Showing papers in "Conservation Genetics in 2007"

Genetic consequences of habitat fragmentation and loss: the case of the Florida black bear (Ursus americanus floridanus)

Abstract: Habitat loss and fragmentation can influence the genetic structure of biological populations. We studied the genetic consequences of habitat fragmentation in Florida black bear (Ursus americanus floridanus) populations. Genetic samples were collected from 339 bears, representing nine populations. Bears were genotyped for 12 microsatellite loci to estimate genetic variation and to characterize genetic structure. None of the nine study populations deviated from Hardy–Weinberg equilibrium. Genetic variation, quantified by mean expected heterozygosity (HE), ranged from 0.27 to 0.71 and was substantially lower in smaller and less connected populations. High levels of genetic differentiation among populations (global FST = 0.224; global RST = 0.245) suggest that fragmentation of once contiguous habitat has resulted in genetically distinct populations. There was no isolation-by-distance relationship among Florida black bear populations, likely because of barriers to gene flow created by habitat fragmentation and other anthropogenic disturbances. These factors resulted in genetic differentiation among populations, even those that were geographically close. Population assignment tests indicated that most individuals were genetically assigned to the population where they were sampled. Habitat fragmentation and anthropogenic barriers to movement appear to have limited the dispersal capabilities of the Florida black bear, thereby reducing gene flow among populations. Regional corridors or translocation of bears may be needed to restore historical levels of genetic variation. Our results suggest that management actions to mitigate genetic consequences of habitat fragmentation are needed to ensure long-term persistence of the Florida black bear.

Impact of urban fragmentation on the genetic structure of the eastern red-backed salamander

Abstract: Urban development is a major cause of habitat loss and fragmentation. Few studies, however, have dealt with fragmentation in an urban landscape. In this paper, we examine the genetic structure of isolated populations of the eastern red-backed salamander (Plethodon cinereus) in a metropolitan area. We sampled four populations located on a mountain in the heart of Montreal (Quebec, Canada), which presents a mosaic of forested patches isolated by roads, graveyards and buildings. We assessed the genetic structure of these populations using microsatellite loci and compared it to the genetic structure of four populations located in a continuous habitat in southern Quebec. Our results indicate that allelic richness and heterozygosity are lower in the urban populations. Exact differentiation tests and pairwise F ST also show that the populations found in the fragmented habitat are genetically differentiated, whereas populations located in the continuous habitat are genetically homogeneous. These results raise conservation concerns for these populations as well as for rare or threatened species inhabiting urban landscapes.

Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition?

Abstract: We investigate using relative amounts of prey DNA recovered from pinniped faeces to obtain diet composition data. Faeces were obtained from captive sea lions being fed a diet containing three fish species (50%, 36% and 14% by mass). Real-time PCR was used to quantify mtDNA in undigested tissue and in the faecal samples. The percent composition of fish mtDNA extracted from tissue corresponded reasonably well to the mass of fish in the mixture. In faecal samples the absolute amount of fish mtDNA recovered varied 100-fold, but the percent composition of the samples was relatively consistent (57.5 ± 9.3%, 19.3 ± 6.6% and 23.2 ± 12.2%). These results indicate there are prey-specific biases in DNA survival during digestion. However, the biases may be less than those commonly observed in conventional diet studies.

The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification

Abstract: To establish longevity of faecal DNA samples under varying summer field conditions, we collected 53 faeces from captive brown bears (Ursus arctos) on a restricted vegetation diet. Each faeces was divided, and one half was placed on a warm, dry field site while the other half was placed on a cool, wet field site on Moscow Mountain, Idaho, USA. Temperature, relative humidity, and dew point data were collected on each site, and faeces were sampled for DNA extraction at <1, 3, 6, 14, 30, 45, and 60 days. Faecal DNA sample viability was assessed by attempting PCR amplification of a mitochondrial DNA (mtDNA) locus (~150 bp) and a nuclear DNA (nDNA) microsatellite locus (180-200 bp). Time in the field, temperature, and dew point impacted mtDNA and nDNA amplification success with the greatest drop in success rates occur- ring between 1 and 3 days. In addition, genotyping errors significantly increased over time at both field sites. Based on these results, we recommend collecting samples at frequent transect intervals and focusing sampling efforts during drier portions of the year when possible.

Hybridization and phylogeography of the Mozambique tilapia Oreochromis mossambicus in southern Africa evidenced by mitochondrial and microsatellite DNA genotyping

Abstract: Many Oreochromis species utilized in aquaculture were extensively introduced outside their native range in Africa. Given their recent evolutionary radiation, these species hybridize easily, posing a threat to the integrity of local adaptation. The objective of this work was to study the genetic diversity of the Mozambique tilapia (Oreochromis mossambicus) in its native range, southern Africa, and provide a method for identifying hybrids with genetic markers. We genotyped the mitochondrial DNA (mtDNA) control region (385 bp) of wild and farmed O. mossambicus, wild and farmed O. niloticus and morphologic wild hybrids. These data were complemented with published sequences of parapatric and sympatric Oreochromis taxa. Phylogeographic analysis showed the presence of two O. mossambicus lineages, the southernmost representing a recent Holocene radiation. Hybridization of O. mossambicus was indicated by the presence of O. niloticus and O. mortimeri–andersonii mtDNA specimens in the Limpopo basin and of O. karongae mtDNA in specimens from Malawi. We also genotyped seven suspected hybrid individuals from the Limpopo River, and 137 wild and farmed Mozambique and Nile tilapia samples with five microsatellite markers. Factorial Component Analysis, Bayesian clustering and assignment analyses consistently delineated an O. mossambicus and an O. niloticus group, with the putative hybrids positioned in between. Different levels of hybridization were detected by the Bayesian assignment. The complex nature of hybridization and introgression between cichlid species raises major concerns for the long-term integrity of Mozambique tilapia.

What is the fitness outcome of crossing unrelated fish populations? A meta-analysis and an evaluation of future research directions

Abstract: Outbreeding has been shown to decrease fitness in a variety of species, including several species of fish. An understanding of the general outcomes following outbreeding is required in order to understand the consequences of conservation-related actions and hybridization in aquaculture. A meta-analysis was conducted on outbreeding studies in fishes using 670 comparisons between parent populations and their hybrid progeny. Five hundred and seventy-six comparisons involved first generation hybrids (F1), and a much smaller number (94) involved second generation hybrids (F2). The overall response to outbreeding in the F1 and F2 generations was positive and significant (F1: d + * = 0.425 ± 0.121; F2: d + * = 0.548 ± 0.295, where d + * is the effect size of studies within generations); however, responses differed when studies were separated into groups describing the experimental environment, taxon, or trait. Findings may be biased by a few studies of large effect. Genetic distance explained little of the variance in effect sizes across studies. Results of the meta-analysis suggest that there is no reliable predictor for the effects of outbreeding in fishes, although inconsistencies in experimental design were noted across studies. Future research should include comparisons in both parental environments in order to detect the underlying mechanisms of outbreeding depression, and should focus on measurement of equivalent sets of fitness-related traits. Experimental design should permit estimation of genetic distances based on quantitative traits, which may in turn be meaningful predictors of the outcomes of outbreeding depression. Concerted and consistent research in this area will provide information of relevance to conservation, aquaculture and evolutionary studies.

Buccal swabs allow efficient and reliable microsatellite genotyping in amphibians

Abstract: Buccal swabs have recently been used as a minimally invasive sampling method in genetic studies of wild populations, including amphibian species. Yet it is not known to date what is the level of reliability for microsatellite genotypes obtained using such samples. Allelic dropout and false alleles may affect the genotyping derived from buccal samples. Here we quantified the success of microsatellite amplification and the rates of genotyping errors using buccal swabs in two amphibian species, the Alpine newt Triturus alpestris and the Green tree frog Hyla arborea, and we estimated two important parameters for downstream analyses, namely the number of repetitions required to achieve typing reliability and the probability of identity among genotypes. Amplification success was high, and only one locus tested required two to three repetitions to achieve reliable genotypes, showing that buccal swabbing is a very efficient approach allowing good quality DNA retrieval. This sampling method which allows avoiding the controversial toe-clipping will likely prove very useful in the context of amphibian conservation.

The genetic structure of the loggerhead sea turtle ( Caretta caretta ) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications

Abstract: The population genetic structure of the loggerhead sea turtle (Caretta caretta) nesting in the eastern Mediterranean was assessed by sequencing a fragment of the control region of the mitochondrial DNA (n = 190) and seven microsatellites (n = 112). The two types of markers revealed genetic structuring (mtDNA: cst = 0.212, P < 0.001; nDNA Fst = 0.006, P < 0.001), thus indicating that both females and males are philopatric and that gene flow between populations is restricted. Mitochondrial DNA data indicate that the female populations nesting on the islands of Crete and Cyprus have suffered a recent bottleneck or coloniza- tion event. However, no bottleneck or founder effect was revealed by nuclear markers, thus indicating male- mediated gene flow from other populations that would increase nuclear genetic variability. Crete, and to a lower extent Cyprus, are thought to play a central role in such male-mediated gene flow that may reduce the negative effect of genetic drift or inbreeding on the small populations of Lebanon and Israel. This popu- lation structure indicates that assessing population relevance only on the basis of genetic variability and size would be misleading, as some populations not fulfilling those requirements may play a relevant role in genetic exchange and hence contribute to the overall genetic variability.

Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template

Abstract: Faecal material has increasingly become an important non-invasive source of DNA for wildlife population genetics. However, DNA from faecal sources can have issues associated with quantity (low-template and/or low target-to-total DNA ratio) and quality (degradation and/or low DNA-to-inhibitor ratio). A number of studies utilizing faecal material assume and compensate for the above properties with minimal characterization of quantity or quality of target DNA, which can unnecessarily increase the risk of downstream technical problems. Here, we present a protocol which quantifies faecal DNA using a two step approach: (1) estimating total DNA concentration using a PicogreenTM fluorescence assay and (2) estimating target nuclear DNA concentration by comparing amplification products of field samples at suspected concentrations to those of control DNA at known concentrations. We applied this protocol to faecal material collected in the field from two species: woodland caribou (Rangifer tarandus) and swift fox (Vulpes velox). Total DNA estimates ranged from 6.5 ng/μl to 28.6 ng/μl (X = 16.2 ng/μl) for the caribou extracts and 1.0–26.1 ng/μl (X = 7.5 ng/μl) for the swift fox extracts. Our results showed high concordance between total and target DNA estimates from woodland caribou faecal extracts, with only 10% of the samples showing relatively lower target-to-total DNA ratios. In contrast, DNA extracts from swift fox scat exhibited low target DNA yields, with only 38% (19 of 50) of the samples showing comparative target DNA amplification of at least 0.1 ng. With this information, we were able to estimate the amount of target DNA entered into PCR amplifications, and identify samples having target DNA below a lower threshold of 0.2 ng and requiring modification to genotyping protocols such as multiple tube amplification. Our results here also show that this approach can easily be adapted to other species where faeces are the primary source of DNA template.

Genetic quality and offspring performance in Chinook salmon: implications for supportive breeding

Abstract: Each year salmon and other fishes are caught and used for supportive breeding programs that attempt to augment natural populations that are threatened with extinction. These programs typically mate individuals randomly and as such they overlook the importance of genetic quality to offspring fitness and ultimately to ensuring population health. Here, we use Chinook salmon (Oncorhynchus tshawytscha) and a fully crossed quantitative genetic breeding design to partition genetic variance in offspring performance (growth and survival) to additive and non-additive genetic effects as well as maternal effects. We show that these three effects contribute about equally to the variation in survival, but only non-additive genetic and maternal effects contribute to variation in growth. Some of the genetic effects could be assigned to variation at the class IIB locus of the major histocompatibility complex, but the maternal effects were not associated with egg size and we found no relationship between dam phenotypic measures and offspring survival or growth. We also found no relationship between sire sexually selected characters and offspring survival or growth, which is inconsistent with a “good genes” hypothesis. Finally, we show that incorporation of genetic quality into supportive breeding programs can increase offspring growth or survival by between 3% and 19% during the endogenous feeding stage alone, and projections to adulthood suggest that survivorship could be over four fold higher.

Detecting introgressive hybridisation in rock partridge populations ( Alectoris graeca ) in Greece through Bayesian admixture analyses of multilocus genotypes

Abstract: The nominal subspecies of rock partridge (Alectoris graeca graeca) is widely distributed in Greece, where populations are declining due to over-hunting and habitat changes. Captive-reared chukars (A. chukar) have been massively released throughout the country, raising fear that introgressive hybridisation might have disrupted local adaptations leading to further population declines. In this study we used mtDNA control-region sequences and Bayesian admixture analyses of multilocus genotypes determined at eight microsatellite loci, to assess the extent of introgressive hybridisation in 319 wild rock partridges collected in Greece. A neighbour-joining tree split the mtDNA haplotypes into three strongly supported clades, corresponding to rock, red-legged (A.␣rufa) and chukar partridges. We did not detect any case of maternal introgression. In contrast, admixture analyses of microsatellite genotypes identified from four to 28 putative hybrids (according to different assignment criteria), corresponding to 1.2–8.8% of the samples, which were widespread throughout all the country. Power and limits of admixture analyses were assessed using simulated hybrid genotypes, which revealed that a small number of markers can detect all first and second generation hybrids (F1 and F2), and up to 90% of the first generation backrossess. Thus, the true proportion of recently introgressed rock partridges in Greece might be ca. 20%. These findings indicate that introgressive hybridisation is widespread, suggesting that released captive-bred partridges have reproduced and hybridised in nature polluting the gene pool of wild rock partridge populations in Greece.

Population genetics of the freshwater mussel, Amblema plicata (Say 1817) (Bivalvia: Unionidae): Evidence of high dispersal and post-glacial colonization

Abstract: Over 70% of North American freshwater mussel species (families Unionidae and Margaritiferidae) are listed as threatened or endangered. Knowledge of the genetic structure of target species is essential for the development of effective conservation plans. Because Ambelma plicata is a common species, its population genetic structure is likely to be relatively intact, making it a logical model species for investigations of freshwater mussel population genetics. Using mtDNA and allozymes, we determined the genotypes of 170+ individuals in each of three distinct drainages: Lake Erie, Ohio River, and the Lower Mississippi River. Overall, within-population variation increased significantly from north to south, with unique haplotypes and allele frequencies in the Kiamichi River (Lower Mississippi River drainage). Genetic diversity was relatively low in the Strawberry River (Lower Mississippi River drainage), and in the Lake Erie drainage. We calculated significant among-population structure using both molecular markers (A.p. Φst = 0.15, θst = 0.12). Using a hierarchical approach, we found low genetic structure among rivers and drainages separated by large geographic distances, indicating high effective population size and/or highly vagile fish hosts for this species. Genetic structure in the Lake Erie drainage was similar to that in the Ohio River, and indicates that northern populations were founded from at least two glacial refugia following the Pleistocene. Conservation of genetic diversity in Amblema plicata and other mussel species with similar genetic structure should focus on protection of a number of individual populations, especially those in southern rivers.

Conservation genetics of snowy plovers ( Charadrius alexandrinus ) in the Western Hemisphere: population genetic structure and delineation of subspecies

Abstract: We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern.

Strongly diverging population genetic patterns of three skipper species: the role of habitat fragmentation and dispersal ability

Abstract: The fragmentation of landscapes has an important impact on the conservation of biodiversity, and the genetic diversity is an important factor for a populations viability, influenced by the landscape structure. However, different species with differing ecological demands react rather different on the same landscape pattern. To address this feature, we studied three skipper species with differing habitat requirements (Lulworth Skipper Thymelicus acteon: a habitat specialist with low dispersal ability, Small Skipper Thymelicus sylvestris: a habitat generalist with low dispersal ability, Essex Skipper Thymelicus lineola: a habitat generalist with higher dispersal ability). We analysed 18 allozyme loci for 1,063 individuals in our western German study region with adjoining areas in Luxembourg and north-eastern France. The genetic diversity of all three species were intermediate in comparison with other butterfly species. The FST was relatively high for T. acteon (5.1%), low for T. sylvestris (1.6%) and not significant for T. lineola. Isolation by distance analyses revealed a significant correlation for T. sylvestris explaining 20.3% of its differentiation, but no such structure was found for the two other species. Most likely, the high dispersal ability of T. lineola in comparison with T. sylvestris leads to a more or less panmictic structure and hence impedes isolation by distance. On the other hand, the isolation of the populations of T. acteon seems to be so strict that the populations develop independently. Although no general genetic impoverishing was observed for the endangered T. acteon, small populations had significantly lower genetic diversities than big populations, and therefore the high degree of isolation among populations might threaten its local and regional survival.

High gene flow in oceanic bottlenose dolphins (Tursiops truncatus) of the North Atlantic

Abstract: Despite the openness of the oceanic environment, limited dispersal and tight social structure often induce genetic structuring in marine organisms, even in large animals such as cetaceans. In the bottlenose dolphin, mitochondrial and nuclear DNA analyses have revealed the existence of genetic differentiation between pelagic (or offshore) and coastal (or nearshore) ecotypes in the western North Atlantic, as well as between coastal populations. Because previous studies concentrated on continental margins, we analysed the population structure of bottlenose dolphins in two of the most isolated archipelagos of the North Atlantic: the Azores and Madeira. We analysed 112 samples collected on live animals in the two archipelagos, and nine samples collected on stranded animals in Madeira and mainland Portugal. Genetic analyses consisted in molecular sexing, sequencing of part of the mitochondrial hyper-variable region, and screening of ten microsatellite loci. We predicted that: (1) there is at least one pelagic and one or more coastal populations in each archipelago; (2) populations are differentiated between and possibly within archipelagos. Contrary to these predictions, results indicated a lack of population structure in the study area. In addition, comparison with published sequences revealed that the samples from the Azores and Madeira were not significantly differentiated from samples of the pelagic population of the western North Atlantic. Thus, bottlenose dolphins occurring in the pelagic waters of the North Atlantic belong to a large oceanic population, which should be regarded as a single conservation unit. Unlike what is known for coastal populations, oceanic bottlenose dolphins are able to maintain high levels of gene flow.

Large mainland populations of South Island robins retain greater genetic diversity than offshore island refuges

Abstract: For conservation purposes islands are considered safe refuges for many species, particularly in regions where introduced predators form a major threat to the native fauna, but island populations are also known to possess low levels of genetic diversity. The New Zealand archipelago provides an ideal system to compare genetic diversity of large mainland populations where introduced predators are common, to that of smaller offshore islands, which serve as predator-free refuges. We assessed microsatellite variation in South Island robins (Petroica australis australis), and compared large mainland, small mainland, natural island and translocated island populations. Large mainland populations exhibited more polymorphic loci and higher number of alleles than small mainland and natural island populations. Genetic variation did not differ between natural and translocated island populations, even though one of the translocated populations was established with five individuals. Hatching failure was recorded in a subset of the populations and found to be significantly higher in translocated populations than in a large mainland population. Significant population differentiation was largely based on heterogeneity in allele frequencies (including fixation of alleles), as few unique alleles were observed. This study shows that large mainland populations retain higher levels of genetic diversity than natural and translocated island populations. It highlights the importance of protecting these mainland populations and using them as a source for new translocations. In the future, these populations may become extremely valuable for species conservation if existing island populations become adversely affected by low levels of genetic variation and do not persist.

Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

Abstract: Asian box turtles (genus Cuora, family Geoemydidae) comprise a clade of 12 aquatic and semiaquatic nominate species distributed across southern China and Southeast Asia. Over the last two decades, turtles throughout Asia have been harvested at an unsustainable rate to satisfy demands for food, traditional Chinese medicine, and the pet trade. Con- sequently, all species of Cuora were recently placed on the IUCN Red List, nine are currently listed as criti- cally endangered by the IUCN, and all species are listed in Appendix II of CITES. We compiled a 67-specimen mitochondrial (~1,650 base pairs (bp) from two mitochondrial genes) and a 40-specimen nuclear-plus-mitochondrial (~3,900 bp total, three nuclear introns plus an additional ~860 bp mitochon- drial gene fragment) DNA data set to reconstruct the phylogeny of Cuora species and to assess genetic diversity and species boundaries for several of the most problematic taxa. Our sampling included 23 C. trifas- ciata ,1 7C. zhoui and 1-4 individuals of the remaining 10 species of Cuora. Maximum likelihood, maximum parsimony and Bayesian analyses all recovered similar, well resolved trees. Within the Cuora clade, mito- chondrial and nuclear sequence data indicated that both C. zhoui and C. mccordi represent old lineages with little or no history of interspecific gene flow, suggesting that they are good genealogical species. Based on mtDNA, Cuora pani was paraphyletic and C. trifasciata was composed of two highly divergent lineages that were not each other's closest relatives; both cases of non-monophyly were due to a mtDNA sequence that was widespread and identical in C. aurocapitata, C. pani and C. trifasciata. However, when combined with nuclear DNA results, our data indicate that C. trifasciata is a single, monophyletic taxon, and that mitochondrial introgression and nuclear-mitochondrial pseudogenes have led to a complex pattern of mitochondrial gene relationships that does not reflect species-level histories. Our results imply that captive ''assurance colonies'' of both C. trifasciata and C. pani should be genotyped to identify pure, non-hybrid members of both taxa, and we recommend that introgressed and pure taxa be man- aged as independent entities until the full evolutionary histories of these critically endangered turtles are resolved.

Reliability of noninvasive genetic census of otters compared to field censuses

Abstract: Conservation and management actions are often highly dependent on accurate estimations of population sizes. However, these estimates are difficult to obtain for elusive and rare species. We compared two census methods for Eurasian otter: snow tracking and noninvasive genetic census based on the genotyping of faecal samples. With the noninvasive genetic census we detected the presence of almost twice as many otters as with snow tracking (23 and 10–15, respectively), and mark-recapture estimates based on the genetic census indicated that the real number of otters could be even higher. Our results indicate that snow tracking tends to underestimate the number of individuals and also that it is more susceptible to subjective assessment. We compared the strengths and weaknesses of the two methods.

Genetic structure in a swarming brown long-eared bat ( Plecotus auritus ) population: evidence for mating at swarming sites

Abstract: Plecotus auritus, a small, gleaning bat species, lives in small, isolated summer colonies in which both males and females show a high degree of natal philopatry. Despite this, colonies have high gene diversities and low inbreeding coefficients. It has been suggested that inbreeding is avoided because mating occurs during autumnal and spring swarming at hibernation sites. We tested this hypothesis by comparing microsatellite profiles, based on eight loci, of bats from six summer colonies and two swarming sites they were known to visit from radiotelemetry studies. We found high gene diversities (Hs = 0.77) at both swarming sites and summer colonies which were not statistically different. There was no detectable isolation by distance and FST was low (0.001). Together, these results suggest high gene flow between sites. Despite this, there was small but significant genetic differentiation amongst summer colonies and between summer colonies and the primary swarming site. We suggest that swarming is important for gene flow and for maintaining genetic diversity in this highly philopatric species and discuss possible reasons for the genetic differentiation observed. The identification and protection of swarming sites should be a major conservation priority for this and other temperate bat species.

Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California

Abstract: The final publication is available at link.springer.com. Link to abstract: http://link.springer.com/article/10.1007/s10592-006-9183-0

Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations

Abstract: Comprehensive evaluations of multiple genetic factors are rarely undertaken in rehabilitation attempts of extirpated populations, despite a growing need to address why some rehabilitation projects succeed and others fail. Using temporally-spaced samples of microsatellite DNA, we tested several genetic hypotheses that might explain an unsuccessful attempt to re-establish Atlantic salmon populations (Salmo salar) in two rivers of the inner Bay of Fundy, Canada. Census sizes (N) in both populations plummeted to near zero from initial increases after reintroduction/human-mediated recolonization occurred. Over the same period (1974–1996), both populations were characterized by low or relatively low effective sizes (N e ) and temporally unstable genetic structuring, whereas neighbouring populations, known historically for their significant salmon production, were not. Despite evidence for genetic bottlenecking and continual linkage disequilibrium over time in both populations, neither exhibited detectable inbreeding or a significant loss of allelic diversity or heterozygosity relative to known donor/source populations. Ratios of N e to N also increased with decreasing N in both populations, implying a buffering capacity against losses of genetic diversity at depressed abundances. Most significantly, multiple lines of evidence were consistent with the hypothesis that there has been substantial and recurrent asymmetric migration (migration rate, m) from neighbouring areas into both populations even after initial rehabilitation. This included migration from a historically productive population that became extirpated during the course of rehabilitation efforts, indicating that both populations might have naturally depended on immigration from neighbouring areas for persistence. Our results highlight the value of incorporating temporal genetic data beyond commonly used metrics of neutral genetic diversity (F ST, allelic richness, heterozygosity) to evaluate rehabilitation successes or failures. They also illustrate how the joint evaluation of multiple genetic concerns in rehabilitation attempts, at spatial scales beyond donor and rehabilitated populations, is useful for focusing future rehabilitation efforts.

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

Abstract: California is home to both the native state- threatened Sierra Nevada red fox (Vulpes vulpes ne- cator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in Cali- fornia, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911-1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant popula- tion differentiation among the modern and historic high-elevation populations (average pairwise FST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise FST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (FST = -0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise FST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecu- lar variance (FCT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (FSC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.

Genetic differentiation of an endangered capercaillie (Tetrao urogallus) population at the Southern edge of the species range

Abstract: The low-latitude limits of species ranges are thought to be particularly important as long-term stores of genetic diversity and hot spots for speciation. The Iberian Peninsula, one of the main glacial refugia in Europe, houses the southern distribution limits of a number of boreal species. The capercaillie is one such species with a range extending northwards to cover most of Europe from Iberia to Scandinavia and East to Siberia. The Cantabrian Range, in North Spain, constitutes the contemporary south-western distribution limit of the species. In contrast to all other populations, which live in pure or mixed coniferous forests, the Cantabrian population is unique in inhabiting pure deciduous forests. We have assessed the existence of genetic differentiation between this and other European populations using microsatellite and mitochondrial DNA (mtDNA) extracted from capercaillie feathers. Samples were collected between 2001 and 2004 across most of the current distribution of the Cantabrian population. Mitochondrial DNA analysis showed that the Cantabrian birds form a distinct clade with respect to all the other European populations analysed, including the Alps, Black Forest, Scandinavia and Russia, which are all members of a discrete clade. Microsatellite DNA from Cantabrian birds reveals the lowest genetic variation within the species in Europe. The existence of birds from both mtDNA clades in the Pyrenees and evidence from microsatellite frequencies for two different groups, points to the existence of a Pyrenean contact zone between European and Cantabrian type birds. The ecological and genetic differences of the Cantabrian capercaillies qualify them as an Evolutionarily Significant Unit and support the idea of the importance of the rear edge for speciation. Implications for capercaillie taxonomy and conservation are discussed.

Genetic diversity within and between remnant populations of the endangered calcareous grassland plant Globularia bisnagarica L.

Abstract: Changes in agricultural production methods over the last century have caused a massive reduction and fragmentation of the area of European semi-natural grasslands. It remains unclear whether small and isolated grassland fragments can support viable plant populations in a sustainable way. In our study area in southern Belgium, the extent of calcareous grasslands was reduced from c. 650 ha in 1775 to less than 30 ha in 2004. We used AFLP markers to quantify the effects of present and historical grassland fragmentation on the genetic structure of 27 populations of the rare perennial plant species Globularia bisnagarica. Given the mixed breeding system of the species and the relatively small area of the studied system, the populations were characterized by high genetic differentiation (F st range: 0.42–0.48; Φst=0.53). A Mantel test revealed significant isolation by distance of the populations. Average within population genetic diversity, measured as expected heterozygosity or gene diversity, was low (H j =0.081) and was negatively related to population isolation. This suggests more gene flow into less isolated populations. Population size and local habitat characteristics did not significantly influence population genetic diversity. Both, high selfing rates in G. bisnagarica and a population genetic response to habitat fragmentation may explain our findings. Finally, a clear geographical clustering was observed, with cluster membership partially explainable by historical grassland connectivity. If populations indeed started to differentiate after fragmentation, this process was not (yet) strong enough to erase the genetic similarity between fragments that historically belonged to the same large grassland fragment.

Genetic variation in island populations of tuatara (Sphenodon spp) inferred from microsatellite markers

Abstract: Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High F ST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.

Phylogeography of the capercaillie in Eurasia: what is the conservation status in the Pyrenees and Cantabrian Mounts?

Abstract: The Western capercaillie (Tetrao urogallus) is a keystone species of Palearctic boreal and altitude coniferous forests. With the increase of mountain leisure activities and habitat loss, populations are declining in most mountain ranges in Western Europe. Recent work has shown that the populations from the Pyrenees and Cantabrian Mountains survived a severe bottleneck during the 19th century, and are still considered as threatened due to habitat fragmentation and isolation with other populations. We present an extensive phylogeographic study based on mitochondrial DNA sequence (control region) extracted non-invasively from faeces collected throughout the species range (from western European mountains to central and eastern Europe, Fenno-Scandia, Russia and Siberia). We also compared our results with DNA sequences of closely related black-billed capercaillie (T. parvirostris). We found that populations from Pyrenees and Cantabrians are closely related but are different from all other capercaillie populations that form a homogenous clade. Therefore, we consider that these South-Western populations should be considered as forming an Evolutionary Significant Unit that needs an appropriate management at a local scale. We also discuss the possible locations of glacial refugia and subsequent colonisation routes in Eurasia, with a Western “aquitanus” lineage from Iberia and Balkans, and an Eastern “urogallus” lineage from Southern Asia. This work might have important implication for capercaillie conservation strategies to define important areas for conservation, and to prevent possible exchange or introductions of individuals originated from other lineages.

Low genetic diversities in isolated populations of the Asian black bear ( Ursus thibetanus ) in Japan, in comparison with large stable populations

Abstract: Populations of the Asian black bear (Ursus thibetanus) are relatively large and continuous in central Honshu, the main island of Japan, but they are isolated in western Honshu. To clarify the degree of genetic isolation of the populations in western Honshu, we compared the genetic diversities of four populations in western Honshu with that of one of the continuous populations of central Honshu. Three of the four western Honshu populations were isolated and the other was continuous with the central Honshu populations on a geographical distribution basis. The genotypes at 10 microsatellite loci of the sampled individuals were determined and the genetic structures of the populations examined. Genetic diversities were significantly lower in the isolated populations than in the continuous populations. The continuous population in central Honshu had high levels of genetic diversity, comparable to those in populations of the American black bear (Ursus americanus) and the brown bear (Ursus arctos). The genetic distances between the two continuous populations were smallest, even though their geographic distance was largest (>200 km) among all the pairs of neighboring populations examined. Low genetic diversity within the isolated populations suggested genetic drift due to the small population size; the genetic differentiation among the populations indicated low rates of gene flow among them.

Mitochondrial markers reveal deep population subdivision in the European protected spider Macrothele calpeiana (Walckenaer, 1805) (Araneae, Hexathelidae)

Abstract: The funnel-web spider genus Macrothele is the only representative of the mygalomorph family Hexathelidae not found in Australia or New Zealand. Its 26 species occur in Central Africa and the Oriental region. Two Macrothele species are found in Europe: M. cretica Kulczynski, 1903 from Crete, and M. calpeiana (Walckenaer, 1805) type species of the genus and the largest European spider, whose distribution extends across the south-eastern Iberian Peninsula, and in two localities of North Africa. Macrothele calpeiana is the only spider protected under European legislation. The fragmentation and destruction of the cork oak forest, with which M. calpeiana was thought to be closely associated, prompted the inclusion of this species in the Bern Convention. Some authors, however, have challenged this view and consider M. calpeiana to be neither a cork oak forest bioindicator nor an endangered species. By contrast, other observations suggest that the distribution of the species is extremely fragmented and that most local populations should be considered as threatened. In this paper, we examine aspects of the conservation status of M. calpeiana in the light of molecular phylogenetic analyses based on mitochondrial markers of sample specimens from major populations. Our data confirm the fragmented distribution of M. calpeiana and reveal high levels of genetic differentiation across its populations. Local population growth cannot be ruled out, though the lineage as a whole has apparently not undergone population growth. Lineage age estimates suggest that M. calpeiana colonized the Iberian Peninsula during the Messinian salinity crisis and that the current population fragmentation originates from the Pliocene and Pleistocene. We argue that the fragmentation and deep genetic divergence across populations, along with evolutionary singularity and endemicity in one of Europe’s main biodiversity hotspots, support the preservation of its legally protected status.

Genetic structure of Saxifraga tridactylites (Saxifragaceae) from natural and man-made habitats

Abstract: In contrast to many declining plant species Saxifraga tridactylites extended its distribution range in the man-made landscape of central Europe. The species naturally colonizes rocks and calcareous grasslands, but has also spread enormously in anthropogenic habitats such as railway constructions during the last decades. To analyze the genetic structure of the species 216 individuals from 8 populations in natural and 5 populations in man-made habitats were studied using AFLPs. The molecular analysis resulted in 250 scorable fragments. Population variability, measured as Nei’s gene diversity, Shannon’s Information Index and percentage of polymorphic bands, was slightly but not significantly higher in populations from natural habitats and was not correlated with population size. Mantel test indicated no significant correlation between pairwise genetic (ΦPT) and geographic distances. An analysis of molecular variance revealed significant differentiation between the two habitat types. About 9% variability were observed between natural and man-made habitats, 21% among populations within these two habitats and 70% within populations. In a neighbour joining cluster analysis populations from natural and man-made habitats were clearly separated from each other. Populations of S. tridactylites from man-made habitats do, therefore, not suffer from reduced genetic diversity. The observed genetic differentiation between populations from man-made and natural habitats could be due to reduced gene flow and/or habitat specific selection. However, the results of the study clearly demonstrate human impact on the genetic structure of plant populations in man-made landscapes.

Allelic dropout from a high-quality DNA source

Abstract: Allelic dropouts are an important source of genotyping error, particularly in studies using non-invasive sampling techniques. This has important implications for conservation biology, as an increasing number of studies are now using non-invasive techniques to study rare species or endangered populations. Previously, allelic dropout has typically been associated with PCR amplification of low quality/quantity template DNA. However, in this study we recorded high levels of allelic dropout (21–57%) at specific loci amplified from a high quality DNA (63.1 ± 7.8 ng/μl) source in the red fox (Vulpes vulpes). We designed a series of experiments to identify the sources of error. Whilst we were able to show that the best method to identify allelic dropout was the dilution of template DNA prior to PCR amplification, our data also showed two specific patterns: (1) allelic dropouts occurred at specific loci; (2) allelic dropouts occurred at specific pair-wise combinations of alleles. These patterns suggest that mechanisms other than low quantity template DNA are responsible for allelic dropout. Further research on the causes of these patterns in this and other studies would further our understanding of genotyping errors and would aid future studies where allelic dropout may be a serious issue.