Bayesian Clustering Methods Research Articles

Hybrid origin of European Vipers (Vipera magnifica and Vipera orlovi) from the Caucasus determined using genomic scale DNA markers.

BackgroundStudying patterns of introgression can illuminate the role of hybridization in speciation, and help guide decisions relevant to the conservation of rare taxa. Vipera magnifica and Vipera orlovi are small vipers that have high conservation status due to their rarity and restricted distributions in an area of the Caucasus region where two other related species are present – V. kaznakovi and V. renardi. Despite numerous observations of hybridization between different species of small vipers, and the potential of a hybrid origin for V. magnifica and V. orlovi based on their distribution with respect to V. kaznakovi and V. renardi, hypotheses of a hybrid origin have not been formally tested. Here we generate genomic-scale data by performing next generation sequencing of double digest restriction-site associated DNA libraries, and use these multilocus data to test whether these two species are of hybrid origin.ResultsWe generated over nine hundred loci for 38 specimens of six taxa, and analysed the dataset using Bayesian clustering and multivariate methods, as well as Patterson D-statistics, which can distinguish between incomplete lineage sorting and introgression as explanations for shared polymorphism. The results demonstrate a pattern of historical admixture in the two purported hybrids that is consistent with past gene flow from V. renardi into V. kaznakovi. The average admixture proportion in individuals was low (6.39 %) in the case of V. magnifica, but was higher in V. orlovi (19.02 %). We also show that the specific individual samples used in D-statistic tests can have a significant impact on inferences regarding the magnitude of introgression, suggesting the importance of including multiple individuals in these analyses.ConclusionsOur results support the conclusion that both V. orlovi and V. magnifica had formed through a hybridization event between V. kaznakovi and V. renardi. Given a low proportion of admixture and absence of clear ecological and morphological differences V. magnifica should be treated as a marginal population of V. kaznakovi. Further studies that include analyses of ecological segregation of V. orlovi from parental taxa and search for evolutionary consequences of hybridisation would clarify if V. orlovi is a distinct hybrid species. Until this we recommend preserving the current taxonomy and protection status of V. orlovi.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0647-7) contains supplementary material, which is available to authorized users.

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

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.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox.

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.

GENETIC DIVERSITY OF THE SIKA DEER CERVUS NIPPON IN LITHUANIA

The sika deer ( Cervus nippon ) are considered to be an invasive species in Europe. The main problem that the European free-living sika deer pose is damage they do to forests as well as hybridisation with the local red deer. The aim of this study was to analyse the genetic diversity of the sika deer and the red deer in Lithuania, and to determine the hybridization, which might be present in red deer population from the past release of sika deer into the nature. Tissue samples were collected from 30 sika deer individuals from enclosures, and 33 wild-living red deer. Samples were genotyped using seven microsatellite (STR) loci; genetic diversity indices were calculated and individuals were classified using Principal Coordinate Analysis (PCoA); the genetic structure of sika deer and red deer was investigated according to Bayesian clustering method using STRUCTURE software. The STR loci were highly polymorphic with up to 17 alleles per locus, and with an average heterozygosity Ho=0.695 and Ho=0.626 for sika deer and red deer respectively. Overall inbreeding coefficient (F IS ) values are 0.004 and 0.127 in sika and red deer respectively. According to the PCoA sika deer samples differ from those of red deer; however, few red deer individuals mix with sika deer. These animals were attributed to red deer according to their phenotype; however according to their genotype they are closer to sika deer. Thus, it can be concluded that wild red deer in Lithuania may hybridise with sika deer.

Using multiple landscape genetic approaches to test the validity of genetic clusters in a species characterized by an isolation-by-distance pattern

Bayesian clustering methods are typically used to identify barriers to gene flow, but they are prone to deduce artificial subdivisions in a study population characterized by an isolation-by-distance pattern (IbD). Here we analysed the landscape genetic structure of a population of wild boars (Sus scrofa) from south-western Germany. Two clustering methods inferred the presence of the same genetic discontinuity. However, the population in question was characterized by a strong IbD pattern. While landscape-resistance modelling failed to identify landscape features that influenced wild boar movement, partial Mantel tests and multiple regression of distance matrices (MRDMs) suggested that the empirically inferred clusters were separated by a genuine barrier. When simulating random lines bisecting the study area, 60% of the unique barriers represented, according to partial Mantel tests and MRDMs, significant obstacles to gene flow. By contrast, the random-lines simulation showed that the boundaries of the inferred empirical clusters corresponded to the most important genetic discontinuity in the study area. Given the degree of habitat fragmentation separating the two empirical partitions, it is likely that the clustering programs correctly identified a barrier to gene flow. The differing results between the work published here and other studies suggest that it will be very difficult to draw general conclusions about habitat permeability in wild boar from individual studies.

Combining molecular and fossil data to infer demographic history of Quercus cerris: insights on European eastern glacial refugia

AbstractAimPhylogeographical studies of Eastern Mediterranean species are rare. We aim to fill a gap in the current understanding of the role of Eastern Mediterranean glacial refugia, and their connections with other refugia across Europe. To this end, we studied the genetic diversity distribution and genetic structure of the modern population of Quercus cerris in relation to its Quaternary demographic history and to more ancient events.LocationMediterranean Basin; Italian, Balkan, Anatolian peninsulas.MethodsA total of 192 populations were genotyped with six polymorphic chloroplast microsatellites, and the genetic diversity and differentiation of the populations were evaluated. The geographical structure of genetic variation was analysed with a Bayesian clustering method using baps 5.2. The demographic history of Q. cerris was explored by an approximate Bayesian computation procedure using diyabc 2.0. To reconstruct the past distribution of Q. cerris, we also considered the chronology and geographical distribution of fossil records.ResultsThirty‐five haplotypes were found, three of which (together) were found in 71.82% of individuals. Bayesian analysis resulted in three genetically and geographically distinct clusters: a Western group, a Central group, and an Eastern group. The approximate Bayesian computation analysis, together with fossil data, showed a possible bottleneck leading to the divergence of the Eastern and Central populations in the Early Pleistocene (Gelasian). The split into two groups of populations in the Italian and Balkan Peninsulas, respectively, was probably caused by a marked population contraction during a glacial phase of the Middle Pleistocene.Main conclusionsThis study provides information on the potential role of Eastern Europe and the Near East as refugia and as a source for ancient westward range expansions in the Mediterranean region. Our study covers a remarkable gap in European oak phylogeography, showing a putative eastern origin of Q. cerris and the presence of large amounts of genetic diversity in this region.

Identifying Activation Centers with Spatial Cox Point Processes Using fMRI Data.

We developed a Bayesian clustering method to identify significant regions of brain activation. Coordinate-based meta data originating from functional magnetic resonance imaging (fMRI) were of primary interest. Individual fMRI has the ability to measure the intensity of blood flow and oxygen to a location within the brain that was activated by a given thought or emotion. The proposed method performed clustering on two levels, latent foci center and study activation center, with a spatial Cox point process utilizing the Dirichlet process to describe the distribution of foci. Intensity was modeled as a function of distance between the focus and the center of the cluster of foci using a Gaussian kernel. Simulation studies were conducted to evaluate the sensitivity and robustness of the method with respect to cluster identification and underlying data distributions. We applied the method to a meta data set to identify emotion foci centers.

Identification of Initiating Trunk Mutations and Distinct Molecular Subtypes: An Interim Analysis of the Mmrf Commpass Study

The Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT145429) is a longitudinal study of 1000 patients with newly-diagnosed multiple myeloma from clinical sites in the United States, Canada, Spain, and Italy. Each patient receives a treatment regimen containing a proteasome inhibitor, immunumodulatory agent, or both. Clinical parameters are collected at study enrollment and every three months through the five-year observation period. To identify molecular determinants of clinical outcome each baseline and progression tumor specimen is characterized using Whole Genome Sequencing, Exome Sequencing, and RNA sequencing. This will be the first public presentation of the interim analysis seven cohort with 760 enrolled patients of whom 565 are molecularly characterized. This cohort of patients includes 14 patients with baseline and secondary samples along with 7 patients with characterized tumor samples from the bone marrow and peripheral blood.Although the median follow-up time for the cohort is only 260 days the patients on proteasome and IMiD based combinations are currently showing a PFS and OS benefit compared to those receiving combinations with each agent alone. From the raw mutational analysis we identified 24 significant genes that are recurrently mutated and the mutated allele is detectably expressed in all but one, DNAH5. Suggesting these mutations are likely contributing to myelomagenesis through an unconventional mechanism. Interestingly, DIS3 mutations are independent of KRAS, NRAS, and BRAF indicating a potential mechanistic link while PRKD2 mutations are associated with t(4;14). To identify events driving the initiation of myeloma we performed a detailed clonality analysis using a bayesian clustering method that corrects for copy number abnormalities and tumor purity to assign mutations into distinct clonal branches versus the initiating trunk mutations. On average 63.8% of mutations are trunk mutations and in 86.7% of patients at least one trunk mutation is associated with somatic hypermutation of an immunoglobulin gene as expected in a late stage B-cell malignancy. This identified many expressed trunk mutations that did not come out in the classic significance analysis like ATM, EGR1, and CCND1. To identify molecular subtypes we performed unsupervised clustering using a consensus clustering approach on independent discovery and validation cohorts, which identified 12 distinct subtypes, using a combination of silhouette score and cumulative distribution of consensus scores. This analysis identified two distinct groups associated with t(4;14) with mutations in FGFR3 and DIS3 being exclusive to one subgroup. In addition, this analysis separates patients with cyclin D translocations into three different groups, with one group having the second lowest PFS proportion. Three patients without CCND1 or CCND3 translocations were found to have IgH translocations targeting CCND2. The MAF subgroup was associated with the lowest OS and PFS proportion, and the three MAF/MAFB translocation negative patients in the subgroup all had MAFA translocations. The remaining 6 subgroups are associated with hyperdiploid copy number profiles and harbor the majority of the IgH-MYC translocation events. Two of the hyperdiploid groups are associated with a low level of NFKB activation compared to the remaining four, one of these is defined by the highest proliferation index but paradoxically the other has the second worst OS proportion. Another group is enriched with FAM46C and NRAS mutations. The genomic profiles of the paired tumors isolated from the peripheral blood and bone marrow are highly similar indicating these are not genetically distinct tumor compartments, at least in this subset of seven patients. Applying our bayesian clustering method to the serial samples resolved additional clonal clusters as mutations with similar cancer cell fractions at diagnosis clearly diverged at later timepoints. These analyses have identified tumor initiating mutations and new subtypes of myeloma, which are associated with distinct molecular events and clinical outcomes. DisclosuresJagannath:Novartis: Honoraria; Bristol Myers Squibb: Honoraria; Celgene: Honoraria; Merck: Honoraria; Janssen: Honoraria. Siegel:Celgene Corporation: Consultancy, Speakers Bureau; Amgen: Speakers Bureau; Takeda: Speakers Bureau; Novartis: Speakers Bureau; Merck: Speakers Bureau. Vij:Takeda, Onyx: Research Funding; Celgene, Onyx, Takeda, Novartis, BMS, Sanofi, Janssen, Merck: Consultancy. Zimmerman:Amgen: Honoraria, Speakers Bureau; Celgene: Honoraria, Speakers Bureau; Millennium: Honoraria, Speakers Bureau; Onyx: Honoraria. Niesvizky:Celgene: Consultancy, Speakers Bureau. Rifkin:Onyx Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millennium Pharmaceuticals, Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Consultancy, Membership on an entity's Board of Directors or advisory committees. Lonial:Millennium: Consultancy, Research Funding; Onyx: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Celgene: Consultancy, Research Funding.

Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa.

The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA.

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

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.

Role of habitat heterogeneity and landscape connectivity in shaping gene flow and spatial population structure of a dominant rodent species in a tropical dry forest

AbstractEvaluating how habitat heterogeneity and landscape connectivity influence fine‐scale population processes of gene flow and spatial population structure is key for understanding animal dispersal. Liomys pictus is a heteromyid rodent that inhabits tropical dry deciduous and semideciduous forests, where it is a dominant, abundant species and a key element on the ecosystem as seed disperser. We evaluated how landscape features shaped the genetic structure and gene flow at a fine scale among L. pictus populations in a well‐conserved natural environment. On the basis of L. pictus ecological characteristics (e.g. dominant species, female philopatry), we predicted that forested areas (irrespective of vegetation type) should facilitate dispersal if the forest vegetation acted as a kind of corridor, and that these patterns will be different between sexes. We tested these assumptions (104 individuals, six sampling localities, 14 microsatellite loci) after checking for discrete genetic groups using Bayesian clustering methods, by assessing the effect of landscape variables on patterns of gene flow combining Mantel and partial Mantel tests, least‐cost path and circuit theories. L. pictus differentiated into genetic clusters delimited by clear landscape boundaries. Accordingly, resistance hypotheses results showed that precipitation and stream channels were the main environmental and landscape attributes influencing gene flow. Exchange of a majority of migrants was detected from the center into other sampling localities, indicating higher dispersal throughout deciduous and semideciduous forest corridors, whereas isolation by distance was found only for females. Our approach allowed us to elucidate animal environmental space use, identifying some of the landscape features linked to the species dispersal patterns, which can serve as a basis for the study and comparison with other tropical forests and species. It can also have conservation applications, for instance, preserving the forested corridors we identified as significant for dispersal can likely benefit other codistributed, threatened rodent species.

Implementing genotypic AmpFlSTR® Identifiler® Plus profiles to infer population groups

In this study Identifiler® Plus was evaluated in its capacity to infer ancestry by comparing genotypic data garnered for several populations.Implementing pairwise F statistics (Fst) and an unsupervised Bayesian clustering method (STRUCTURE) significant genetic structure was observed between the African, European and Asian population groups. The Khoi-San group Ju\\’hoansi showed the highest differentiation (Fst) with the non-African populations.High correct assignment rates were obtained using likelihood ratios with low error rates, this highlights the significant population structure found. A frequentist method was employed to identify Fst outliers and locus TH01 was shown to be under positive selective pressure.In this study a forensic kit for human identification has been shown to contain important ancestry information which may aid forensics case work if a sufficiently large reference database is established.

Evidence of post‐glacial secondary contact and subsequent anthropogenic influence on the genetic composition of Fennoscandian moose (Alces alces)

AbstractAimTo determine whether a contemporary population of the moose (Alces alces), a large northern ungulate, retains genetic signatures of post‐glacial recolonization and/or the effects of anthropogenic factors. We focused on investigating spatial genetic structure and the distribution of genetic diversity of this species to clarify its still obscure history.LocationEastern Fennoscandia, Northern Europe.MethodsIn total, 574 Finnish and Russian Karelian moose were genotyped at 16 microsatellite loci, and the mitochondrial control region was sequenced from 224 individuals. Spatially explicit Bayesian clustering, multivariate and spatial autocorrelation methods were applied alongside traditional F‐statistics to study the effects of landscape on genetic structure. The demographic history of our study populations was explored with coalescent analysis and Bayesian skyline plots.ResultsA major mitochondrial divergence of moose was discovered between northern parts of Finland and the rest of the studied area. Landscape genetic analyses on the microsatellite data identified three genetic clusters connected by clines, with coalescent analysis indicating the division to be of ancient origin. Additionally, recent population bottlenecks were detected using Bayesian skyline plots.Main conclusionsOur results indicate a post‐glacial secondary contact between two distinct moose mitochondrial lineages that diverged during the Pleistocene, whereas admixture of three diverged genetic subpopulations was detected using microsatellites. The emergence of these subpopulations was estimated to have occurred after the post‐glacial recolonization of Fennoscandia. The observed genetic bottlenecks coincide with recorded historical population declines in the 18th century. We conclude that the contemporary genetic composition of the moose population in eastern Fennoscandia has been affected by both ancient and recent factors.

Population Structure of and Conservation Strategies for Wild Pyrus ussuriensis Maxim. in China.

Pyrus ussriensis Maxim. is native to the northern part of China, but whose habitats are currently being destroyed by environmental changes and human deforestation. An investigation of population structure and genetic diversity of wild Ussurian pear is a priority in order to acquire fundamental knowledge for conservation. A total of 153 individuals of wild Ussurian pear from the main habitats, Heilongjiang, Jilin, and Inner Mongolia in China, possessed low genetic diversity as a result of habitat fragmentation. The genetic diversity of the populations in Inner Mongolia and north east of Heilongjiang was especially low and there was the possibility of inbreeding. Wild Ussurian pears were divided into 5 groups based on the Bayesian clustering method using 20 nuclear SSRs (nSSRs) and 5 groups by haplotype distributions using 16 chloroplast SSRs (cpSSRs), and the populations in Inner Mongolia and north east of Heilongjiang represented unique genotypes. AMOVA indicated there was a 20.05% variation in nSSRs and a 44.40% variation in cpSSRs among populations. These values are relatively high when compared to those of other tree species. Haplotype E, positioned in the center of the cpSSR analysis network and showed the largest number of connections with other haplotypes, represented the most important haplotype. Inner Mongolia and the north east of Heilongjiang are two areas that need urgent conservation because of their genetic vulnerability and peculiarity. We determined 4 conservation units based on the clustering by nSSRs and cpSSRs, and geographic factor. This information is helpful in deciding the conservation strategies for wild Ussurian pear in China.

Genetic diversity and population structure of Polistes nimpha based on DNA microsatellite markers.

The Eurasiatic Polistes nimpha belongs to primitively eusocial wasps for which no data are available on its population’s genetic structure and relatedness/relationships of individuals. The purpose of this research is to determine the amplification efficiency in P. nimpha of microsatellite primers developed for P. dominula and using these primers, to explore genetic diversity, population structure and relatedness/relationship of P. nimpha in the context of its reproductive options. Eight out of twelve microsatellite markers analyzed on 59 individuals (pupae and larvae) were polymorphic (mean PIC = 0.545) and mutated following the stepwise mutation model. The Bayesian clustering method gave the probability of >0.898 of there being 10 clusters within the pooled sample of 15 nests. In two or three nest clusters, full- and/or half-siblings and unrelated individuals occurred. A significant correlation between genetic and geographic distances was detected. There are three main possibilities that come into play to explain our genetic results and direct field observations: cooperative nest foundation, visitations, and/or usurpation events. So far there is no conclusive evidence to exclude or support any of these possibilities.Electronic supplementary materialThe online version of this article (doi:10.1007/s00040-015-0421-7) contains supplementary material, which is available to authorized users.

Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting

We examined the evolutionary history of the diploid representatives of the genus Leucanthemum Mill. (Compositae, Anthemideae), which constitutes an extensive polyploid complex comprising around 41 species with ploidy levels ranging from 2x to 22x. The inference of phylogenetic relationships even on the diploid level is complicated in this genus due to the overlay of hybridisation and incomplete lineage sorting processes leading to incongruence among gene trees based on nuclear and plastid sequence information. Species tree and network reconstructions were based on gene trees from nine low-copy nuclear markers and the concatenated sequence information for five intergenic spacer regions of the chloroplast genome, either sequenced by Roche 454 pyrosequencing techniques or traditional Sanger sequencing techniques. Additional phylogenetic information came from multi-locus AFLP-fingerprinting of representative individuals of all diploid taxa under study and the subsequent analysis of AFLP patterns with Bayesian clustering and network reconstruction methods. To distinguish between hybridisation and incomplete lineage sorting, we developed and utilized a new ‘hybrid index’ calculation for individual taxa of the data set, which was compared to a simulated null-distribution assuming the occurrence of incomplete lineage sorting alone for pinpointing taxa with a significant hybrid signal. As a result, two species groups with contrasting patterns of gene flow and/or hybrid speciation signals could be identified in the diploids of Leucanthemum: (a) an early-diverging stock of allopatrically distributed diploid species with a lack of evidence for recent hybridisation events among its members and (b) a more recently radiated taxon assemblage with morphologically less clearly circumscribed taxa and a pronounced signal of gene flow among lineages and several candidate taxa, for which a homoploid hybrid origin may be considered.

Limited genetic differentiation among chinstrap penguin (Pygoscelis antarctica) colonies in the Scotia Arc and Western Antarctic Peninsula

Long-term monitoring of seabird numbers around Antarctica has revealed that the chinstrap penguin (Pygoscelis antarctica) is largely declining throughout its range in the Scotia Arc. Whether archipelagos across this large area remain connected via dispersal or represent genetically isolated groups has not yet been established. The purpose of this study was to assess the level of genetic differentiation between four breeding colonies on the Western Antarctic Peninsula (WAP), South Shetland, South Orkney, and South Sandwich Islands using microsatellite-based analysis of population structure. All colonies had similar levels of genetic diversity (mean heterozygosity, H O = 0.583) but colonies from the WAP and South Orkney Island had significant inbreeding coefficients. Hierarchical and pairwise F-statistics revealed very limited population structure in the Scotia Arc, with weak differentiation between colonies from the WAP, South Shetland and South Orkney Islands relative to the South Sandwich Islands, which are situated at least 1000 km apart from these other archipelagos. Bayesian model-based clustering methods found no evidence of significant population structuring, suggesting that whilst some isolation by distance may occur, there are no strong barriers to dispersal across this wide geographic range. No evidence of sex-biased dispersal was detected. We conclude that chinstrap penguin colonies across the Scotia Arc represent one interconnected breeding population. High levels of gene flow may be important in maintaining smaller, less stable colonies, and this status should be preserved by creating dispersal corridors throughout the Scotia Arc.

Invasion genetics of the Pacific oyster Crassostrea gigas in the British Isles inferred from microsatellite and mitochondrial markers

The Pacific oyster, Crassostrea gigas, native to northeast Asia, is one of the most important cultured shellfish species. In Europe, Pacific oysters first settled along the Atlantic coasts of France at the end of the 1960s but rapidly spread and are now widely established. Twenty-two sites in the United Kingdom (UK), Ireland, Denmark, France and Spain were sampled to assess genetic diversity and differentiation. Hatchery-propagated stocks from two hatcheries located in the UK also were included. Two main genetic clusters were identified from pairwise genetic differentiation indexes, Bayesian clustering methods or neighbour-joining analysis, based on 7 microsatellite loci: (1) a Northeast cluster (including feral samples from East England, Ireland and Denmark as well as UK hatchery stocks) and (2) a Southwest cluster (including samples from South Wales, South West England, France and Spain). The Southwest cluster had significantly higher allelic richness (A) and expected heterozygosity (H e ) (A: 45.68, H e : 0.928) than in the Northeast (A: 26.58, H e : 0.883); the two diverging by a small but significant F ST value (F ST = 0.017, 95 % CI 0.014–0.021). A 739-bp fragment of the major noncoding region of the mitochondrial genome was sequenced in 248 oysters from 12 of the studied samples in Europe and in 25 oysters from Miyagi prefecture (Japan). A total of 81 haplotypes were found. Haplotype frequency analyses identified the same two clusters observed using microsatellites. This study highlights how the number and size of introduction events, aquaculture practices, genetic bottlenecks followed by genetic drift and natural dispersal can act concurrently to shape the genetic diversity and structure of introduced populations.

Genetic characterisation of new host‐specialised biotypes and novel associations with bacterial symbionts in the pea aphid complex

Abstract The pea aphid, Acyrthosiphon pisum Harris, constitutes a complex of sympatric populations that are specialised to distinct species of Fabaceae. So far, 12 such populations have been characterised genetically as genetic clusters associated with one or few legumes species. These clusters form a continuum of genetic divergence linking host‐associated races, which show moderate hybridization, to nascent species. They are also known to be associated with different species of endosymbiotic bacteria, which have environmentally dependent effects on aphid fitness. Here, we report on the genetic characterisation of new host‐associated populations in this species complex. We sampled pea aphids in eastern France on Genista tinctoria, G. sagittalis, Onobrychis viciifolia, and Hippocrepis comosa. Bayesian clustering methods based on genotypes obtained at 25 microsatellite loci showed that each sampled plant species hosted a specific pea aphid population. Comparison with previously characterised biotypes showed that the population associated with Hippocrepis comosa was no different from that on Securigera varia. Migrant aphids from other host plants and hybrids were found at various frequencies on the newly sampled plant species. They were particularly frequent on Onobrychis viciifolia, occasional between the two Genista‐associated populations, and rare on Hippocrepis comosa. PCR‐based screening of bacterial species revealed new associations between aphid biotypes and facultative endosymbionts, chiefly the combination of Serratia symbiotica and Hamiltonella defensa within most individuals collected on Genista. The newly identified biotypes, which add up to a total of 15 within the pea aphid complex, offer new material to study the mechanisms and genetic bases of host‐specialisation and ecological speciation in this model aphid.

Evaluating the resolution power of new microsatellites for species identification and stock delimitation in the Cape hakes Merluccius paradoxus and Merluccius capensis (Teleostei: Merlucciidae).

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep-water hake Merluccius paradoxus and the shallow-water hake Merluccius capensis. A total of 14 microsatellites were polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (FST < 0·006) that will be valuable to delimit and characterize genetic stocks.