Genetic lineages and postglacial colonization of grayling (Thymallus thymallus, Salmonidae) in Europe, as revealed by mitochondrial DNA analyses

In stark contrast to other species within the Salmonidae family, phylogeographic information on European grayling, Thymallus thymallus, is virtually nonexistent. In this paper, we utilized mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (mtDNA PCR-RFLP) and sequence variation to infer the postglacial dispersal routes of T. thymallus into and within northern Europe, and to locate geographically, potential evolutionarily distinct populations. Mitochondrial analyses revealed a total of 27 T. thymallus haplotypes which clustered into three distinct lineages. Average pairwise interlineage divergence was four and nine times higher than average intralineage divergence for RFLP and sequence data, respectively. Two European grayling individuals from the easternmost sample in Russia exhibited haplotypes more genetically diverged from any T. thymallus haplotype than T. arcticus haplotype, and suggested that hybridization/introgression zone of these two sister species may extend much further west than previously thought. Geographic division of the lineages was generally very clear with northern Europe comprising of two genetically differentiated areas: (i) Finland, Estonia and north-western Russia; and (ii) central Germany, Poland and western Fennoscandia. Average interpopulation divergence in North European T. thymallus was 10 times higher than that observed in a recent mtDNA study of North American T. arcticus. We conclude that (i) North European T. thymallus populations have survived dramatic Pleistocene temperature oscillations and originate from ancient eastern and central European refugia; (ii) genetic divergence of population groups within northern Europe is substantial and geographically distinct; and (iii) the remainder of Europe harbours additional differentiated assemblages that likely descend from a Danubian refugium. These findings should provide useful information for developing appropriate conservation strategies for European grayling and exemplify a case with a clear need for multinational co-operation for managing and conserving biodiversity.     

Mitochondrial and nuclear DNA phylogeography of European grayling (Thymallus thymallus): evidence for secondary contact zones in central Europe

Mitochondrial and microsatellite DNA markers were applied to infer the phylogeography, intraspecific diversity and dynamics of the distributional history of European grayling (Thymallus thymallus) with focus on its central and northern European distribution range. Phylogenetic and nested clade analyses revealed at least four major mtDNA lineages, which evolved in geographical isolation during the Pleistocene. These lineages should be recognized as the basic evolutionary significant units (ESUs) for grayling in central and northern Europe. In addition, and in contrast to previous work on grayling, the results of Bayesian analysis of individual admixture coefficients, two-dimensional scaling analysis and spatial analysis of molecular variance provided evidence for a high level of admixture among major lineages in contact zones between drainages (e.g. the low mountain range of Germany), most likely resulting from glacial perturbations and ancient river connections between drainages during the Pleistocene glaciations. Even within river systems, a high level of differentiation among populations was revealed as indicated by the microsatellite data. Grayling sampled from 29 sites displayed high levels of differentiation (overall F(ST) = 0.367), a high number of private alleles and high bootstrap support for the genetic distance-based population clusters across 12 loci. We specifically discuss our results in context of phylogeograpic studies on other European freshwater fish species with habitat preferences similar to those of grayling. Our study shows that both large-scale phylogeographical and detailed genetic analyses on a fine scale are mandatory for developing appropriate conservation guidelines of endangered species.     

Interpopulation genetic divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation

In order to provide guidelines for conservationand management of the severely declining LakeSaimaa (eastern Finland) European grayling(Thymallus thymallus, Salmonidae), weinvestigated the microgeographic geneticstructure of three populations from the watersystem using 17 microsatellite loci andmitochondrial DNA polymerase chainreaction-restriction fragment lengthpolymorphism analysis. Microsatellites revealedlow levels of intrapopulation genetic diversityand substantial divergence between populationssampled from spawning sites separated by aslittle as 55 kilometers. Mitochondrial analysisindicated the occurrence of two compositehaplotypes within Lake Saimaa. The nucleotidesubstitution estimates between the haplotypessuggested their separation to markedly predatethe late Pleistocene period. The populationsexhibited marked frequency differences for thetwo mitochondrial haplotypes, reinforcing theview of limited interpopulation gene flowwithin Lake Saimaa. An individual basedmicrosatellite Neighbor-Joining dendrogramdemonstrated clustering of all the specimensaccording to their sampling origin. Individualassignment tests revealed 100% assignmentsuccess of individuals into their population oforigin and 100% exclusion (p <0.05) from all alternative referencepopulations. These findings exemplify that T. thymallus populations may be genetically highly structured over small geographical scales and provide a good starting point for the development of appropriate conservation strategies for Lake Saimaa grayling.     

Intraspecific genetic structure,divergence and high rates of clonality in an amphi‐Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species’ distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria–Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo‐Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations’ genetic divergence could be observed between some populations.     

Microsatellite variation in Bavarian populations of European grayling (Thymallus thymallus): Implications for conservation

European grayling populations in Bavaria have shown steady declines during the last 10–20years. In order to provide guidelines for conservation strategies and future management programs, we investigated the genetic structure of 15 grayling populations originating from three major Central European drainages (the Danube, the Elbe and the Rhine/Main) using 20 microsatellite loci. Genetic divergence between the three drainage systems was substantial as illustrated by highly significant heterogeneity of genotype frequencies, high number of drainage-specific private alleles, high between-drainage F _ST values, high assignment success of individuals to their drainage of origin and the high bootstrap support for the genetic distance based drainage-specific population clusters. In agreement with earlier studies, microsatellites revealed relatively low levels of intrapopulational genetic diversity in comparison to the overall level of variation across populations. Maximum likelihood methods using the coalescent approach revealed that the proportion of common ancestors was generally high in native populations and that the estimates of N _e were correlated with the genetic diversity parameters in all drainages. The number of effective immigrants per generation (N _e m) was less than one for all pairwise comparisons of populations within the drainages, indicating restricted interpopulational gene flow. Based on these findings we recommend a drainage and sub-drainage specific conservation of grayling populations in order to preserve their overall genetic diversity and integrity. For large-scale stocking actions to supplement declining or to restore extinct populations, creation of separate broodstocks for major conservation units (ESUs and MUs) is warranted. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic differentiation of European grayling populations across the Main, Danube and Elbe drainages in Bavaria

Analysis of mitochondrial ( ND-1/3/4 genes) and nuclear ( GH-1 gene, four microsatellite loci) DNA markers of European grayling Thymallus thymallus populations identified strong genetic differentiation between the Rhine/Main, Elbe and Danube drainages in Bavaria, as a result of both present processes and past history. The Danube and the Main-Elbe group diverged about five times earlier than the populations of Main and Elbe. These data suggest that exchange and transfer of grayling stocking material between these drainages should be avoided, to maintain the genetic diversity and integrity of populations.     

Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus,based on complete sequencing of the mitochondrial DNA control region

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well-supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human-mediated stock transfers, parsimony-network-based nested-clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre-dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter- and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.     

Genetic variation of European grayling (Thymallus thymallus) populations in the Western Balkans

In order to elucidate genetic composition of European grayling (Thymallus thymallus) populations in the Western Balkans, the partial mitochondrial DNA (mtDNA) control region was sequenced and 12 microsatellite loci genotyped in 14 populations originating from tributaries of the Adriatic and Danube drainages. Eleven mtDNA haplotypes were found, one confined to the Adriatic clade, one to the Alpine group and the rest to the ‘Balkan’ grayling phylogenetic clade. Haplotypes from the Balkan clade were confined to the Danube drainage and constituted two groups: northern group with haplotypes found in the Slovenian part of the Danube drainage, and southern group, consisting from Bosnia–Herzegovina and Montenegro. Substantial genetic distance between northern and southern groups of haplotypes (0.75–1.8%) and well supported divisions within the northern group indicate very structured grayling population within the studied Danube basin that most probably did not evolve due to vicariance but rather as a consequence of multiple colonization waves that might have occurred during the Pleistocene. Furthermore, genetic distance of ~4% between Adriatic and Danube populations’ haplotypes, suggest that their separation occurred in mid-Pliocene. These findings imply a complex colonization pattern of the Western Balkans drainages. Microsatellite data also confirm high genetic diversity in Western Balkans populations of grayling (on average 7.5 alleles per microsatellite locus and H _exp 0.58). Limited stocking activities were detected based on microsatellites and mtDNA data. Regarding current knowledge of grayling phylogeography appropriate management strategies were proposed to preserve unique, autochthonous grayling populations in Western Balkan.     

Evolutionary distinctness of grayling {Thymallus thymallus) inhabiting the Adriatic river system, as based on mtDNA variation

The northern part of the peri-Adriatic river system is inhabited by a native grayling population. In comparison with the Danubian population most of the Adriatic population is regarded as morphologically distinct and therefore recognized as racially differentiated. DNA sequence analysis of the 394-bp fragment of the mtDNA control region and 363-bp fragment of the cytochrome b gene region from grayling specimens of the Adriatic, Danubian and Atlantic river systems revealed nine composite mtDNA haplotypes. The genetic divergence of the Adriatic and the Danubian-Atlantic haplotypes ranged from 2.52 to 3.10% and from 3.38 to 3.92% in the cytochrome b gene and control region, respectively. On the basis of sequence data an attempt was made to elucidate the phylogeography of the Adriatic population. The molecular data indicate an ancient monophyletic origin and also confirm its distinct position within the Thymallus thymallus species, in spite of the fact that stocking with the Danubian type occurred in the Adriatic river system. Therefore the Adriatic population deserves special attention. As a first step in its preservation, its formal distinction by using the name Adriatic grayling is proposed.     

The benefits of increasing the number of microsatellites utilized in genetic population studies: an empirical perspective

One of the key issues concerning the application of microsatellite DNA data in evolutionary studies is how the number of loci applied may influence the stability of genetic distances and corresponding phylograms. While computer simulations have suggested that over 30 microsatellites are required for accurate evolutionary inference, we show that a median of only six loci have been generally applied in studies of wild populations. Factors contributing to this contrast include: i) uncertainty regarding the potential benefits that can be gained from a realistic increase in the number of loci used; and ii) the lack of empirical studies assessing the influence of the number of microsatellites on the reliability of genetic distance estimation and phylogeny construction. In order to address these issues, we applied resampling techniques to microsatellite data in widely distributed populations of European grayling (Thymallus thymallus, Salmonidae). In agreement with expectations based on simulated data, we demonstrate empirically that the stability of commonly used genetic distances (DCE, DA and (deltamu)2) and the corresponding neighbor-joining phylograms is positively associated with the number of microsatellites utilized. For instance, increasing the number of loci from six to 17 resulted in a striking 75% increase in the proportion of DCE phylogram nodes supported by a bootstrap estimate of over 70%. Our results demonstrate that even moderately increasing the number of loci can be very beneficial--a finding extremely relevant for studies of natural populations for which optimally high microsatellite numbers are out of reach. Furthermore, the number of loci most commonly used to date may lead to erroneous inference of the evolutionary relationships between populations.     

The influence of history and contemporary stream hydrology on the evolution of genetic diversity within species: an examination of microsatellite DNA variation in bull trout,Salvelinus confluentus (Pisces: Salmonidae)

An understanding of the relative roles of historical and contemporary factors in structuring genetic variation is a fundamental, but understudied aspect of geographic variation. We examined geographic variation in microsatellite DNA allele frequencies in bull trout (Salvelinus confluentus, Salmonidae) to test hypotheses concerning the relative roles of postglacial dispersal (historical) and current landscape features (contemporary) in structuring genetic variability and population differentiation. Bull trout exhibit relatively low intrapopulation microsatellite variation (average of 1.9 alleles per locus, average He = 0.24), but high levels of interpopulation divergence (F(ST) = 0.39). We found evidence of historical influences on microsatellite variation in the form of a decrease in the number of alleles and heterozygosities in populations on the periphery of the range relative to populations closer to putative glacial refugia. In addition, one region of British Columbia that was colonized later during deglaciation and by more indirect watershed connections showed less developed and more variable patterns of isolation by distance than a similar region colonized earlier and more directly from refugia. Current spatial and drainage interconnectedness among sites and the presence of migration barriers (falls and cascades) within individual streams were found to be important contemporary factors influencing historical patterns of genetic variability and interpopulation divergence. Our work illustrates the limited utility of equilibrium models to delineate population structure and patterns of genetic diversity in recently founded populations or those inhabiting highly heterogeneous environments, and it highlights the need for approaches incorporating a landscape context for population divergence. Substantial microsatellite DNA divergence among bull trout populations may also signal divergence in traits important to population persistence in specific environments.     

A comparison of biallelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar)

Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic markers (in total 7 loci) to those estimated with 14 microsatellite loci in 21 Atlantic salmon (Salmo salar) populations from northern Europe. Pairwise FST values were significantly correlated between biallelic loci and microsatellite datasets, as was overall heterozygosity when both anadromous and nonanadromous populations were analyzed together. However, when the anadromous and nonanadromous samples were analyzed separately, only genetic divergence correlations remained significant. Biallelic markers alone were not sufficient for reliable neighbor-joining clustering of populations but gave highly similar isolation-by-distance signals when compared with microsatellites. Finally, although several population prioritization measures for conservation exhibited significant correlation between different marker types, the specific populations highlighted as being most valuable for conservation purposes varied depending on the marker type and conservation criteria applied. This study demonstrates that a relatively small set of biallelic markers can be sufficient for obtaining concordant results in most of the analyses compared with microsatellites, although estimates of genetic distance are generally more concordant than estimates of genetic diversity. This suggests that a relatively small number of biallelic markers can provide useful information for various population genetic applications. However, we emphasize that the use of much higher number of loci is preferable, especially when the genetic differences between populations are subtle or individual multilocus genotype-based analyses are to be performed.     

Colonization, extinction, and phylogeographic patterning in a freshwater crustacean

Phylogeographic analyses have revealed the importance of Pleistocene vicariance events in shaping the distribution of genetic diversity in freshwater fishes. However, few studies have examined the patterning of variation in freshwater organisms with differing dispersal syndromes and life histories. The present investigation addresses this gap, examining the phylogeography of Sida crystallina, a species whose production of diapausing eggs capable of passive dispersal was thought to constrain its regional genetic differentiation. By contrast, the present analysis has revealed deep allozyme and cytochrome oxidase I mitochondrial DNA divergence between populations from North America and Europe. Moreover, North American populations are separated into four allopatric assemblages, whose distribution suggests their derivation from different Pleistocene refugia. These lineages show higher haplotype diversity and deeper sequence divergence than those of any fish from temperate North America. Its distinctive life history traits have evidently sheltered lineages of Sida from extinction, contributing to a remarkably comprehensive and high resolution phylogeographic record.     

Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.     

Deriving evolutionary relationships among populations using microsatellites and (deltamu)(2): all loci are equal,but some are more equal than others..

Numerous studies have relied on microsatellite DNA data to assess the relationships among populations in a phylogenetic framework, converting microsatellite allelic composition of populations into evolutionary distances. Among other coefficients, (deltamu)(2) and R(st) are often employed because they make use of the differences in allele sizes on the basis of the stepwise mutation model. While it has been recognized that some microsatellites can yield disproportionate interpopulation distance estimates, no formal investigation has been conducted to evaluate to what extent such loci could affect the topology of the corresponding dendrograms. Here we show that single loci, displaying extremely large among-population variance, can greatly bias the topology of the phylogenetic tree, using data from European grayling (Thymallus thymallus, Salmonidae) populations. Importantly, we also demonstrate that the inclusion of a single disproportionate locus will lead to an overestimation of the stability of trees assessed using bootstrapping. To avoid this bias, we introduce a simple statistical test for detecting loci with significantly disproportionate variance prior to phylogenetic analyses and further show that exclusion of offending loci eliminates the false increase in phylogram stability.     

Genetic structure and diversity of a rare woodland bat, <Emphasis Type="Italic">Myotis bechsteinii</Emphasis>: comparison of continental Europe and Britain

The Bechstein’s bat (Myotis bechsteinii) is a rare sedentary bat considered to be highly reliant on the presence of ancient woodland. Understanding the genetic connectivity and population structure of such elusive mammals is important for assessing their conservation status. In this study, we report the genetic diversity and structure of M. bechsteinii across Britain and Europe. Assessments were made using 14 microsatellite markers and a 747 bp region of the mitochondrial cytochrome b gene. Nuclear DNA (microsatellites) showed high levels of genetic diversity and little inbreeding across the species range, though genetic diversity was slightly lower in Britain than in mainland Europe. Bayesian and spatial PCA analysis showed a clear separation between the British and European sites. Within Europe, the Italian population south of the Alps was isolated from the other sites. In Britain, there was genetic structuring between the northern and southern part of the geographical range. Despite there being little genetic divergence in mitochondrial DNA (mtDNA) sequences throughout most of Europe, the mtDNA patterns in Britain confirmed this separation of northern and southern populations. Such genetic structuring within Britain—in the absence of any obvious physical barriers—suggests that other factors such as land-use may limit gene-flow.     

Levels and patterns of population genetic diversity in the red seaweed Chondrus crispus (Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites

Single nucleotide polymorphisms (SNPs) are predicted to supersede microsatellites as the marker of choice for population genetic studies in the near future. To date, however, very few studies have directly compared both marker systems in natural populations, particularly in non‐model organisms. In the present study, we compared the utility of SNPs and microsatellites for population genetic analysis of the red seaweed Chondrus crispus (Florideophyceae). Six SNP loci yielded very different patterns of intrapopulation genetic diversity compared to those obtained using seven moderately (mean 5.2 alleles) polymorphic microsatellite loci, although Bayesian clustering analysis gave largely congruent results between the two marker classes. A weak but significant pattern of isolation‐by‐distance was observed across scales from a few hundred metres to approximately 200 km using the combined SNP and microsatellite data set of 13 loci. Over larger scales, however, there was little correlation between genetic divergence and geographical distance. Our findings suggest that even a moderate number of SNPs is sufficient to determine patterns of genetic diversity across natural populations, and also highlight the fact that patterns of genetic variation in seaweeds arise through a complex interplay of short‐ and long‐term natural processes, as well as anthropogenic influence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 251–262.     

Genetic assessment of spatiotemporal evolutionary relationships and stocking effects in grayling (Thymallus thymallus, Salmonidae)

Domestically reared introduced (or escaped) individuals can have detrimental genetic effects on the indigenous populations into which they are released. Consequently, numerous studies have attempted to estimate whether non-native specimens have contributed to the gene pool of wild populations. So far, the key limiting factor of such studies has been their lack of appropriate baseline genetic material. Here, microsatellite DNA analyses of historical scale samples and contemporary wild and introduced populations were used to assess spatiotemporal population structure and stocking effects among endangered Lake Saimaa (eastern Finland) grayling ( Thymallus thymallus , Salmonidae). Significant decreases in genetic differentiation were detected between wild and introduced populations since the commencement of stocking in 1986. Accordingly, up to 15% of the contemporary wild grayling were confidently identified to be of pure hatchery origin, and recent hybridization between the hatchery and indigenous individuals appeared likely. Despite these clear genetic imprints of stocking, the contemporary populations exhibited evolutionary relationships congruent with the sampling locations, and up to 73% of contemporary individuals were identified to be of pure indigenous origin. The use of historical baseline material should prove efficient for monitoring gene flow between domesticated and wild populations in other species also, e.g. salmonids, game animals and plants.     

Genetic diversity, clonality and sexuality in Toxoplasma gondii

The majority of Toxoplasma gondii strains from a variety of human and animal sources have been grouped into three highly clonal but closely related lineages. The low occurrence of nucleotide differences among the three predominant lineages and their unusual dimorphic allelic composition suggest that they have arisen from a recent common ancestry. Less than 1% of the previously studied strains contain unique genotypes and high divergence of DNA sequence, and therefore are considered 'exotic' or 'atypical' strains. The seemingly low genetic diversity in T. gondii may have been underestimated because most parasite strains in previous studies were collected from human patients and domestic animals in North America and Europe. To investigate the genetic diversity of T. gondii, we analysed parasite strains isolated from remote geographical regions by multilocus microsatellite sequencing and phylogenetic analysis. The genetic diversity indices, the molecular analysis of microsatellite genotypes and the constructed phylogram considered together suggest that the global T. gondii population is highly diversified and not characteristic of a clonal organism. The most parsimonious hypothesis is that T. gondii presents a complex population structure with a mix of clonal and sexual propagation as a function of the environmental conditions. The comparison between domestic strains data on one hand and wild strains data on the other hand is in favour of more frequent sexual recombinations in wild environment even though Toxoplasma subpopulation in human and domestic animals is largely clonal.     

Development and characterization of ten novel microsatellite markers from olive ridley sea turtle (Lepidochelys olivacea)

Olive ridleys, one of the widely distributed marine turtle species has undergone declines in recent years due to multiple anthropogenic factors warranting conservation efforts for which assessment of genetic variability in existing populations become critical. Here we describe development of ten new microsatellite markers from a short sequence repeat-enriched partial genomic DNA library, which are found to be highly informative for genetic studies. Eight of these markers when tested on 83 olive ridley turtles revealed high allelic diversity (4–27 alleles per marker), and high observed and expected heterozygosity estimates that ranged from 0.29 to 0.82 and 0.62 to 0.94, respectively. Two microsatellites were monomorphic in the tested olive ridley samples, but were found to be informative/polymorphic when tested on related marine turtle species. More importantly, nine of the new markers showed robust cross-species amplifications in three related species Dermochelys coriacea, Chelonia mydas and Eretmochelys imbricata. Thus, this study describes ten new microsatellite markers and also demonstrates their potential as efficient genetic markers in studies related to parentage analysis, population structure, phylogeography and species relationships of olive ridleys and other marine turtle species.