The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.     

Gene flow and immigration: genetic diversity and population structure of lions (Panthera leo) in Hwange National Park,Zimbabwe

The genetic diversity and population structure of a population of African lions in Hwange National Park, Zimbabwe, was studied using 17 microsatellite loci. Spatial genetic analysis using Bayesian methods suggested a weak genetic structure within the population and high levels of gene flow across the study area. We were able to identify a few individuals with aberrant or admixed ancestry, which we interpreted as either immigrants or as descendants thereof. This, together with relatively high genetic diversity, suggests that immigrants from beyond the study area have influenced the genetic structure within the park. We suggest that the levels of genetic diversity and the observed weak structure are indicative of the large and viable Okavango-Hwange population of which our study population is a part. Genetic patterns can also be attributed to still existing high levels of habitat connectivity between protected areas. Given expected increases in human populations and anthropogenic impacts, efforts to identify and maintain existing movement corridors between regional lion populations will be important in retaining the high genetic diversity status of this population. Our results show that understanding existing levels of genetic diversity and genetic connectivity has implications, not only for this lion population, but also for managing large wild populations of carnivores.     

A multi‐method approach for analyzing hierarchical genetic structures: a case study with cougars Puma concolor

Genetic data are increasingly used to describe the structure of wildlife populations and to infer landscape influences on functional connectivity. To accomplish this, genetic structure can be described with a multitude of methods that vary in their assumptions, advantages and limitations. While some methods discriminate distinct subpopulations separated by sharp genetic boundaries (i.e. barrier detection or clustering methods), other methods estimate gradient genetic structures using individual‐based genetic distances. We present an analytical framework based on individual ancestry values that combines these different approaches and can be used to a) test for local barriers to gene flow and b) evaluate effects of landscape gradients through individual‐based genetic distances that account for hierarchical genetic structure. We illustrate the approach with a data set of 371 cougars Puma concolor from a 217 000 km² study area in Idaho and western Montana (USA) that were genotyped at 12 microsatellite loci. Results suggest that cougars in the region show a complex, hierarchical genetic structure that is influenced by a local barrier to gene flow (an urban population cluster connected by high traffic volumes), different landscape features (the Snake River Plain, forested habitat), and geographic distance. Our novel approach helped to elucidate the relative influence of these factors on different hierarchical levels of population structure, which was not possible when using either clustering methods or standard genetic distances. Results obtained with our analytical framework highlight the need for multi‐scale management of cougars in the region and show that landscape heterogeneity can create complex genetic structures, even in generalist species with high dispersal capabilities.     

Genetic diversity, structure, and size of an endangered brown bear population threatened by highway construction in the Pindos Mountains, Greece

One of the major negative effects of roads is the creation of barriers to the movement of wildlife, ultimately disconnecting populations and increasing extinction risk. We collected genetic data from a threatened brown bear population in the central part of the Pindos mountain range in northwestern Greece to provide information about this, as yet genetically undescribed, population and to evaluate its status prior to the construction of a major highway. We used noninvasive genetic sampling methods and microsatellite analysis to investigate nuclear genetic diversity, population genetic structure, demographic history, relatedness within the population and estimated effective and total population size. Brown bears in the study area were found to possess a relatively high level of nuclear genetic diversity and low levels of inbreeding; the population did not show any signs of substructuring but seems to have gone through a genetic bottleneck in the recent past. The estimated effective population size was 29, and the total population size estimate obtained by two different methods was 33 and 51 individuals, respectively. Our results indicate a good conservation status of this bear population and provide baseline genetic data for the future evaluation of the effects on bears from the construction of a major highway, for monitoring the genetic status of this and other bear populations in Greece and for assessing gene flow in bear populations in southern Europe.     

Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population

Molecular forensic methods are being increasingly used to help enforce wildlife conservation laws. Using multilocus genotyping, illegal translocation of an animal can be demonstrated by excluding all potential source populations as an individual's population of origin. Here, we illustrate how this approach can be applied to a large continuous population by defining the population genetic structure and excluding suspect animals from each identified cluster. We aimed to test the hypothesis that recreational hunters had illegally introduced a group of red deer into a hunting area in Luxembourg. Reference samples were collected over a large area in order to test the possibility that the suspect individuals might be recent immigrants. Due to isolation-by-distance relationships in the data set, inferring the number of genetic clusters using Bayesian methods was not straightforward. Biologically meaningful clusters were only obtained by simultaneously analysing spatial and genetic information using the program baps 4.1. We inferred the presence of three genetic clusters in the study region. Using partial Mantel tests, we detected barriers to gene flow other than distance, probably created by a combination of urban areas, motorways and a river valley used for viticulture. The four focal animals could be excluded with a high certainty from the three genetic subpopulations and it was therefore likely that they had been released illegally.     

Inferring the ancient population structure of the vulnerable albatross Phoebastria albatrus, combining ancient DNA, stable isotope, and morphometric analyses of archaeological samples

The history of population structure is a key to effective wildlife management and conservation. However, inferring the history of population structure using present genetic structures is problematic when the method is applied to species that have experienced severe population bottlenecks. Ancient DNA analysis seemed to be a promising, direct method for inferring ancient population structures. However, the usual methods for inferring modern population structure, i.e. the phylogeographic approach using mitochondrial DNA and the Bayesian approach using microsatellite DNA, are often unsuitable for ancient samples. In this study, we combined ancient DNA obtained from zooarchaeological bones with carbon/nitrogen stable isotope ratios and morphological variations to infer ancient population structure of the short-tailed albatross Phoebastria albatrus. The results showed that the bird existed in two populations, between which the genetic distance was greater than that of distinct sister albatross species, although no subspecies of P. albatrus have been proposed. Our results suggest that the birds at the present two breeding regions (Torishima in the Izu Islands and two islets of the Senkaku Islands) are descended from these two ancient populations, and that reevaluation of the status and conservation strategy for the species is required. Our results also indicate that lineage breeding on the Senkaku Islands has drastically reduced genetic diversity, while that on Torishima has not. The approach proposed in this study would be useful for inferring ancient population structure, using samples of highly mobile animals and/or samples from archaeological sites, and the reconstructed ancient population structure would be useful for conservation and management recommendations.     

Population Genetics of Indigenous Quercus robur L. Populations and of Derived Half‐Sib Families has Implications for the Reproductive Management of the Species

Abstract: In the Netherlands indigenous Quercus robur L. populations are rare and have been maintained as patches in ancient woodland. For adequate conservation of these populations, information about genetic variation and population structure is necessary. In order to assess the genetic variation and structure of these populations, microsatellite polymorphisms were studied in two autochthonous populations. These two populations differed slightly for their gene diversity, which was as high as was observed for Q. robur populations in France and Germany. For reforestation purposes there is an interest in the genetic variation of a half‐sib family harvested from one tree. The gene diversity of the two studied half‐sib families ‐ obtained from a forest and an urban area ‐ was similar, but relatively low. This indicates that, for reforestation purposes, seeds should be harvested from many different trees in order to obtain a population with a genetic variation as high as was observed for an autochthonous population.     

Evidence of wolf dispersal in anthropogenic habitats of the Polish Carpathian Mountains

In the course of their maturation, most young wolves leave their natal pack and disperse in search for mating partners, improved food availability and new territories. We investigated whether this dispersal is affected by anthropogenic infrastructure in a 5,000 km2 area of the eastern region of the Polish Carpathian Mountains occupied by wolves. A radio-collared male wolf covered 230 km while dispersing through forested hills and densely populated valleys. To test if such dispersal is common in the population we analysed by microsatellite genotyping 39 samples taken from live-trapped wolves or wolves found dead in the study area. Although the obtained genotypes were assigned to different clusters in Bayesian tests, we could not ascribe this structure to landscape features, but rather to shared ancestry of wolf individuals found in distant locations. Moreover, we could not detect a spatial genetic structure in the wolf population, indicating a random occurrence of genotypes within the study area. Observation of the dispersing wolf and the absence of spatial genetic structure imply that wolves are still able to roam the entire area despite high densities of roads and a dense human population. Thus, we concluded that the existing anthropogenic infrastructure does not restrict wolf dispersal in the area and the studied wolves represent a coherent part of the Polish Carpathian wolf population.     

Principal components analysis of protein structure ensembles calculated using NMR data

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations.     

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

Red Junglefowl (Gallus gallus) are among the few remaining ancestors of an extant domesticated livestock species, the domestic chicken, that still occur in the wild. Little is known about genetic diversity, population structure, and demography of wild Red Junglefowl in their natural habitats. Extinction threats from habitat loss or genetic alteration from domestic introgression exacerbate further the conservation status of this progenitor species. In a previous study, we reported extraordinary adaptive genetic variation in the MHC B‐locus in wild Red Junglefowl and no evidence of allelic introgression between wild and domestic chickens was observed. In this study, we characterized spatial genetic variation and population structure in naturally occurring populations of Red Junglefowl in their core distribution range in South Central Vietnam. A sample of 212 Red Junglefowl was obtained from geographically and ecologically diverse habitats across an area of 250 × 350 km. We used amplified fragment‐length polymorphism markers obtained from 431 loci to determine whether genetic diversity and population structure varies. We found that Red Junglefowl are widely distributed but form small and isolated populations. Strong spatial genetic patterns occur at both local and regional scales. At local scale, population stratification can be identified to approximately 5 km. At regional scale, we identified distinct populations of Red Junglefowl in the southern lowlands, northern highlands, and eastern coastal portions of the study area. Both local and long‐distance genetic patterns observed in wild Red Junglefowl may reflect the species’ ground‐dwelling and territorial characteristics, including dispersal barriers imposed by the Annamite Mountain Range. Spatially explicit analyses with neutral genetic markers can be highly informative and here elevates the conservation profile of the wild ancestors of domesticated chickens.     

StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk , medmeak , maxmedk and maxmeak ) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy‐to‐use software limits the use of these appealing new estimators. Here, we developed a web‐based user‐friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure , admixture or faststructure as input files. It reports the “best” K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/ .     

Do rivers and human-induced habitat fragmentation affect genetic diversity and population structure of the European ground squirrel at the edge of its Pannonian range?

The European ground squirrel (EGS) (Spermophilus citellus) populations of Vojvodina (Serbia) represent the southernmost part of its distribution in the Pannonian lowland. For species with low dispersal abilities a presence of even weak barriers can have significant influence on genetic structure among adjacent populations. We examined here the effects of habitat fragmentation and river barriers on the genetic structure of the EGS based on 12 microsatellite loci. Bayesian clustering methods were used as additions to classical population genetic approaches. We found that EGS populations in Vojvodina are highly fragmented, but their genetic variation is still higher than in peripheral populations in Central Europe. Populations in Vojvodina consistently grouped into three genetic clusters. The Danube, but not the Tisza River, represents an important barrier to gene flow. EGS populations in the studied area did not show the signs of recent genetic bottlenecks, as would be expected from observations of recent population declines. Conservation strategy should be focused on maintenance of remained suitable habitats and optimal population sizes.     

Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.     

Genetic structure of La Cabrera, Spain, from surnames and migration matrices

The genetic structure of La Cabrera (province of Léon, Spain), a highly isolated and inbred population (alpha3 = 0.00482), is analyzed by applying multivariate methods (nonmetric multidimensional scaling, Mantel test, Monmonier's algorithm) to different biodemographic data sets. Isonymy, parent-offspring migration (total, males, females), and marital migration matrices were obtained from 5,714 marriages recorded in 37 parishes (clustered in 4 municipalities) between 1880 and 1989. The aim of the study is to investigate the relationships between the genetic and geographic structures of the area. Endemicity values (diagonal of parent-offspring migration matrices), calculated for both sexes at two hierarchical levels (parishes and municipalities), show that female mobility follows the virilocal migration model at the higher (municipalities) level and the uxorilocal model at the parish level. Analysis of isonymy and parent-offspring migration matrices shows high correspondence between the genetic structure and geographic location of the parishes. In fact, the main reproductive barriers, constructed using Monmonier's algorithm, generally coincide with geographic barriers, highlighting increasing isolation patterns from northwest to southeast. Moreover, the analysis of isonymous relationships, which are influenced by earlier population movements, identifies three parishes whose outlier positions are explained by historical-cultural or geographic reasons. The positive and highly significant values (0.32 < or = r < or = 0.51;p < or = 0.001) given by the Mantel tests underline the dependence of the genetic structure on geographic distance. In confirmation of the endemicity results, the lowest correlation value (r = 0.32) is given by the female migration matrix. When the outlier parishes are omitted from the analysis, the correlation between isonymy and geographic distance increases from 0.35 to 0.46, and the values from the other migration matrices remain unchanged. In conclusion, the combination of different data sets and methods allows a wider and more coherent reconstruction of the historical changes in the genetic structure of the La Cabrera population.     

Genetic Structure of Populations of the Colorado Potato Beetle Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The genetic structure of a Colorado potato beetle population from Kiev oblast was examined by cluster analysis of individual RAPD patterns. The obtained clustering indicates that the population is structured. This may be explained by adaptation to pyrethroid insecticides used for controlling the population size of this pest. Microevolutionary factors affecting the genetic structure of local populations of Colorado potato beetle are discussed.     

Genetic structure of populations of the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The genetic structure of a Colorado potato beetle population from Kiev oblast was examined by cluster analysis of individual RAPD patterns. The obtained clustering indicates that the population is structured. This may be explained by adaptation to pyrethroid insecticides used for controlling the population size of this pest. Micro-evolutionary factors affecting the genetic structure of local populations of Colorado potato beetle are discussed.     

Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea

Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.     

Analysis of the Alu insertion polymorphism in urban and rural populations of Siberia]

Polymorphic Alu-repeat loci of human genome are commonly used as effective genetic markers in population and evolution studies. In this work, the data on genetic structure of two Russian populations from Siberia obtained via analysis of five polymorphic Alu repeats are presented. The urban population was characterized by a slightly higher level of genetic diversity compared to the rural population. The value of genetic differentiation coefficient for the populations studied was 0.57%, pointing to the absence of genetic subdivision within the urban and rural populations. Phylogenetic analysis of these populations, together with literature data, shows that, with respect to the markers examined, the gene pool structure of Russian population is similar to that of other Caucasoid populations.     

Non-invasive genetic monitoring of wild central chimpanzees

Background

An assessment of population size and structure is an important first step in devising conservation and management plans for endangered species. Many threatened animals are elusive, rare and live in habitats that prohibit directly counting individuals. For example, a well-founded estimate of the number of great apes currently living in the wild is lacking. Developing methods to obtain accurate population estimates for these species is a priority for their conservation management. Genotyping non-invasively collected faecal samples is an effective way of evaluating a species'' population size without disruption, and can also reveal details concerning population structure.

Methodology/Principal Findings

We opportunistically collected wild chimpanzee faecal samples for genetic capture-recapture analyses over a four-year period in a 132 km² area of Loango National Park, Gabon. Of the 444 samples, 46% yielded sufficient quantities of DNA for genotyping analysis and the consequent identification of 121 individuals. Using genetic capture-recapture, we estimate that 283 chimpanzees (range: 208–316) inhabited the research area between February 2005 and July 2008. Since chimpanzee males are patrilocal and territorial, we genotyped samples from males using variable Y-chromosome microsatellite markers and could infer that seven chimpanzee groups are present in the area. Genetic information, in combination with field data, also suggested the occurrence of repeated cases of intergroup violence and a probable group extinction.

Conclusions/Significance

The poor amplification success rate resulted in a limited number of recaptures and hence only moderate precision (38%, measured as the entire width of the 95% confidence interval), but this was still similar to the best results obtained using intensive nest count surveys of apes (40% to 63%). Genetic capture-recapture methods applied to apes can provide a considerable amount of novel information on chimpanzee population size and structure with minimal disturbance to the animals and represent a powerful complement to traditional field-based methods.