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P _SAxy data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P _SAxy were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.     

Genetic divergence between cave and surface populations of Astyanax in Mexico (Characidae,Teleostei)

A study of genetic diversity at microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b gene was carried out to assess genetic relationships among four Mexican cave (Pachon, Sabinos, Tinaja, Chica) and four surface populations of Astyanax fasciatus (Characidae) from northeast Mexico and the Yucatan. With the exception of Chica, the cave populations were all characterized by extremely low microsatellite variability, which most likely resulted from bottleneck events. Population analyses of the microsatellite data indicated no measurable levels of gene flow between all cave and surface populations (F(ST) > 0.0707). Phylogenetic analyses of mtDNA data showed that only two cave populations - Sabinos and Tinaja - group together to the exclusion of surface populations. From the microsatellite data these cave populations cluster with the Pachon cave fish population. The mtDNA thus appears to have been replaced in Pachon because of introgressive hybridization. It is likely that these three cave populations have descended from a surface ancestor in common with current surface populations, rather than evolving recently from one of the extant surface populations. Like Pachon, the Chica population clustered with the surface populations according to mtDNA data, but was not clearly associated with either the surface or the other cave populations according to the microsatellite data. Our data indicate that the Chica population evolved recently from a surface population, and subsequently hybridized with a phylogenetically older cave population. In conclusion, both the microsatellite and mtDNA data suggest multiple origins of cave populations and the Chica and Sabinos/Tinaja/Pachon were founded after at least two independent invasions from surface populations.     

Isolation and characterization of microsatellites in Sparganium emersum and cross‐species amplification in the related species S. erectum

We developed seven novel polymorphic microsatellite loci for the aquatic macrophyte Sparganium emersum (Sparganiaceae). These were characterized on 62 individuals collected from nine different populations. In this set of individuals, seven to 20 alleles per locus were detected and observed heterozygosity ranged between 0.16 and 0.95. Cross‐species amplification was tested in the related species Sparganium erectum, and was successful for five of the seven microsatellite loci.     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Gene flow connects coastal populations of a habitat specialist,the Clapper Rail Rallus crepitans

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographical range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of the USA, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks and a weak pattern of genetic differentiation that increased with geographical distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the Atlantic coast of the USA, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioural factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.     

Population genetics of Tuberolachnus salignus,an obligate parthenogenetic aphid

• 1 This study reports the results obtained in an investigation of the putatively parthenogenetic aphid species Tuberolachnus salignus Gmelin. Tuberolachnus salignus is one of the largest aphid species in the world but where and how it overwinters is not known. It has recently become noteworthy because it is increasingly found on commercially grown willows used in bioenergy production.
• 2 Seven newly‐developed polymorphic microsatellite markers were used to investigate the genetic diversity of the species, and also to confirm its reproduction strategy.
• 3 Tuberolachnus salignus shows very low clonal diversity; only 16 genotypes were found in 660 specimens from 27 populations in five countries.
• 4 There was limited geographical structuring in the samples, although the two most common genotypes, which comprised more than half of the specimens collected, had a very wide distribution.
• 5 Furthermore, we determined that these aphids, which live in very dense colonies, can consist of more than one genotype, suggesting aggregation of colonizing T. salignus. These results confirm the parthenogenetic nature of T. salignus and demonstrate the presence of common genotypes that are widespread in time and space.

     

Drifting fronds and drifting alleles: range dynamics,local dispersal and habitat isolation shape the population structure of the estuarine seaweed Fucus ceranoides

Aim The seaweed Fucus ceranoides is restricted to spatially discrete estuarine habitats and lacks planktonic dispersal phases; it is therefore expected to exhibit strong population differentiation. Its cold‐temperate affinities and mtDNA variation imply that the northern part of the species’ range, where F. ceranoides is now ubiquitous, was recently colonized after the onset of the last deglaciation, potentially resulting in areas with greater genetic homogeneity. Here we examine the population structure of F. ceranoides to test these predictions, emphasizing the contrasting genetic signatures of limited dispersal in refugial versus recently colonized regions. Location North‐eastern Atlantic estuaries from Portugal to Norway. Methods A total of 504 individuals from 21 estuarine sites spanning the entire range of F. ceranoides were sampled and genotyped for nine microsatellite loci. Population structure was inferred from several genotypic and allele‐frequency analyses. Geographical patterns of genetic diversity were used to reconstruct the historical biogeography of the species. Results Genetic diversity and regional population differentiation showed a consistent decline with increasing latitude. Southernmost populations harboured most of the endemic variation, whereas the northern populations (> 55° N) were almost fixed for the same alleles across loci. In southern and central regions of its distribution, F. ceranoides showed striking population subdivision, with many of the sampled estuaries corresponding to coherent genetic units that were easily discriminated from one another with standard clustering methods. Main conclusions The geographical pattern of genetic diversity supports the long‐term refugial status of Iberia and a post‐glacial range expansion of F. ceranoides into previously glaciated latitudes. Despite the species’ capacity to colonize newly available habitats, the genetic structure of F. ceranoides outside the recently (re)colonized range reveals that gene flow between populations is extremely low. This study provides a remarkable example of how infrequent and spatially limited dispersal can have contrasting effects at the scales of meta‐population (connectivity) versus range dynamics (habitat tracking), and of how dispersal restrictions can result in either genetic divergence or homogeneity depending on the maturity and demographic conditions of the populations.     

Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean Sea

We investigated hierarchical patterns of genetic subdivision, and assessed kinship within and between social groups of striped dolphins (Stenella coeruleoalba) in the Tyrrhenian Sea. A total of 165 samples were analysed at eight microsatellite DNA loci, including outgroup samples from the Adriatic, Scotland and Spain for population-level comparisons. We found population genetic structure within the Mediterranean basin, including small but significant differentiation between the Adriatic and Tyrrhenian Seas (FST=0.0047, P=0.008), and between putative 'inshore' and 'offshore' (FST=0.0217, P=0.005) populations in the Tyrrhenian Sea. Assessment of kinship within and among 12 association groups showed higher average kinship for females within than between groups, and smaller groups showed higher average kinship. Comparisons of relatedness for both sexes showed a significant difference between males and females, with females more likely to associate with adult kin. Together these data emphasize the importance of the social cohesion of kin in small groups to the structuring of striped dolphin populations in this environment.     

Dispersal and population genetic structure of Telmatherina antoniae,an endemic freshwater Sailfin silverside from Sulawesi,Indonesia

Population genetic structure in the presence of substantial dispersal provides a unique perspective on the evolution of reproductive isolation. We sampled Telmatherina antoniae, an endemic fish species, at 10 sites in Lake Matano, Indonesia. Significant genetic structure (F_ST = 0.03) was found, despite a migration rate of 10.2% and a mean dispersal distance of 13.6 km, estimated by genotype assignment. Neither dispersal distance nor direction differed from random expectations, indicative of no dispersal barrier in Lake Matano. However, Bayesian genotype cluster assignment identified a population structure consisting of four to six clusters that did not coincide with sample site distribution, but explained two to three times more genetic variance than sample site. The mechanism for continued isolation of those genetic clusters is unknown, but assortative mating and temporal isolation are obvious candidates. Our results resolve the apparent paradox of population genetic structure coupled with frequent dispersal, and highlight the importance of considering cryptic genetic structure.     

Multiple paternity and mating patterns in the American alligator, Alligator mississippiensis

Eggs were sampled from 22 wild American alligator nests from the Rockefeller Wildlife Refuge in south-west Louisiana, along with the females guarding the nests. Three nests were sampled in 1995 and 19 were sampled in 1997. Females and offspring from all clutches were genotyped using five polymorphic microsatellite loci and the three nests from 1995 were also genotyped using one allozyme locus. Genotypes of the hatchlings were consistent with the guarding females being the mothers of their respective clutches. Multiple paternity was found in seven of the 22 clutches with one being fathered by three males, and the remaining six clutches having genotypes consistent with two males per clutch. Paternal contributions of multiply sired clutches were skewed. Some males sired hatchlings of more than one of the 22 clutches either as one of two sires of a multiple paternity clutch, as the sole sire of two different clutches, or as the sole sire of one clutch and one of two sires of a multiply sired clutch. There was no significant difference between females that had multiple paternity clutches and those that had singly sired clutches with respect to female total length (P = 0.844) and clutch size (P = 0.861). Also, there was no significant correlation between genetic relatedness of nesting females and pairwise nest distances (r2 = 0.003, F1,208 = 0.623, P = 0.431), indicating that females in this sample that nested close to one another were no more related than any two nesting females chosen at random. Eleven mutations were detected among hatchlings at the five loci over the 22 clutches. Most of these mutations (eight of 11) occurred at Ami(mu)-17, the only compound microsatellite locus of the five used in this study, corresponding to a mutation rate of 1.7 x 10-3. Finally, most of the mutations (82%) were homoplasious, i.e., mutating to an allelic state already present in this Louisiana population.     

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.     

The influence of sample size on two approaches to estimate Black Grouse Lyrurus tetrix population size using non-invasive sampling methods

Population size is an important parameter to monitor for species conservation and management. This is especially important for rare and endangered species, as declines can give information about anthropogenic impacts and the need for new conservation measures. To estimate population size, various methods of analysis can be used, for which sample size is an important factor. Sample size is particularly important to consider when applying non-invasive sampling strategies such as sampling faeces or feathers/hairs as a source of DNA, as a means to limit disturbance and stress for the species of concern. We investigated a Black Grouse Lyrurus tetrix population in the eastern part of the Alps, in East Tyrol (Austria), and estimated population size using two approaches: capture–recapture and rarefaction. With a set of 12 polymorphic microsatellite markers, we identified genotypes from faeces and feathers (backed up with 23 tissue samples) and checked for population substructure and gene flow among sampling sites. We estimated population size using four different models from the two approaches (molecular capture–recapture: TIRM, TIRMpart; rarefaction: hyperbolic function – Kohn, exponential function – Eggert). To evaluate the impact of sample size on the estimations, we used the full dataset of 500 samples (‘complete’ dataset) and half the dataset of 250 samples (‘half’ dataset). We also estimated the population size for each sex separately using complete and half datasets to check for sex-specific differences in population size. We found similar results in three of four models (capture–recapture: capwire TIRM, capwire TIRMpart; rarefaction: rarefaction Kohn). Using just half of the data increased the uncertainties in the estimation of population size in all models used and deviations were particularly large in females, which indicated a sex bias. Only the complete dataset of males had an observation rate of more than two observations/individual, and this observation rate meets the recommendation for using the capwire models. This indicates that, for species with different sex-specific detectability, larger sample sizes do not generally imply higher observation rates. We conclude that calculating the observation rates and population-size estimations for each sex separately can improve overall population-size estimation, especially in species with biased sex ratios and those that exhibit sex-specific behaviour.