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193 results for “Population connectivity”
Data from: Population genomics and connectivity of the blue mussel species complex: Insights from a North-east Atlantic hybrid zone
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Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population
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The demographic contributions of connectivity versus local dynamics to population growth of an endangered bird
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Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves
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Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania
<p>Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically-linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. Elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean FST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean AR = 9.96), heterozygosity (mean µHE = 0.73), and effective population sizes (mean Ne = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.</p>
Data from: Restricted connectivity and population genetic fragility in a globally endangered hammerhead shark
Vagile, large-bodied marine organisms frequently have wide range dispersion but also dependence on coastal habitats for part of their life-history. These characteristics may induce complex population genetic structure patterns, with resulting implications for the management of exploited populations. The scalloped hammerhead, Sphyrna lewini, is a cosmopolitan, migratory shark in tropical and warm temperate waters, inhabiting coastal bays during parturition and juvenile development and the open ocean as adults. Here, we investigated the genetic connectivity and diversity of S. lewini in the western Atlantic using large sample coverage (N=308), and data from whole mitochondrial control region (mtCR) sequences and ten nuclear microsatellite loci. We detected significant population genetic structure with both mtCR and microsatellites markers (mtCR: ΦST = 0.60; p < 0.001; microsatellites: Dest 0.0794, p = 0.001, FST = 0.046, p < 0.05), and isolation by distance (mtCR r = 0.363, p = 0.009; microsatellites r = 0.638, p = 0.007). The migration and gene flow patterns, based on mtCR and microsatellites were asymmetric, and female reproductive philopatry is postulated to explain such population subdivision patterns. The notable population differentiation at microsatellites markers indicates low-levels of male-mediated gene flow in the western Atlantic. The overall effective population size was estimated as 299 (215 – 412 Confidence Interval), and there was no evidence of strong or recent bottleneck effects. Findings of at least three management units, moderate genetic diversity, and low effective population size in the context of current overfishing calls for intensive management aimed at short and long-term conservation for this endangered species in the western Atlantic Ocean.
Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific
<p>Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on <em>Pocillopora damicornis</em> sensu stricto (or <em>Pocillopora </em>PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. <em>Pocillopora </em>PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region.</p> <p>This dataset contains the microsatellite genotypes analysed (458 <em>Pocillopora</em> PSH04 colonies × 13 loci).</p>
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
Data from: Herbivore control in connected seascapes: habitat determines when population regulation occurs in the life history of a key herbivore
Herbivore outbreaks often trigger catastrophic overgrazing events in marine macrophyte ecosystems. The sea urchin Paracentrotus lividus, the dominant herbivore of shallow Mediterranean seascapes, is capable of precipitating shifts to barrens when its populations explode. P. lividus is found ubiquitously in rocky macroalgal communities and in sandy seagrass meadows of Posidonia oceanica, two of the most important subtidal habitats in the Mediterranean. We explored if habitat-specific regulation across the principal stages of the urchin life cycle could help explain the persistence of these populations in connected mosaics. We measured each of three relevant ecological process (i.e. settlement, post-settlement survival and predation) across a wide stretch of the Mediterranean coast (ca. 600km). Our results show that habitat-specific regulation is critical in determining urchin populations: each habitat limited urchin sub-populations at different life stages. Settlement was never limiting; urchins settled at similar rates in both habitats across the coast. Post-settlement survival was a clear bottleneck, particularly in seagrass meadows where no juvenile urchins were recorded. Despite this bottleneck in seagrasses, adult urchin populations were very similar in both seagrass and macroalgal habitats indicating that other processes (potentially migration) could be key in determining adult distributions across the mosaic. The fact that population regulation is clearly habitat-specific suggests that sea urchin populations may be significantly buffered from bottlenecks in mixed seascapes where both habitats co-occur. Sea urchin populations can therefore persist across the seascape despite strong habitat-specific regulation either by maintaining reproductive output in one habitat or by migrating between them. By affording these regulatory escapes to habitat-modifying species, patchy mosaics may be much more prone to herbivore outbreaks and a host of cascading effects that come in their wake.
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data
Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.
Data from: Predicting global population connectivity and targeting conservation action for snow leopard across its range
Movements of individuals within and among populations help to maintain genetic variability and population viability. Therefore, understanding landscape connectivity is vital for effective species conservation. The snow leopard is endemic to mountainous areas of Central Asia and occurs within 12 countries. We assess potential connectivity across the species' range to highlight corridors for dispersal and genetic flow between populations, prioritizing research and conservation action for this wide-ranging, endangered top-predator. We used resistant kernel modeling to assess snow leopard population connectivity across its global range. We developed an expert-based resistance surface that predicted cost of movement as functions of topographical complexity and land cover. The distribution of individuals was simulated as a uniform density of points throughout the currently accepted global range. We modeled population connectivity from these source points across the resistance surface using three different dispersal scenarios that likely bracket the lifetime movements of individual snow leopard: 100km, 500km and 1000km. The resistant kernel models produced predictive surfaces of dispersal frequency across the snow leopard range for each distance scenario. We evaluated the pattern of connectivity in each of these scenarios and identified potentially important movement corridors and areas where connectivity might be impeded. The models predicted two regional populations, in the north and south of the species range respectively, and revealed a number of potentially important connecting areas. Discrepancies between model outputs and observations highlight unsurveyed areas of connected habitat that urgently require surveying to improve understanding of the global distribution and ecology of snow leopard, and target land management actions to prevent population isolation. The connectivity maps provide a strong basis for directed research and conservation action, and usefully direct the attention of policy makers.
Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands
Harnessing the power of genomic scans, we test the debated 'species pump' hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically inter-connected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75–130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification.
Data from: Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species' southern range margin
Low-latitudinal range margins of temperate and boreal plant species typically consist of scattered populations that persist locally in microrefugia. It remains poorly understood how their refugial habitats affect patterns of gene flow and connectivity, key components for their long-term viability and evolution. We examine landscape-scale patterns of historical and contemporary gene flow in refugial populations of the widespread European forest tree Pedunculate oak (Quercus robur) at the species' southwestern range margin. We sampled all adult trees (n = 135) growing in a 20 km long valley and genotyped 724 acorns from 72 mother trees at 17 microsatellite loci. The ten oak stands that we identified were highly differentiated and formed four distinct genetic clusters, despite sporadic historical dispersal being detectable. By far most contemporary pollination occurred within stands, either between local mates (85.6%) or through selfing (6.8%). Pollen exchange between stands (2.6%) was remarkably rare given their relative proximity and was complemented by long-distance pollen immigration (4.4%) and hybridization with the locally abundant Quercus pyrenaica (0.6%). The frequency of between-stand mating events decreased with increasing size and spatial isolation of stands. Overall, our results reveal outstandingly little long-distance gene flow for a wind-pollinated tree species. We argue that the distinct landscape characteristics of oaks' refugial habitats, with a combination of a rugged topography, dense vegetation and humid microclimate, are likely to increase plant survival but to hamper effective long-distance pollen dispersal. Moreover, local mating might be favoured by high tree compatibility resulting from genetic purging in these long-term relict populations.
Data from: Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents
This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups; (1) samples from the Zanzibar channel, (2) Mozambique, (3) Madagascar, and (4) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (DEST), but the three predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale – across national boarders.
Data from: Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)
Pelagic larval duration (PLD) has been hypothesized to be the primary predictor of connectivity in marine fishes; however, few studies have examined the effects that adult reproductive behaviour may have on realized dispersal. We assessed gene flow (connectivity) by documenting variation in microsatellites and mitochondrial DNA sequences in two protogynous species of groupers, the aggregate spawning red hind, Epinephelus guttatus, and the single-male, harem-spawning coney, Cephalopholis fulva, to ask if reproductive strategy affects connectivity. Samples of both species were obtained from waters off three islands (Puerto Rico, St. Thomas, and St. Croix) in the Caribbean Sea. Despite the notion that aggregate spawning of red hind may facilitate larval retention, stronger signals of population structure were detected in the harem-spawning coney. Heterogeneity and/or inferred barriers, based on microsatellites, involved St. Croix (red hind and coney) and the west coast of Puerto Rico (coney). Heterogeneity and/or inferred barriers, based on mitochondrial DNA, involved St. Croix (coney only). Genetic divergence in both species was stronger for microsatellites than for mitochondrial DNA, suggesting sex-biased dispersal in both species. Long-term migration rates, based on microsatellites, indicated asymmetric gene flow for both species in the same direction as mean surface currents in the region. Red hind had higher levels of variation in microsatellites and lower levels of variation in mitochondrial DNA. Long-term effective size and effective number of breeders were greater for red hind; estimates of θf a proxy for long-term effective female size, were the same in both species. Patterns of gene flow in both species appear to stem in part from shared aspects of larval and adult biology, local bathymetry, and surface current patterns. Differences in connectivity and levels of genetic variation between the species, however, likely stem from differences in behaviour related to reproductive strategy.
Data from: Loss of functional connectivity in migration networks induces population decline in migratory birds
Migratory birds rely on a habitat network along their migration routes by temporarily occupying stopover sites between breeding and non-breeding grounds. Removal or degradation of stopover sites in a network might impede movement, and thereby reduce migration success and survival. The extent to which the breakdown of migration networks, due to changes in land use, impacts the population sizes of migratory birds is poorly understood. We measured the functional connectivity of migration networks of waterfowl species that migrate over the East Asian-Australasian Flyway from 1992-2015. We analysed the relationship between changes in non-breeding population sizes and changes in functional connectivity, while taking into account other commonly-considered species traits, using a Phylogenetic Linear Mixed Model. We found that population sizes significantly declined with a reduction in the functional connectivity of migration networks; no other predictor variables were important. We conclude that the current decrease in functional connectivity, due to habitat loss and degradation in migration networks, can negatively and crucially impact population sizes of migratory birds. Our findings provide new insights into the underlying mechanisms that affect population trends of migratory birds under environmental changes. Establishment of international agreements leading to the creation of systematic conservation networks associated with migratory species' distributions and stopover sites may safeguard migratory bird populations.
Data from: Consistent scaling of population structure across landscapes despite intraspecific variation in movement and connectivity
Understanding the spatial scale of population structure is fundamental to long-standing tenets of population biology, landscape ecology and conservation. Nonetheless, identifying such scales has been challenging because a key factor that influences scaling – movement among patches or local populations – is a multicausal process with substantial phenotypic and temporal variation. We resolve this problem via a novel application of network modularity. When applied to movements, modularity provides a formal description of the functional aggregation of populations and identifies potentially critical scales for ecological and evolutionary dynamics. We first test for modularity using several different types of biologically relevant movements across the entire geographic range of an endangered bird, the snail kite (Rostrhamus sociabilis plumbeus). We then ask whether variation in movement based on (i) age, (ii) sex and (iii) time (annual, seasonal and within-season movements) influences spatial population structure (i.e. modularity) in snail kites. We identified significant modularity in annual dispersal of snail kites (all adults, males only, females only, and juveniles only) and in within-breeding season movements of adults, yet no evidence of modularity in seasonal (non-breeding) movements. For those movements with observed modular structure, we found striking similarities in the spatial configuration of population structure, even though movement properties varied considerably among these different types of movements. Our results suggest that the emergence of modularity in population networks can be robust despite movement heterogeneity and differences in patch-based measures of connectivity. Furthermore, our comparison of the population structure and connectivity across multiple movement phases helps to identify wetland patches most critical to population connectivity at multiple spatiotemporal scales. We argue that understanding modularity in populations may provide a robust complement to existing measures of population structure and connectivity and will help to clarify the limiting roles of movement for populations. Such information is increasingly needed for interpreting population persistence and guiding effective conservation strategies with ongoing environmental change.
Data from: Genetic variation and seasonal migratory connectivity in Wilson's warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations
There is growing interest in understanding patterns of seasonal migratory connectivity between breeding and wintering sites, both because differences in migratory behavior can be associated with population differentiation and because knowledge of migratory connectivity is essential for understanding the ecology, evolution, and conservation of migratory species. We present the first broad survey of geographic variation in the nuclear genome of breeding and wintering Wilson's warblers (Wilsonia pusilla), which have previously served as a research system for the study of whether genetic markers and isotopes can reveal patterns of migratory connectivity. Using 153 samples surveyed at up to 257 variable amplified fragment length polymorphism (AFLP) markers, we show that Wilson's warblers consist of highly distinct western and eastern breeding groups, with all winter samples grouping with the western breeding group. Within the west there is weak geographic differentiation, at a level insufficient for use in assignment of wintering samples to specific areas. The distinctiveness of western and eastern genetic groups, with no known intermediates, strongly suggests that these two groups are cryptic species. Analysis of mitochondrial cytochrome b sequence variation shows that the estimated coalescence time between western and eastern clades is roughly 2.3 million years ago, a surprisingly old time of divergence that is more typical of distinct species than of subspecies. Given their morphological similarity but strong genetic differences, western and eastern Wilson's warblers present a likely case of association between divergence in migratory behavior and the process of speciation.
Data from: Divergent landscape effects on population connectivity in two co-occurring amphibian species
The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi-species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern U.S. and estimated the influence of specific landscape features on observed genetic patterns. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.
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