Showing papers in "Conservation Genetics in 2016"

The ecology of environmental DNA and implications for conservation genetics

Abstract: Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the “ecology” of eDNA—myriad interactions between extraorganismal genetic material and its environment—and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

Constraints to and conservation implications for climate change adaptation in plants

Abstract: Contemporary climate change is having widespread impacts on plant populations. Understanding how plants respond to this change is essential to our efforts to conserve them. The key climate responses of plant populations can be categorised into one of three types: migration, in situ adaptation, or extirpation. If populations are to avoid extirpation then migration and/or in situ adaptation is essential. In this review we first articulate the current and future constraints of plant populations, but trees in particular, to the different adaptation strategies (e.g. space availability, rate of change, habitat fragmentation, niche availability). Secondly, we assess the use of the most appropriate methods (e.g. natural environmental gradients, genome and transcriptome scans) for assessing and understanding adaptive responses and the capacity to adapt to future challenges. Thirdly, we discuss the best conservation approaches (e.g. assisted migration, biodiversity corridors, ex situ strategies) to help overcome adaptive constraints in plants. Our synthesis of plant, and particularly tree, responses and constraints to climate change adaptation, combined with the identification of conservation strategies designed to overcome constraints, will help deliver effective management actions to assist adaptation in the face of current and future climate change.

Landscape genetics of a tropical rescue pollinator

Abstract: Pollination services are increasingly threatened by the loss and modification of natural habitats, posing a risk to the maintenance of both native plant biodiversity and agricultural production. In order to safeguard pollination services, it is essential to examine the impacts of habitat degradation on the population dynamics of key pollinators and identify potential “rescue pollinators” capable of persisting in these human-altered landscapes. Using a landscape genetic approach, we assessed the impact of landscape structure on genetic differentiation in the widely-distributed tropical stingless bee Trigona spinipes (Apidae: Meliponini) across agricultural landscape mosaics composed of coffee plantations and Atlantic forest fragments in southeastern Brazil. We genotyped 115 bees at 16 specific and highly polymorphic microsatellite loci, developed using next-generation sequencing. Our results reveal that T. spinipes is capable of dispersing across remarkably long distances, as we did not find genetic differentiation across a 200 km range, nor fine-scale spatial genetic structure. Furthermore, gene flow was not affected by forest cover, land cover, or elevation, indicating that reproductive individuals are able to disperse well through agricultural landscapes and across altitudinal gradients. We also found evidence of a recent population expansion, suggesting that this opportunistic stingless bee is capable of colonizing degraded habitats. Our results thus suggest that T. spinipes can persist in heavily-altered landscapes and can be regarded as a rescue pollinator, potentially compensating for the decline of other native pollinators in degraded tropical landscapes.

Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans

Abstract: Most hard corals have broad distributions, and historically this was attributed to their capability for extensive dispersal leading to high evolutionary and demographic inter-dependence among regions. More recently there has been a paradigm shift in the understanding of coral dispersal, driven largely by genetic evidence, which has put greater emphasis on self-recruitment and larval retention. There is now a growing body of evidence that morphologically cryptic species exist within many recognized ‘species’ of stony corals. Here, we characterise levels of genetic divergence within and between five species of Acropora sampled from disparate populations spanning the Indo-Pacific Oceans. We find that strong regional genetic differentiation corresponding to the separation of the Indian and Pacific Ocean basins is a consistent pattern in three of the five species examined. Furthermore, the extent of allopatric divergence within species is similar to that observed between species, implying negligible contemporary gene flow between regions in four of the five species examined. This is consistent with the presence of numerous morphologically cryptic allopatric subspecies or incipient Acropora species. If this is confirmed, the conservation status of several species, which are already demonstrably threatened, would require re-evaluation so that risks including silent extinctions and inappropriate translocations are properly managed.

Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot

Abstract: The ecology of a species strongly influences genetic variation and population structure. This interaction has important conservation implications because taxa with low dispersal capability and inability to use different habitats are more susceptible to anthropogenic stressors. Ocelots (Leopardus pardalis albescens) and bobcats (Lynx rufus texensis) are sympatric in Texas and northeastern Mexico; however, their ecology and conservation status are markedly different. We used 10 microsatellite loci and a 397-bp segment of the mitochondrial control region to examine how historical and ecological differences in these two species have influenced current patterns of genetic diversity in a landscape heavily altered by anthropogenic activities. Substantially higher genetic diversity (heterozygosity and haplotype diversity) and population connectivity was observed for bobcats in comparison to ocelots. The level of divergence among proximate ocelot populations ( 100 km. Ocelot populations in the US have never recovered from reductions experienced during the twentieth century, and their low genetic variation and substantial isolation are exacerbated by strong preference for dense native thornshrub and avoidance of open habitat. In contrast, despite continued legal harvesting and frequent road-related mortality, bobcats have maintained wide distribution, high abundance, and population connectivity. Our study illustrates that sympatric species with a similar niche can still have sufficient ecological differences to alter their response to anthropogenic change. Sensitive species, such as the ocelot, require additional conservation actions to sustain populations. Ecological differences among species occupying a similar guild are important to consider when developing conservation plans.

Large-scale genetic census of an elusive carnivore, the European wildcat (Felis s. silvestris)

Abstract: The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently.

Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range

Abstract: The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (FST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average FST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.

Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution

Abstract: Molecular markers can reveal interesting aspects of organismal ecology and evolution, especially when surveyed in rare or elusive species. Herein, we provide a preliminary assessment of golden eagle (Aquila chrysaetos) population structure in North America using novel single nucleotide polymorphisms (SNPs). These SNPs included one molecular sexing marker, two mitochondrial markers, 85 putatively neutral markers that were derived from noncoding regions within large intergenic intervals, and 74 putatively nonneutral markers found in or very near protein-coding genes. We genotyped 523 eagle samples at these 162 SNPs and quantified genotyping error rates and variability at each marker. Our samples corresponded to 344 individual golden eagles as assessed by unique multilocus genotypes. Observed heterozygosity of known adults was significantly higher than of chicks, as was the number of heterozygous loci, indicating that mean zygosity measured across all 159 autosomal markers was an indicator of fitness as it is associated with eagle survival to adulthood. Finally, we used chick samples of known provenance to test for population differentiation across portions of North America and found pronounced structure among geographic sampling sites. These data indicate that cryptic genetic population structure is likely widespread in the golden eagle gene pool, and that extensive field sampling and genotyping will be required to more clearly delineate management units within North America and elsewhere.

Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

Abstract: The Central Texas endemic freshwater mussel, Quadrula mitchelli (Simpson in Dall, 1896), had been presumed extinct until relict populations were recently rediscovered. To help guide ongoing and future conservation efforts focused on Q. mitchelli we set out to resolve several uncertainties regarding its evolutionary history, specifically its unknown generic position and untested species boundaries. We designed a molecular matrix consisting of two loci (cytochrome c oxidase subunit I and internal transcribed spacer I) and 57 terminal taxa to test the generic position of Q. mitchelli using Bayesian inference and maximum likelihood phylogenetic reconstruction. We also employed two Bayesian species validation methods to test five a priori species models (i.e. hypotheses of species delimitation). Our study is the first to test the generic position of Q. mitchelli and we found robust support for its inclusion in the genus Fusconaia. Accordingly, we introduce the binomial, Fusconaia mitchelli comb. nov., to accurately represent the systematic position of the species. We resolved F. mitchelli individuals in two well supported and divergent clades that were generally distinguished as distinct species using Bayesian species validation methods, although alternative hypotheses of species delineation were also supported. Despite strong evidence of genetic isolation within F. mitchelli, we do not advocate for species-level status of the two clades as they are allopatrically distributed and no morphological, behavioral, or ecological characters are known to distinguish them. These results are discussed in the context of the systematics, distribution, and conservation of F. mitchelli.

On applications of landscape genetics

Abstract: Recent assertions in the literature (e.g., Keller et al. 2015) suggest that landscape genetic research has been infrequently applied by practitioners. We were interested to test this assertion, which is difficult to assess, since applications may not be detectable through searches of peer-reviewed literature. Producing publications may not be a goal of practitioners. We developed a method to search the internet for evidence of research applications and evaluated 25 different research fields in the natural sciences. We found that fields with more publications also had more applications, but the field of landscape genetics was less applied than expected based on the number of peer-reviewed publications—only about 4 % of landscape genetics articles were applied. In fact, all research fields in genetics or evolutionary biology were under-applied compared to ‘whole organism’, ecological research fields. This result suggests the lack of applications in landscape genetics may be due to a systemic under-application of genetics research, perhaps related to a lack of understanding of genetics by practitioners. We did find some evidence of landscape genetic applications however, which we sorted into 5 categories: (1) identification of evolutionarily significant units for conservation, (2) managing pathogens and invasive species, (3) natural heritage systems planning, (4) assessing population status, and (5) restoration of populations.

Effects of habitat deterioration on the population genetics and conservation of the jaguar

Abstract: Over the past century, human activities and their side effects have significantly threatened both ecosystems and resident species Nevertheless, the genetic patterns of large felids that depend heavily on large and well-conserved continuous habitat remain poorly studied Using the largest-ever contemporary genetic survey of wild jaguars (Panthera onca), we evaluated their genetic diversity and population structure in natural (Brazilian Amazon) and highly modified habitats (eg Cerrado, Caatinga) including those close to the northern (Yucatan, Mexico) and southern (Pantanal) edge of the species’ distribution range Data from our set of microsatellites revealed a pronounced genetic structure, with four genetically differentiated geographic areas Geographic distance was not the only factor influencing genetic differentiation through the jaguar range Instead, we found evidence of the effects of habitat deterioration on genetic patterns: while the levels of genetic diversity in the Amazon forest, the largest continuum habitat for the species, are high and consistent with panmixia across large distances, genetic diversity near the edge of the species distribution has been reduced through population contractions Mexican jaguar populations were highly differentiated from those in Brazil and genetically depauperated An isolated population from the Caatinga showed the genetic effects of a recent demographic decline (within the last 20–30 years), which may reflect recent habitat degradation in the region Our results demonstrate that the jaguar is highly sensitive to habitat fragmentation especially in human-dominated landscapes, and that in Brazil, the existing but limited genetic connectivity in the central protected areas should be maintained These conclusions have important implications for the management of wide-ranging species with high dispersal and low population density The restoration of ecological connectivity between populations over relatively large scales should be one of the main priorities for species conservation

Genetic structure of a commercially exploited bivalve, the great scallop Pecten maximus, along the European coasts

Abstract: The great scallop Pecten maximus is harvested in several European countries and fisheries targeting this species are severely regulated by fishing quotas. In addition, hatchery-based population enhancement has been developed in some countries to provide alternative or complementary production. The genetic structure of wild populations of P. maximus and the potential impact of aquaculture on the genetic diversity of this species remains poorly documented. In this study, we explored the genetic structure of P. maximus using 12 microsatellite markers, considering 14 populations sampled from Galicia (Spain) to the North of Norway, and one population of Pecten jacobaeus (L., 1758) from the Lion Gulf (Mediterranean Sea). Results indicated a clear differentiation between Norwegian and Atlantic (from Ireland to Spain) populations, but very little to no difference between populations within these two groups. A decrease of the genetic diversity was observed with latitude. No significant reduction of the genetic diversity was observed in the Bay of Brest, where hatchery-based population enhancement has been performed intensively since 1983. Our results are discussed in the light of the inferred recent evolutionary history, phylogeography and connectivity of populations in Europe, and of the phenotypic variability reported in previous studies between northern and southern populations.

Threat or fiction: is the pond slider (Trachemys scripta) really invasive in Central Europe? A case study from Slovenia

Abstract: Using samples of non-native pond sliders (Trachemys scripta) from three different climatic zones in Slovenia, we perform parentage analyses and use population genetic approaches to find out whether they successfully reproduce and are able to establish populations. Based on 14 highly polymorphic microsatellite loci, we provide evidence for successful reproduction and invasiveness of pond sliders not only for the Mediterranean and sub-Mediterranean regions of Slovenia, but also for the central part of the country having a temperate continental climate. Our results suggest that the pond slider should be classified as an invasive species (introduced species spreading in a non-native region) for Slovenia and other European regions with similar climatic conditions. Since the negative impact of pond sliders is out of question for native European turtle species, we suggest the immediate removal of pond sliders from all habitats. Our study provides for the first time hard evidence for the capability of pond sliders to reproduce in Central Europe. Thus, it contributes to the understanding of the invasiveness of pond sliders in Europe and delivers an important foundation for decision-makers in conservation.

Integrating ecological and genetic structure to define management units for caribou in Eastern Canada

Abstract: Genetic diversity is a key parameter to delineate management units, but many organisms also display ecological characteristics that may reflect potential local adaptations. Here, we used ecological and genetic information to delineate management units for a complex system involving several ecotypes of caribou (Rangifer tarandus) from Quebec and Labrador, eastern Canada. We genotyped 560 caribou at 16 microsatellite loci and used three Bayesian clustering methods to spatially delineate and characterize genetic structure across the landscape. The different approaches employed did not converge on the same solution, and differed in the number of inferred genetic clusters that best fit the dataset but also in the spatial distribution of genetic variation. We reconciled variability among the methods using a synthetic approach that considers the sum of the partitions obtained by each of them and retrieved six genetically distinct groups that differ in their spatial extent across the range of caribou in the study area. These genetic groups are not consistent with the presently defined ecological designations for this species. Combining both genetic and ecological criteria, we distinguished eight independent management units. Overall, the management units we propose should be the focus of conservation and management actions aimed to maximize genetic and ecological diversity and ensure the persistence of caribou populations inhabiting increasingly disturbed landscapes.

Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses ( Ceratotherium simum ): the conservation consequences of species definitions

Abstract: The probable extinction of the last confirmed population of northern white rhinoceros (Ceratotherium simum cottoni) in the world has ignited debate regarding its species status compared to the southern white rhinoceros (Ceratotherium simum simum). Previous studies, based on partial mitochondrial sequences, have reported conflicting results regarding the species status of the northern white rhinoceros. We use whole mitochondrial genomes obtained using Next Generation Sequencing of four northern white rhinoceros and three southern white rhinoceros using novel primers in three overlapping fragments. Phylogenetic relationships were constructed, using Maximum Likelihood, and recovered monophyletic clades for northern white rhinoceros and southern white rhinoceros. The divergence time between the two mitochondrial DNA lineages was estimated to be between 0.46 and 0.97 million years ago using Bayesian inferences. Since there are currently only three surviving northern white rhinoceros individuals these results put into sharp focus the ongoing debate regarding the methods of species definition, and in particular the consequences of such definitions in conservation management of endangered species and subspecies. We conclude that the designation of sub-species status is more applicable to northern and southern white rhinoceros.

Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia

Abstract: Distinguishing the relative influence of historic (i.e. natural) versus anthropogenic factors in metapopulation structure is an important but often overlooked step in management programs of threatened species. Biotas in freshwater wetlands and floodplains, such as those in the Murray–Darling Basin (MDB)—one of Australia’s most impacted ecosystems, are particularly susceptible to anthropogenic fragmentation. Here we present a comprehensive multilocus assessment of genetic variation in the threatened southern pygmy perch Nannoperca australis (578 individuals; 45 localities; microsatellite, allozyme and mitochondrial DNA datasets), an ecological specialist with low dispersal potential. We assess patterns of spatial structure and genetic diversity in populations spanning the highly fragmented MDB and test whether recent anthropogenic modification has disrupted range-wide connectivity. We detected strong and hierarchical population structure, very low genetic diversity and lack of contemporary gene flow across the MDB. In contrast, the apparent absence of pronounced or long-term phylogeographic structure suggests that observed population divergences generally do not reflect deeply historic natural fragmentation. Coalescent-based analyses supported this inference, revealing that divergence times between populations from the upper and lower MDB fall into the period of European settlement. It appears that the observed contemporary isolation of populations is partly explained by the severe modification of the MDB post-dating the onset of European settlement. Our integrated approach substantially improves the interpretation of how fragmentation impacts present-day biodiversity. It also provides novel contributions for risk-assessing management actions in the context of captive breeding and translocations of small freshwater fishes, a group of increasing global conservation concern.

The effect of reintroductions on the genetic variability in Eurasian lynx populations: the cases of Bohemian–Bavarian and Vosges–Palatinian populations

Abstract: Over the past ~40 years, several attempts were made to reintroduce Eurasian lynx to suitable habitat within their former distribution range in Western Europe. In general, limited numbers of individuals have been released to establish new populations. To evaluate the effects of reintroductions on the genetic status of lynx populations we used 12 microsatellite loci to study lynx populations in the Bohemian–Bavarian and Vosges–Palatinian forests. Compared with autochthonous lynx populations, these two reintroduced populations displayed reduced genetic diversity, particularly the Vosges–Palatinian population. Our genetic data provide further evidence to support the status of ‘endangered’ and ‘critically endangered’ for the Bohemian–Bavarian and Vosges–Palatinian populations, respectively. Regarding conservation management, we highlight the need to limit poaching, and advocate additional translocations to bolster genetic variability.

Population genetic structure and ancestry of steelhead/rainbow trout (Oncorhynchus mykiss) at the extreme southern edge of their range in North America

Abstract: Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.

The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines

Abstract: Coral reefs within the Coral Triangle (CT) are home to the greatest marine diversity on the globe and are an important supplier of marine resources to densely populated coastal regions. Many coral reefs within the CT and around the world are under threat from over-exploitation. Marine protected areas (MPAs) have been proven to be effective tools in restoring fish stocks. However, the role that MPAs play in promoting connectivity at greater distances through larval dispersal is still unknown. RADseq was used to discover 4253 SNPs from 81 individuals of the dusky parrotfish (Scarus niger) collected from three sites within the Philippines. A lack of population structure suggested a high rate of gene flow (F ST = 0.007). Estimates of Ne from linkage disequilibrium are relatively large, ranging from 1200 to 2000. A sibling analysis revealed one pair of well-supported full siblings (r = 0.773) and one pair of putative half siblings (r = 0.191) between sites separated by more than 500 km. The low F ST values indicate a high degree of gene flow between the reefs within the sampling area while the sibling analysis suggests demographic connectivity between the Sibuyan Sea and the Sulu Sea. The Mindoro–Panay throughflow is a likely vector by which larvae are transported between these sites, suggesting that reefs in Romblon are sources for reefs near Basay, 400 km to the south. Given the reliance of a vast majority of coral reef fishes on larval dispersal, this study reveals that MPAs established within the central Philippines can supply varying levels of larvae to overfished reefs.

The role of very small fragments in conserving genetic diversity of a common tree in a hyper fragmented Brazilian Atlantic forest landscape

Abstract: In hyper fragmented biomes, conservation of extant biota relies on preservation and proper management of remnants. The maintenance of genetic diversity and functional connectivity in a landscape context is probably key to long-term conservation of remnant populations. We measured the genetic diversity in seedlings and adults of tree Copaifera langsdorffii and evaluated whether edge and density-dependent effects drive natural regeneration in a set of very small and degraded Brazilian Atlantic forest fragments. We evaluated the role of small remnants in the conservation of genetic diversity in a hyper fragmented landscape and discuss the challenge of long-term population sustainability of such altered habitats. High genetic diversity in adults indicated these fragments are valuable targets for C. langsdorffii in situ conservation, but both genetic diversity and divergence among patches decreased in seedlings. In our landscape, regeneration increased as it neared edges and adults; suggesting this population is resilient to fragmentation. However, at a broader scale, current levels of gene flow have not been sufficient to prevent the loss of genetic diversity across generations. Restoration plans, even at a small scale, are necessary to promote fragment connectivity and spatially expand opportunities for the fairly restricted gene flow observed in this severely fragmented Brazilian Atlantic forest region.

Massive genetic introgression in threatened northern crested newts (Triturus cristatus) by an invasive congener (T. carnifex) in Western Switzerland

Abstract: Genetic pollution through introgressive hybridization of local species by exotic relatives is a major, yet neglected aspect of biological invasions, particularly in amphibians where human introductions are frequent. In Western Switzerland, crested newts make an interesting case: the Italian species Triturus carnifex was introduced at least a century ago within the range of the native and threatened T. cristatus. To understand the genetic consequences of this introduction and inform wildlife management authorities, we conducted a genetic survey on the remaining northern crested newt populations known in the area, using newly-developed species-diagnostic nuclear (microsatellites) and mitochondrial (control region) DNA markers. We documented massive nuclear introgression by the T. carnifex genome, which has completely replaced T. cristatus in most populations, especially in the Geneva area where the introduction was originally reported. However, many of these individuals retained the ancestral T. cristatus mtDNA, which could be explained by asymmetric introgression between the two species, stemming from demographic and/or selective processes. Analyses of genetic diversity support multiple events of T. carnifex releases, most-likely of proximate North Italian origin. We pinpointed the last indigenous populations in the region and recommend to prioritize their protection. Our study demonstrates the invasive potential of introduced taxa through introgressive hybridization, alerts about the underestimated rate of illegal amphibian translocations, and emphasizes the need for genetic analyses to monitor such invasions.

Does higher connectivity lead to higher genetic diversity? Effects of habitat fragmentation on genetic variation and population structure in a gypsophile

Abstract: Habitat fragmentation is a major threat to the maintenance of genetic diversity in many plant populations. Genetic effects of population size have received far more attention than the effects of isolation—or connectivity—but both are key components of the fragmentation process. To analyze the consequences of fragment size and connectivity on the neutral genetic variation and population genetic structure of the dominant gypsophile Lepidium subulatum, we selected 20 fragments along two continuous gradients of size and degree of isolation in a fragmented gypsum landscape of Central Spain. We used eight polymorphic microsatellite markers, and analyzed a total of 344 individuals. Populations were characterized by high levels of genetic diversity and low inbreeding coefficients, which agrees with the mainly outcrossing system of L. subulatum and its high abundance in gypsum landscapes. Bayesian clustering methods, pairwise F ST values and analysis of molecular variance revealed low among-population differentiation, with no significant isolation by distance. However, several genetic diversity indices such as allelic richness, number of effective alleles, expected heterozygosity and number of private alleles were negatively related to population isolation. The higher genetic diversity found on more connected fragments suggests higher rates of gene flow among more connected populations. Overall, our results highlight that fragmentation can have important effects on intra-population genetic processes even for locally abundant, dominant species. This, together with previously documented effects of connectivity on fitness of gypsophile species highlights the importance of including habitat connectivity in management and conservation strategies of this type of semiarid systems.

Genetic diversity and population structure of the roughskin sculpin ( Trachidermus fasciatus Heckel) inferred from microsatellite analyses: implications for its conservation and management

Abstract: Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F (ST) estimates were significant after false discovery rate correction (overall average F (ST) = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.

Effective number of breeders in relation to census size as management tools for Atlantic salmon conservation in a context of stocked populations

Abstract: Monitoring short-term fluctuations in effective population sizes (N e) and effective number of breeders (N b), as well as their ratio to adult census population size (N e/N c and N b/N c), provide insight into population demography and inform conservation programs towards limiting long-term loss of evolutionary potential in wild populations. In this study, we monitored short-term variations of N b and N b/N c over three consecutive years for nine Atlantic salmon populations from Quebec, Canada. We documented how these population genetic parameters were influenced by anadromous population size as well as yearly and long-term stocking intensity. Towards this end, 15 microsatellites were used to genotype about 100 one-year-old parrs for each of three consecutive years for nine genetically distinct populations (total n = 2506) from Quebec, Canada. Yearly stocking intensity had a negative effect on N b/N c, possibly as a consequence of a reduced reproductive contribution of stocked relative to wild fish. However, the impact of long-term stocking intensity on N b/N c was not significant, which may indicate relatively weak carry-over effects of stocking on future generations. Also, N b/N c was negatively correlated with N C, suggesting compensatory mechanisms, as previously reported in other salmonids. Overall, this study provides evidence of relatively weak and short-term effect of stocking on N b/N c ratio in Atlantic salmon populations and suggests potential biological mechanisms leading to the significant negative relationship between N b/N c and N c.

Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure, range expansion, and possible introgression

Abstract: The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the range expansion is unknown, yet has resulted in overlap between Lesser and Greater Prairie-Chickens (T. cupido) increasing the potential for hybridization. Our objectives were to characterize connectivity and genetic diversity among populations, identify source population(s) of recent range expansion, and examine hybridization with the Greater Prairie-Chicken. We analyzed 640 samples from across the range using 13 microsatellites. We identified three to four populations corresponding largely to ecoregions. The Shinnery Oak Prairie and Sand Sagebrush Prairie represented genetically distinct populations (F ST > 0.034 and F ST > 0.023 respectively). The Shortgrass/CRP Mosaic and Mixed Grass ecoregions appeared admixed (F ST = 0.009). Genetic diversity was similar among ecoregions and N e ranged from 142 (95 % CI 99–236) for the Shortgrass/CRP Mosaic to 296 (95 % CI 233–396) in the Mixed Grass Prairie. No recent migration was detected among ecoregions, except asymmetric dispersal from both the Mixed Grass Prairie and to a lesser extent the Sand Sagebrush Prairie north into adjacent Shortgrass/CRP Mosaic (m = 0.207, 95 % CI 0.116–0.298, m = 0.097, 95 % CI 0.010–0.183, respectively). Indices investigating potential hybridization in the Shortgrass/CRP Mosaic revealed that six of the 13 individuals with hybrid phenotypes were significantly admixed suggesting hybridization. Continued monitoring of diversity within and among ecoregions is warranted as are actions promoting genetic connectivity and range expansion.

Rainfall and topography predict gene flow among populations of the declining northern quoll (Dasyurus hallucatus)

Abstract: Landscape attributes often shape the spatial genetic structure of species. As the maintenance of genetic connectivity is increasingly a conservation priority, the identification of landscape features that influence connectivity can inform targeted management strategies. The northern quoll (Dasyurus hallucatus) is a carnivorous marsupial that has experienced dramatic population declines in recent decades. To inform management of surviving D. hallucatus populations across north-western Australia we examined the genetic structure of populations, and identified landscape features that influence gene flow within the Kimberley region. We sampled 249 individuals from 28 populations in three regions of north-western Australia, including the Kimberley, Pilbara and Kakadu. Genetic structuring was evident between the three regions and to a lesser extent between the north and central Kimberley. Landscape genetic analysis of Kimberley populations suggest this structuring may be due in part to the indirect effects of differences in rainfall between these two areas. Also, D. hallucatus populations with large areas of open habitat between them tended to be more genetically similar. Managing threats such as the occurrence of intense and frequent fires, and the density of introduced herbivores, could support the persistence of D. hallucatus populations, particularly in areas with high rainfall and flat terrain, where greater genetic connectivity confers a better chance of long-term population survival.

Limited genetic structure in a wood frog (Lithobates sylvaticus) population in an urban landscape inhabiting natural and constructed wetlands

Abstract: Urbanization has been linked to amphibian population declines globally. Habitat fragmentation can negatively impact gene flow among populations but what role artificially constructed wetlands have in maintaining gene flow in urban amphibian populations remains uncertain. We assessed gene flow in a population of wood frogs (Lithobates sylvaticus) inhabiting both constructed and natural wetlands located in Edmonton, Alberta, Canada. We genotyped 10 microsatellite loci in 182 frogs from eight wetlands and tested for genetic differentiation between wetlands. We tested if bottlenecks had occurred at constructed wetlands and if there were differences in allelic richness between natural wetlands and constructed wetlands. We found no evidence of bottlenecks, no differences in allelic richness among subpopulations, and no genetic structure within the population. Although significant differences in pair-wise comparisons of allele frequency distributions between wetlands were detected, all F ST values were low (0.003–0.053) and Bayesian clustering indicated the presence of a single genetic cluster. Despite extensive urbanization within our study area, genetic homogeneity has been preserved indicating that it may be possible to use constructed wetlands to maintain amphibian populations and preserve gene flow among subpopulations living within urbanized landscapes.

Genetic diversity is maintained in the endangered New Zealand long-tailed bat (Chalinolobus tuberculatus) despite a closed social structure and regular population crashes

Abstract: Maintaining the genetic diversity of populations is important in conservation because it strongly influences the ability to adapt to changing environments. We characterised the genetic structure of the endemic and endangered New Zealand (NZ) long-tailed bat (Chalinolobus tuberculatus) in two valleys in Fiordland, NZ. Fiordland is one of the last strongholds of the species, which has drastically declined throughout NZ. C. tuberculatus has suffered from recent habitat fragmentation and episodic predation by exotic mammals over the last 150 years. Gene flow and structuring were measured using nine nuclear microsatellite loci. In addition, the hyper-variable domain HVI of the mitochondrial control region was sequenced to analyse population structure at the maternal level. Our results show that the nine colonies studied have retained high genetic diversity, with moderate signs of genetic bottlenecks. Furthermore, low F ST and F IS values indicated that all colonies are still connected by gene flow and do not show signs of inbreeding. Substantial gene flow among colonies was also demonstrated by Bayesian clustering and PCA analysis. At the mitochondrial level, substantial differentiation between colonies has resulted from strong natal philopatry in females. Overall, our results indicate that genetic diversity is maintained in the Fiordland population of C. tuberculatus despite regular population crashes and habitat fragmentation. Management should ensure that remaining habitat linkages are preserved and further predator-induced population bottlenecks are prevented so that current genetic diversity is maintained in the long-term.

Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii)

Abstract: The Bell’s Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.

Morphological and genetic variation in Cisco (Coregonus artedi) and Shortjaw Cisco (C. zenithicus): multiple origins of Shortjaw Cisco in inland lakes require a lake-specific conservation approach

Abstract: The study of cisco diversity in inland lakes of North America has been plagued by taxonomic uncertainty linked to high phenotypic plasticity and an ongoing reliance on morphology to differentiate species. More recently, this uncertainty has hindered the development of conservation plans and status assessments of ciscoes. This study presents the first range-wide comparison of morphological and genetic variation between Cisco (Coregonus artedi) and Shortjaw Cisco (C. zenithicus). Using morphological and genetic data from 17 lakes, three sets of analyses were undertaken to evaluate alternate hypotheses explaining the pattern of cisco phenotypic diversity in inland lakes. Morphotypes (MTs) representing the two taxa were phenotypically distinct (largely reflective of differences in gill raker number and jaw morphology) within lakes but highly variable across lakes. Shortjaw Cisco was only recognizable when compared to sympatric Cisco and some populations were morphologically similar to Cisco from other lakes. Analysis of AFLP data revealed two genetic clusters that conformed to differences in geography (eastern and western groups), rather than hypothesized taxonomic boundaries. Genetic variation strongly suggests that each of these unique sympatric pairs of MTs originated recently and locally, in parallel, from the ancestral Cisco. Phenotypic and genetic distinctiveness between MTs were not related. MTs were sometimes clearly recognizable despite a lack of genetic differentiation, suggesting that the canalization of phenotypic plasticity is unevenly completed across lakes. These results provide evidence that the taxon-based approach is clearly inadequate for the protection of Shortjaw Cisco. In Canada, status assessment should aim to identify lake-specific designatable units (DU). Given the idiosyncratic nature of each instance of Shortjaw Cisco, it is expected that the strength of morphological, biological, ecological and genetic evidence for individual DUs will vary among lakes.