Coyote movements and social structure along a cryptic population genetic subdivision

A recent region-wide study determined that the central California coyote (Canis latrans) population was genetically subdivided according to habitat bioregions, supporting the hypothesis that coyotes exhibit a dispersal bias toward their natal habitat type. Here, we further investigated this hypothesis using radio-collared coyotes captured on a 150-km(2) study site on the border of (i.e. overlapping) two bioregions (Great Valley and Cascade Mountains). As predicted, most coyotes were assigned (based on a priori genetic criteria) to genetic clusters corresponding to one of these two bioregions. All of those assigned to the Great Valley genetic cluster were caught in (and for the most part, remained in) the Great Valley bioregion. However, contrary to expectations, the coyotes assigned to the Cascades genetic cluster occurred commonly in both bioregions. Nearly all resident individuals on the study site, regardless of the particular bioregion, were assigned to the Cascades genetic cluster, whereas a sizable fraction of nonresident (transient or dispersing) coyotes caught in the Great Valley bioregion were assigned to the Great Valley cluster. Even among resident coyotes, interrelatedness of packs was greater within than between bioregions, and packs with territories overlapping both bioregions were more closely related to those with territories completely within the Cascades bioregion than territories completely within the Great Valley bioregion. Finally, direct estimates indicated that gene flow was twice as high from the Cascades bioregion to the Great Valley bioregion than in the reverse direction. Collectively, these findings reveal the anatomy of the genetic subdivision as beginning abruptly at the bioregion boundary and ending diffusely within the Great Valley bioregion.     

Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences

To help stem the precipitous decline of coral reef ecosystems world-wide, conservation efforts are focused on establishing interconnected reserve networks to protect threatened populations. Because many coral reef organisms have a planktonic or pelagic larval dispersal phase, it is critical to understand the patterns of ecological connectivity between reserve populations that result from larval dispersal. We used genetics to infer dispersal patterns among 24 Indo-West Pacific populations of the mantis shrimp, Haptosquilla pulchella. Contrary to predictions of high dispersal facilitated by the strong currents of the Indonesian throughflow, mitochondrial DNA sequences from 393 individuals displayed striking patterns of regional genetic differentiation concordant with ocean basins isolated during periods of lowered sea level. Patterns of genetic structuring indicate that although dispersal within geographical regions with semicontiguous coastlines spanning thousands of kilometres may be common, ecologically meaningful connections can be rare among populations separated by as little as 300 km of open ocean. Strong genetic mosaics in a species with high dispersal potential highlight the utility of genetics for identifying regional patterns of genetic connectivity between marine populations and show that the assumption that ocean currents will provide ecological connectivity among marine populations must be empirically tested in the design of marine reserve networks.     

The number of breeders explains genetic connectivity in an endangered bird

Connectivity is central to ecology and evolution as it focuses on the movement of individuals or genes across landscapes. Genetic connectivity approaches aim to understand gene flow but often estimate it indirectly based on metrics of genetic differentiation, which can also be affected by other evolutionary forces such as genetic drift. Gene flow and genetic drift are driven by separate ecological mechanisms with potentially differing effects on genetic differentiation and interpretations of genetic connectivity. The ecological mechanisms contributing to gene flow and genetic drift are primarily effective dispersal, or movement followed by successful reproduction, and the number of breeders in a local population, N_b, respectively. Yet, rarely are these ecological mechanisms and genetic connectivity measured simultaneously across landscapes. We examine the roles of effective dispersal and N_b on genetic connectivity across the entire range of the endangered snail kite (Rostrhamus sociabilis plumbeus), between 2006–2015. We find that both N_b and effective dispersal are important predictors of genetic connectivity across this landscape, but that N_b has a 3 × stronger effect on genetic connectivity. Furthermore, N_b is positively correlated with heterozygosity and allelic richness within patches, suggesting a potentially important role of genetic drift, in addition to gene flow, on genetic connectivity. These results emphasize that conservation efforts should focus on not only between‐patch processes of movement but also within‐patch processes regarding habitat quality and local population size for increasing genetic connectivity.     

Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti

In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high‐population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.     

Does life history predict past and current connectivity for rocky intertidal invertebrates across a marine biogeographic barrier?

The southeast Australian coast potentially includes a complex biogeographic barrier, largely lacking exposed rocky shore that may limit the dispersal of rocky intertidal taxa and contribute to the maintenance of two biogeographic regions. Surprisingly, within the 300-km barrier region, several species considered exposed rocky shore specialists occurred within sheltered sites. We analysed COI sequence variation for 10 rocky intertidal invertebrate species, with a range of life histories, to test the hypotheses that larval type and habitat specificity are strong predictors of gene flow between biogeographic regions. Our data revealed that the southeast corner of Australia includes a strong barrier to gene flow for six of eight species with planktonic larvae, and a coalescence analysis of sequence differentiation (IM model) suggests that a barrier has existed since the Pleistocene. In contrast, two direct developers were not affected by the barrier. Our comparative approach and data from earlier studies (reviewed here) do not support the hypothesis that larval type predicts gene flow across this barrier, instead we found that the ability to utilize sheltered habitat provides a clearer explanation of the phylogeographic break. Indeed, the species that displayed little or no evidence of a phylogeographic break across the barrier each displayed unexpectedly relaxed habitat specificity.     

长山列岛南部三岛岩相潮间带群落多样性格局

对长山列岛南部南长山、北长山和大黑山岛屿岩相潮间带群落种类组成的调查表明,3岛屿岩礁潮间带的群落结构差异不大,表现在决定群落结构和外貌的前5位优势种群及其优势度序列基本相同;而砾石潮间带的群落结构存在一定差异,表现在北长山群落中优势种群及其优势度序列显著地区别于南长山和大黑山,但后二者趋同-3岛屿岩礁潮间带的景观和群落外貌与结构由东方小藤壶(Chthamalus chal-lengeri)、牡蛎（Ostrea spp.)、大型藻类和短滨螺(Littorina breuicula)控制,砾石潮间带则由东方小藤壶、大型藻类和平背蜞（Gaetice depressus)决定．群落多样性由物种丰富度(R)、均匀度(J)和多样性(HB、Hlv、DR、DIv)衡量,3岛屿岩礁潮间带群落的各种多样性指数呈现一致性,群落多样性以北长山最高,大黑山最低;而砾石潮间带群落的各种多样性指数存在一定差异,南长山高于北长山和大黑山,北长山潮间带群落中物种分布的均匀度最高,南长山和大黑山趋同．比较3岛屿两种基质潮间带的群落多样性发现,砾石潮间带高于岩礁潮间带。     

Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history

We examine estimates of dispersal in a broad range of marine species through an analysis of published values, and evaluate how well these values represent global patterns through a comparison with correlates of dispersal. Our analysis indicates a historical focus in dispersal studies on low-dispersal/low-latitude species, and we hypothesize that these studies are not generally applicable and representative of global patterns. Large-scale patterns in dispersal were examined using a database of correlates of dispersal such as planktonic larval duration (PLD, 318 species) and genetic differentiation (FST, 246 species). We observed significant differences in FST (p<0.001) and PLD (p<0.001) between taxonomic groups (e.g. fishes, cnidarians, etc.). Within marine fishes (more than 50% of datasets), the prevalence of demersal eggs was negatively associated with PLD (R2=0.80, p<0.001) and positively associated with genetic structure (R2=0.74, p<0.001). Furthermore, dispersal within marine fishes (i.e. PLD and FST) increased with latitude, adult body size and water depth. Of these variables, multiple regression identified latitude and body size as persistent predictors across taxonomic levels. These global patterns of dispersal represent a first step towards understanding and predicting species-level and regional differences in dispersal, and will be improved as more comprehensive data become available.     

Demographic and genetic connectivity: the role and consequences of reproduction,dispersal and recruitment in seagrasses

Accurate estimation of connectivity among populations is fundamental for determining the drivers of population resilience, genetic diversity, adaptation and speciation. However the separation and quantification of contemporary versus historical connectivity remains a major challenge. This review focuses on marine angiosperms, seagrasses, that are fundamental to the health and productivity of temperate and tropical coastal marine environments globally. Our objective is to understand better the role of sexual reproduction and recruitment in influencing demographic and genetic connectivity among seagrass populations through an integrated multidisciplinary assessment of our present ecological, genetic, and demographic understanding, with hydrodynamic modelling of transport. We investigate (i) the demographic consequences of sexual reproduction, dispersal and recruitment in seagrasses, (ii) contemporary transport of seagrass pollen, fruits and seed, and vegetative fragments with a focus on hydrodynamic and particle transport models, and (iii) contemporary genetic connectivity among seagrass meadows as inferred through the application of genetic markers. New approaches are reviewed, followed by a summary outlining future directions for research: integrating seascape genetic approaches; incorporating hydrodynamic modelling for dispersal of pollen, seeds and vegetative fragments; integrating studies across broader geographic ranges; and incorporating non‐equilibrium modelling. These approaches will lead to a more integrated understanding of the role of contemporary dispersal and recruitment in the persistence and evolution of seagrasses.     

Exploring patterns of population subdivision in the net-winged midge, Elporia barnardi (Diptera: Blephariceridae), in mountain streams of the south-western Cape, South Africa

1. The net-winged midges (Diptera: Blephariceridae) are a highly specialized group whose morphological characteristics and specific habitat requirements suggest a limited potential for dispersal. Levels of genetic variation were examined within streams, between streams in the same range and between mountain ranges in larval populations of Elporia barnardi in the south-western Cape of South Africa. The aim was to examine the hypothesis that population structure would reflect the poor potential for dispersal.
2. Significant deviations from Hardy–Weinberg equilibrium in 17 of the 57 individual comparisons indicate a non-random mating population. Given the swarming behaviour and life history traits, larvae sampled may reflect the product of limited matings.
3. Analysis of population substructuring revealed significant levels of differentiation among geographically proximate populations. Large differences between streams within Table Mountain, similar in magnitude to those between mountain ranges, suggest that movement of individuals out of the stream catchment is rare. Observed F _ST values are more similar to those of fully aquatic species than other lotic insects with winged adult stages.
4. Results suggest that mountain ridges provided effective physical barriers to the dispersal of E. barnardi , with the catchment representing the effective population unit.     

Restoration of genetic connectivity among Northern Rockies wolf populations

Probably no conservation genetics issue is currently more controversial than the question of whether grey wolves (Canis lupus) in the Northern Rockies have recovered to genetically effective levels. Following the dispersal‐based recolonization of Northwestern Montana from Canada, and reintroductions to Yellowstone and Central Idaho, wolves have vastly exceeded population recovery goals of 300 wolves distributed in at least 10 breeding pairs in each of Wyoming, Idaho and Montana. With >1700 wolves currently, efforts to delist wolves from endangered status have become mired in legal battles over the distinct population segment (DPS) clause of the Endangered Species Act (ESA), and whether subpopulations within the DPS were genetically isolated. An earlier study by vonHoldt et al. (2008) suggested Yellowstone National Park wolves were indeed isolated and was used against delisting in 2008. Since then, wolves were temporarily delisted, and a first controversial hunting season occurred in fall of 2009. Yet, concerns over the genetic recovery of wolves in the Northern Rockies remain, and upcoming District court rulings in the summer of 2010 will probably include consideration of gene flow between subpopulations. In this issue of Molecular Ecology, vonHoldt et al. (2010) conduct the largest analysis of gene flow and population structure of the Northern Rockies wolves to date. Using an impressive sampling design and novel analytic methods, vonHoldt et al. (2010) show substantial levels of gene flow between three identified subpopulations of wolves within the Northern Rockies, clarifying previous analyses and convincingly showing genetic recovery.     

The role of altitude and associated habitat stability in determining patterns of population genetic structure in two species of Atalophlebia (Ephemeroptera: Leptophlebiidae)

1. Previous studies have identified lowland areas as barriers to gene flow (dispersal) between distinct mountain ranges in montane species of aquatic insects. In this study, we investigated the population genetic structure of two closely related Atalophlebia (mayfly) species inhabiting lowland areas of south‐east Queensland, Australia, with the expectation of widespread gene flow throughout the low‐altitude environment and associated homogeneous genetic structure. 2. In particular, we asked whether species with lower‐altitude distributions demonstrate greater spatial distribution of mtDNA (COI) alleles than the upland species studied previously. This pattern would be expected if good dispersal ability is associated with population persistence in these drought‐prone habitats. 3. The two species demonstrated contrasting genetic population structure. Atalophlebia sp. AV13 D revealed strong population structure, with populations on each side of the low‐altitude area isolated from each other for a long time (c.350 kya), and the presence of an isolation‐by‐distance pattern over relatively small geographical distances (<40 km). In contrast, Atalophlebia sp. AV13 A was panmictic at the scale investigated (≤160 km), with no history of past population fragmentation. 4. Examination of sample distribution along the altitudinal gradient reveals that Atalophlebia sp. AV13 D may have a more upland distribution (associated with greater habitat stability) than previously supposed, while Atalophlebia sp. AV13 A inhabits more xeric lowland areas, where freshwater habitats are less stable. We consequently hypothesise that these contrasting genetic population structures result from differences in habitat stability along the altitudinal gradient, only species with good dispersal ability being able to persist in unstable habitats. These findings may be applicable to other regions of the globe where habitat instability is associated with altitudinal gradients.     

Stable genetic polymorphism in heterogeneous environments: balance between asymmetrical dispersal and selection in the acorn barnacle

Elucidating the processes responsible for maintaining polymorphism at ecologically relevant genes is intimately related to understanding the interplay between selection imposed by habitat heterogeneity and a species' capacity for dispersal in the face of environmental constraints. In this paper, we used a model-based approach to solve equilibria of balanced polymorphism, given values of fitness and larval dispersal among different habitats in the acorn barnacle Semibalanus balanoides from the Gulf of St Lawrence. Our results showed that allele frequencies observed at both MPI* and GPI* loci represented stable equilibria, given empirical estimates of fitness values, and that considerably more larvae dispersed from one region (north) to the other (south) than vice versa. Dispersal conditions were predicted to be similar for the maintenance of polymorphism at both loci. Moreover, the values of asymmetrical dispersal required by the model to reach stable equilibria were compatible with empirical estimates of larval dispersal and oceanic circulation documented in this system. Overall, this study illustrated the usefulness of a modified and computable version of Bulmer's model (1972) in order to test hypotheses of balanced polymorphism resulting from interactions between spatial selection and asymmetrical dispersal.     

Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that populations within species are highly differentiated in terms of their morphology, behaviour, ecology and molecular genetic variation. Despite this level of variability, differences between species are sometimes small, possibly reflecting the fact that reproductive isolation is not always complete and there exists the opportunity for genetic exchange between taxa through hybridization. The present study uses sequence data from a mitochondrial gene to further investigate genetic variation in Society Island Partula. Most populations are found in this study to be highly differentiated, but within individual species there seems to be no simple relationship either between genetic distance and geographical proximity, or between variation in mitochondria and that in allozymes or morphological characteristics. Among species there appears to be no simple correlation between degrees of reproductive isolation and genetic relatedness according to mitochondrial DNA. The results suggest that past events as well as ongoing drift and selection may have been important in affecting patterns of variation. Similarities among species at specific localities suggest that there must have been some genetic exchange in the past, although this may not necessarily reflect ongoing rates of hybridization. The discrepancy between results for different markers probably reflects the differential effects of drift and selection on mitochondrial and nuclear genes.     

Spatial genetic analysis of two polyploid macrophytes reveals high connectivity in a modified wetland

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Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish

Detecting patterns of spatial genetic structure (SGS) can help identify intrinsic and extrinsic barriers to gene flow within metapopulations. For marine organisms such as coral reef fishes, identifying these barriers is critical to predicting evolutionary dynamics and demarcating evolutionarily significant units for conservation. In this study, we adopted an alternative hypothesis‐testing framework to identify the patterns and predictors of SGS in the Caribbean reef fish Elacatinus lori. First, genetic structure was estimated using nuclear microsatellites and mitochondrial cytochrome b sequences. Next, clustering and network analyses were applied to visualize patterns of SGS. Finally, logistic regressions and linear mixed models were used to identify the predictors of SGS. Both sets of markers revealed low global structure: mitochondrial Φ_ST = 0.12, microsatellite F_ST = 0.0056. However, there was high variability among pairwise estimates, ranging from no differentiation between sites on contiguous reef (Φ_ST = 0) to strong differentiation between sites separated by ocean expanses ≥ 20 km (maximum Φ_ST = 0.65). Genetic clustering and statistical analyses provided additional support for the hypothesis that seascape discontinuity, represented by oceanic breaks between patches of reef habitat, is a key predictor of SGS in E. lori. Notably, the estimated patterns and predictors of SGS were consistent between both sets of markers. Combined with previous studies of dispersal in E. lori, these results suggest that the interaction between seascape continuity and the dispersal kernel plays an important role in determining genetic connectivity within metapopulations.     

Linking movement and reproductive history of brook trout to assess habitat connectivity in a heterogeneous stream network

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A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50‐km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free‐living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.