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opencc-zeroDec 2010View details →

Data from: Temporal population-genetic structure of eastern mosquitofish in a dynamic aquatic landscape

We analyzed the effect of periodic drying in the Florida Everglades on spatio-temporal population genetic structure of eastern mosquitofish (Gambusia holbrooki). Severe periodic drying events force individuals from disparate sources to mix in dry-season relatively deep-water refuges. In 1996 (a wet year) and 1999 (a dry year), we sampled mosquitofish at 20 dry-season refuges distributed in three water-management regions and characterized genetic variation for 10 allozyme and 3 microsatellite loci. In 1996, most of the ecosystem did not dry, while in 1999, many of our sampling locations were isolated by expanses of dried marsh surface. In 1996, most spatial genetic variation was attributed to heterogeneity within regions. In 1999, spatial genetic variation within regions was not significant. In both years, a small but significant amount of variation (less than 1% of the total variation) was partitioned among regions. Variance was consistently greater than zero among long-hydroperiod sites within a region, but not among short-hydroperiod sites within a region, where hydroperiod was measured as time since last marsh surface dry-down forcing fishes into local refuges. In 1996, all sites were in Hardy-Weinberg equilibrium. In 1999, we observed fewer heterozygotes than expected for most loci and sites suggesting a Wahlund effect arising from fish leaving areas that dried and mixing in deep-water refuges.

Data from: The role of predation and food limitation on claims for compensation, reindeer demography and population dynamics

1. A major challenge in biodiversity conservation is to facilitate viable populations of large apex predators in ecosystems where they were recently driven to ecological extinction due to resource conflict with humans. 2. Monetary compensation for losses of livestock due to predation is currently a key instrument to encourage human–carnivore coexistence. However, a lack of quantitative estimates of livestock losses due to predation leads to disagreement over the practise of compensation payments. This disagreement sustains the human–carnivore conflict. 3. The level of depredation on year-round, free-ranging, semi-domestic reindeer by large carnivores in Fennoscandia has been widely debated over several decades. In Norway, the reindeer herders claim that lynx and wolverine cause losses of tens of thousands of animals annually and cause negative population growth in herds. Conversely, previous research has suggested that monetary predator compensation can result in positive population growth in the husbandry, with cascading negative effects of high grazer densities on the biodiversity in tundra ecosystems. 4. We utilized a long-term, large-scale dataset to estimate the relative importance of lynx and wolverine predation and density-dependent and climatic food limitation on claims for losses, recruitment and population growth rates in Norwegian reindeer husbandry. 5. Claims of losses increased with increasing predator densities, but with no detectable effect on population growth rates. Density-dependent and climatic effects on claims of losses, recruitment and population growth rates, were much stronger than the effects of variation in lynx and wolverine densities. 6. Synthesis and applications. Our analysis provides a quantitative basis for predator compensation and estimation of the costs of reintroducing lynx and wolverine in areas with free-ranging semi-domestic reindeer. We outline a potential path for conflict management which involves adaptive monitoring programs, open access to data, herder involvement, and development of management strategy evaluation (MSE) models to disentangle complex responses including multiple stakeholders and individual harvester decisions.

opencc-zeroDec 2016View details →

Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus

Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

Data from: Gene flow between wolf and shepherd dog populations in Georgia (Caucasus)

We studied the distribution of the mitochondrial DNA haplotypes and microsatellite genotypes at eight loci in 102 grey wolves, 57 livestock guarding dogs, and 9 mongrel dogs from Georgia (Caucasus). Most of the studied dogs had mitochondrial haplotypes clustered with presumably East Asian dog lineages, and most of the studied wolves had the haplotypes clustered with European wolves, but 20% of wolves and 37% of dogs shared the same mitochondrial haplotypes. Bayesian inference with STRUCTURE software suggested that over 13% of the studied wolves had detectable dog ancestry and over 10% of the dogs had detectable wolf ancestry. 2-3% of the sampled wolves and dogs were identified, with a high probability, as first generation hybrids. These results were supported by the relatedness analysis which showed that 10% of wolves and 20% of dogs had closest relatives from an opposite group. The results of the study suggest that wolf-dog hybridization is a common event in the areas where large livestock guarding dogs are held in a traditional way, and that gene flow between dogs and grey wolves was an important force influencing gene pool of dogs for millennia since early domestication events. This process may have been terminated (1) in areas outside the natural range of grey wolves and (2) since very recent time, when humans started to more tightly control contacts of purebred dogs.

Data from: Successful eradication of a suburban Pallas's squirrel Callosciurus erythraeus (Pallas 1779) (Rodentia, Sciuridae) population in Flanders (northern Belgium)

Despite a growing catalogue of eradication projects, documented successful vertebrate eradications on the mainland remain scarce. Reporting on successful campaigns is crucial to counter pessimism on ambitious programmes to tackle invasive species and to allow conservation practitioners, wildlife managers and scientist to learn from previous experience. Moreover, there is a need for basic information on the effectiveness of control methods and management strategies that can be used. In this note we report on a successful low-tech eradication campaign of a local population of Pallas's squirrel Callosciurus erythraeus, a species of tree squirrel with documented ecological and socio-economic impacts in its invasive range. The population was eradicated from a suburban park of about 15 ha using baited mesh wire life traps, in five consecutive capture campaigns between October 2005 and January 2011. Using maximum likelihood estimation from catch-effort data we calculated initial densities in the park at 3 squirrels ha−1. Although control started quickly and the extent of the invasion was limited, the campaign took over 5 years and required an estimated investment of over €200,000 including 1.5 years of post-eradication surveying. We provide basic data on the methods used to eradicate this invasive rodent. Critical success factors and possible improvements with respect to the specific context of this case are discussed. Adding this species to the list of species of EU concern currently under development could provide incentive to minimise impact of this tree squirrel at the continental scale.

opencc-zeroDec 2015View details →

Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration

Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species. Results: Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2–5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours. Conclusions: Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.

Data from: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating-type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.

opencc-zeroDec 2017View details →

Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)

In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) have been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single nucleotide polymorphisms (SNPs) capable of discriminating between northern and southern clusters, we examined fine-scale genetic structure of scallops among 27 sample locations, spanning the largest geographic range evaluated in this species to date (~37-51°N). Here, we confirmed previous observations of northern and southern groups, but we show that the boundary between northern and southern clusters is not a discrete latitudinal break. Instead, at latitudes near the previously described boundary, we found unexpected patterns of fine-scale genetic structure occurring between inshore and offshore sites. Scallops from offshore sites, including St. Pierre Bank and the eastern Scotian Shelf, clustered with southern stocks, whereas inshore sites at similar latitudes clustered with northern stocks. Our analyses revealed significant genetic divergence across small spatial scales (i.e., 129 to 221 km distances), and that spatial structure over large and fine scales was strongly associated with temperature during seasonal periods of thermal minima. Clear temperature differences between inshore and offshore locations may explain the fine-scale structuring observed, such as why southern lineages of scallop occur at higher latitudes in deeper, warmer offshore waters. Our study supports growing evidence that fine-scale population structure in marine species is common, often environmentally associated, and that consideration of environmental and genomic data can significantly enhance the identification of marine diversity and management units.

Data from: Rapid buildup of genetic diversity in founder populations of the gynodioecious plant species Origanum vulgare after semi-natural grassland restoration

In most landscapes the success of habitat restoration is largely dependent on spontaneous colonization of plant species. This colonization process, and the outcome of restoration practices, can only be considered successful if the genetic makeup of founding populations is not eroded through founder effects and subsequent genetic drift. Here we used 10 microsatellite markers to investigate the genetic effects of recent colonization of the long-lived gynodioecious species Origanum vulgare in restored semi-natural grassland patches. We compared the genetic diversity and differentiation of fourteen recent populations with that of thirteen old, putative source populations, and we evaluated the effects of spatial configuration of the populations on colonization patterns. We did not observe decreased genetic diversity in recent populations, or inflated genetic differentiation among them. Nevertheless, a significantly higher inbreeding coefficient was observed in recent populations, although this was not associated with negative fitness effects. Overall population genetic differentiation was low (FST = 0.040). Individuals of restored populations were assigned to on average 6.1 different source populations (likely following the 'migrant pool' model). Gene flow was, however, affected by the spatial configuration of the grasslands, with gene flow into the recent populations mainly originating from nearby source populations. This study demonstrates how spontaneous colonization after habitat restoration can lead to viable populations in a relatively short time, overcoming pronounced founder effects, when several source populations are nearby. Restored populations can therefore rapidly act as stepping stones and sources of genetic diversity, likely increasing overall metapopulation viability of the study species.

Data from: Contrasting genetic responses to population fragmentation in a coevolving fig and fig wasp across a mainland-island archipelago

Interacting species of pollinator–host systems, especially the obligate ones, are sensitive to habitat fragmentation, due to the nature of mutual dependence. Comparative studies of genetic structure can provide insights into how habitat fragmentation contributes to patterns of genetic divergence among populations of the interacting species. In this study, we used microsatellites to analyse genetic variation in Chinese populations of a typical mutualistic system – Ficus pumila and its obligate pollinator Wiebesia sp. 1 – in a naturally fragmented landscape. The plants and wasps showed discordant patterns of genetic variation and geographical divergence. There was no significant positive relationship in genetic diversity between the two species. Significant isolation-by-distance (IBD) patterns occurred across the populations of F. pumila and Wiebesia sp. 1 as whole, and IBD also occurred among island populations of the wasps, but not the plants. However, there was no significant positive relationship in genetic differentiation between them. The pollinator populations had significantly lower genetic variation in small habitat patches than in larger patches, and three island pollinator populations showed evidence of a recent bottleneck event. No effects of patch size or genetic bottlenecks were evident in the plant populations. Collectively, the results indicate that, in more fragmented habitats, the pollinators, but not the plants, have experienced reduced genetic variation. The contrasting patterns have multiple potential causes, including differences in longevity and hence number of generations experiencing fragmentation; different dispersal patterns, with the host's genes dispersed as seeds as well as a result of pollen dispersal via the pollinator; asymmetrical responses to fluctuations in partner populations; and co-existence of a rare second pollinating wasp on some islands. These results indicate that strongly interdependent species may respond in markedly different ways to habitat fragmentation.

Data from: Murky waters: searching for structure in genetically depauperate blue threadfin populations of Western Australia

The blue threadfin (Eleutheronema tetradactylum) is an exploited fishery species in southeast Asia and Australia. Demographic studies have revealed fine-scale stock structure throughout the Australian coastline, with demographically isolated populations separated by only tens of km. Similarly, population genetic analysis revealed fine-scale structure across most of its Australian range with important implications for fisheries management. However, in northern Western Australia, genetic stock structure analysis showed a contradictory lack of structure. In the present study, one mtDNA marker and a suite of five microsatellite loci were used to further investigate the stock structure of Western Australian blue threadfin populations. By increasing sample sizes from previously investigated areas: Roebuck Bay (n = 93 adults) and Eighty-mile Beach (n = 92 adults and 163 recruits from two settlement cohorts), we were able to detect subtle genetic differentiation that was previously obscured by low levels of genetic polymorphism. Therefore, the same fine-scale stock structure that has been observed elsewhere in this species also appears to exist in Western Australia. This has clear ramifications for a revised management strategy that incorporates the fine scale structuring of northwest Western Australian stocks of the blue threadfin.

Data from: Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations

We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking). To illustrate and test our approach, we focus on western Lake Erie's yellow perch (Perca flavescens) population during 2006–2007, using microsatellite DNA and otolith microchemistry from larvae and juveniles as natural tags. Particle backtracking showed that not all larvae collected near a presumed hatching location may have originated there, owing to passive drift during the larval stage that was influenced by strong river- and wind-driven water circulation. Re-assigning larvae to their most probable hatching site (based on probabilistic dispersal trajectories from the particle backtracking model) improved the use of genetics and otolith microchemistry to discriminate among local breeding subpopulations. This enhancement, in turn, altered (and likely improved) the estimated contributions of each breeding subpopulation to the mixed population of juvenile recruits. Our findings indicate that particle backtracking can complement existing tools used to identify the origin of individuals in mixed populations, especially in flow-dominated systems.

opencc-zeroDec 2016View details →

Data from: Balancing ecological costs and benefits of fire for population viability of disturbance-dependent butterflies

Disturbance is a fundamental ecological process and driver of population dynamics. Ecologists seek to understand the effects of disturbance on ecological systems and to use disturbance to modify habitats degraded by anthropogenic change. Demographic responses by plants to disturbance are often well described, but demographic responses by animals are less understood. This limits development of applied strategies that leverage disturbance to augment animal populations. We estimated demographic and behavioural responses of an endangered butterfly, Fender's blue, Plebejus icarioides fenderi, to experimental burning in Oregon, USA. We monitored butterfly vital rates for four years post-fire. Prescribed fire killed Fender's blue larvae. However, fecundity was higher relative to reference/unburned areas for two years after the burn and overwinter larval survivorship was higher for a year after the burn. Fire treatments did not influence adult movement behaviour. We used matrix models to project butterfly population dynamics in fire-driven successional landscapes. We compared optimal burn strategies given targeted burns, such as prescribed fire, to undirected burns, such as wildfires. Disturbance enhances population growth rate under both strategies, and the optimal proportion of landscape burned is similar in both cases. However, targeted burning leads to substantially higher population growth rates. Synthesis and applications. Demographic models allow planning of long-term and large-scale disturbance by balancing initial costs of disturbance with subsequent benefits. We use matrix models to project population growth in fire-driven successional landscapes and contrast prescribed burns with undirected burns (wildfires). We also use these models to evaluate the influence of local vs. non-local dispersal. Because random (non-local) dispersal allows individuals to disperse into areas that were just burned, non-local dispersal always increases population growth rates in this system. This contrasts with source-sink dynamics in stationary environments, in which local dispersal leads to higher population growth rates. Our matrix modelling approach has broad application to other disturbance-dependent taxa surviving in anthropogenically modified landscapes, and could be more widely applied to animal populations.

Data from: Investigation of genetic structure between deep and shallow populations of the southern rock lobster, Jasus edwardsii in Tasmania, Australia

The southern rock lobster, Jasus edwardsii, shows clear phenotypic differences between shallow water (red coloured) and deeper water (pale coloured) individuals. Translocations of individuals from deeper water to shallower waters are currently being trialled as a management strategy to facilitate a phenotypic change from lower value pale colouration, common in deeper waters, to the higher value red colouration found in shallow waters. Although panmixia across the J. edwardsii range has been long assumed, it is critical to assess the genetic variability of the species to ensure that the level of population connectivity is appropriately understood and translocations do not have unintended consequences. Eight microsatellite loci were used to investigate genetic differentiation between six sites (three shallow, three deep) across southern Tasmania, Australia, and one from New Zealand. Based on analyses the assumption of panmixia was rejected, revealing small levels of genetic differentiation across southern Tasmania, significant levels of differentiation between Tasmania and New Zealand, and high levels of asymmetric gene flow in an easterly direction from Tasmania into New Zealand. These results suggest that translocation among Tasmanian populations are not likely to be problematic, however, a re-consideration of panmictic stock structure for this species is necessary.

Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation

Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of the introduced Guanacos. Genetic variation estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci were compared among 154 Guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variation on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island Guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.

opencc-zeroDec 2018View details →

Data from: Integrated modeling predicts shifts in waterbird population dynamics under climate change

Climate change has been identified as one of the most important drivers of wildlife population dynamics. The in-depth knowledge of the complex relationships between climate and population sizes through density dependent demographic processes is important for understanding and predicting population shifts under climate change, which requires integrated population models (IPMs) that unify the analyses of demography and abundance data. In this study we developed an IPM based on Gaussian approximation to dynamic N-mixture models for large scale population data. We then analyzed four decades (1972-2013) of Mallard (Anas platyrhynchos) breeding population survey, band-recovery, and climate data covering a large spatial extent from North American prairies through boreal habitat to Alaska. We aimed to test the hypothesis that climate change will cause shifts in population dynamics if climatic effects on demographic parameters that have substantial contribution to population growth vary spatially. More specifically, we examined the spatial variation of climatic effects on density dependent population demography, identified the key demographic parameters that are influential to population growth, and forecasted population responses to climate change. Our results revealed that recruitment, which explained more variance of population growth than survival, was sensitive to the temporal variation of precipitation in the southern portion of the study area but not in the north. Survival, by contrast, was insensitive to climatic variation. We then forecasted a decrease in Mallard breeding population density in the south and an increase in the northwestern portion of the study area, indicating potential shifts in population dynamics under future climate change. Our results implied that different strategies need to be considered across regions to conserve waterfowl populations in the face of climate change. Our modelling approach can be adapted for other species and thus has wide application to understanding and predicting population dynamics in the presence of global change.

opencc-zeroDec 2017View details →

Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison to the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based in Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.

Data from: Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern

The North America deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using Isolation-with-Migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The Likelihood Ratio Test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia, and define this species as a single evolutionarily significant unit for conservation purposes.

Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.

Discrepancies between morphology-based taxonomy and phylogenetic systematics are common in Scleractinian corals. In Pocillopora corals, nine recently identified genetic lineages disagree fundamentally with the 17 recognized Pocillopora species, including 5 major Indo-Pacific reef-builders. Pocillopora corals hybridize in the Tropical Eastern Pacific, so it is possible that some of the disagreement between the genetics and taxonomy may be due to introgressive hybridization. Here we used 6769 genome-wide SNPs from Restriction-site Associated DNA sequencing (RAD-Seq) to conduct phylogenomic comparisons among three common, Indo-Pacific Pocillopora species - P.'damicornis, P. eydouxi and P. elegans - within and between populations in the Tropical Eastern Pacific (TEP) and the Central Pacific. Genome-wide RAD-Seq comparisons of Central and TEP Pocillopora confirm that the morphospecies P.'damicornis, P. eydouxi and P. elegans are not monophyletic, but instead fall into three distinct genetic groups. However, hybrid samples shared fixed alleles with their respective parental species and, even without strict monophyly, P. damicornis share a common set of 33 species- specific alleles across the Pacific. RAD-Seq data confirm the pattern of one-way introgressive hybridization among TEP Pocillopora, suggesting that introgression may play a role in generating shared, polyphyletic lineages among currently recognized Pocillopora species. Levels of population differentiation within genetic lineages indicate significantly higher levels of population differentiation in the Tropical Eastern Pacific than in the Central West Pacific.

Data from: An invasive non-native mammal population conserves genetic diversity lost from its native range

Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species' native range in Great Britain, we reveal the opposite effect. We demonstrate that the New Zealand stoat population contains four mitochondrial haplotypes that have not been found in the native range. Stoats in Britain rely heavily on introduced rabbits Oryctolagus cuniculus as their primary prey and were introduced to New Zealand in a misguided attempt at biological control of rabbits, which had also been introduced there. While invasive stoats have since decimated the New Zealand avifauna, native stoat populations were themselves decimated by the introduction to Britain of Myxoma virus as a control measure for rabbits. We highlight the irony that while introduced species (rabbits) and subsequent biocontrol (myxomatosis) have caused population crashes of native stoats, invasive stoats in New Zealand, which were also introduced for biological control, now contain more genetic haplotypes than their most likely native source.