Population genetics of the endangered South American freshwater turtle, Podocnemis unifilis, inferred from microsatellite DNA data

We studied the population genetics of Podocnemis unifilis turtles within and among basins in the Orinoco and Amazon drainages using microsatellites. We detected high levels of genetic diversity in all sampled localities. However, ‘M-ratio’ tests revealed a substantial recent population decline in ten localities, in accord with current widespread exploitation. Our results reveal a consistent pattern across multiple analyses, showing a clear subdivision between the populations inhabiting the Amazon and Orinoco drainages despite a direct connection via the Casiquiare corridor, and suggesting the existence of two biogeographically independent and widely divergent lineages. Genetic differentiation followed an isolation-by-distance model concordant with hypotheses about migration. It appears that migration occurs via the flooded forest in some drainages, and via river channels in those where geographic barriers preclude dispersal between basins or even among nearby tributaries of the same basin. These observations caution against making generalizations based on geographically restricted data, and indicate that geographically proximate populations may be demographically separate units requiring independent management.     

Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest

From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan‐tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra.     

Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae)

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.     

Polymorphic microsatellite markers for endangered spotted suslik,Spermophilus suslicus

Spotted suslik Spermophilus suslicus is one of the most endangered mammal species in Poland. Over the last 50 years, it lost more than 90% of its populations and about 70% of its individuals. In order to establish a conservation and reintroduction program, the knowledge of population structure of the species is crucial. We have developed nine polymorphic microsatellite loci to analyse the population structure. Six of the primer sets also amplify polymorphic markers in the European suslik Spermophilus citellus.     

Microsatellite DNA markers for Lysiphlebus testaceipes

Microsatellite loci were isolated from the aphid parasitoid Lysiphlebus testaceipes (Hymenoptera: Braconidae). Ten loci were obtained from an enriched partial genomic library. Genetic diversity was analysed at seven of these loci and two natural populations, one on oleander and one on citrus. The observed number of alleles ranged from one to 17, and the observed heterozygosity ranged from 0.37 to 0.82. In both populations, no departure from Hardy–Weinberg equilibrium was detected except for one locus. The differentiation between the two populations was characterized by an F_ST of 0.09.     

Characterization of microsatellite DNA markers for the alligator snapping turtle,Macrochelys temminckii

Two trinucleotide and seven tetranucleotide microsatellite loci were isolated from an alligator snapping turtle Macrochelys temminckii. To assess the degree of variability in these nine microsatellite loci, we genotyped 174 individuals collected from eight river drainage basins in the southeastern USA. These markers revealed a moderate degree of allelic diversity (six to 16 alleles per locus) and observed heterozygosity (0.166–0.686). These polymorphic microsatellite loci provide powerful tools for population genetic studies for a species that is afforded some level of conservation protection in every state in which it occurs.     

Microsatellite DNA markers for delineating population structure and kinship among the endangered Kirtland's warbler (Dendroica kirtlandii)

We document the isolation and characterization of 23 microsatellite DNA markers for the endangered Kirtland's warbler (Dendroica kirtlandii), a Nearctic/Neotropical migrant passerine. This suite of markers revealed moderate to high levels of allelic diversity (averaging 7.7 alleles per locus) and heterozygosity (averaging 72%). Genotypic frequencies at 22 of 23 (95%) markers conformed to Hardy–Weinberg equilibrium expectations, and no linkage disequilibrium was observed in blood samples taken from 14 warblers found on the wintering grounds in the Bahamas archipelago. Multilocus genotypes resulting from this suite of markers should reduce the amount of resources required for initiating new genetic studies assessing breeding structure, parentage, demographics, and individual‐level ecological interactions for D. kirtlandii.     

Microsatellite DNA markers for the pea aphid Acyrthosiphon pisum

Microsatellite loci were isolated from enriched partial genomic libraries of Acyrthosiphon loti and Acyrthosiphon pisum. Twenty of those loci were characterized in A. pisum. Fifteen of those loci were polymorphic. Genetic diversity varied across loci, allele repeat number ranging from two to 15, and observed heterozygosity from 0.1 and 0.96. An additional eight microsatellite loci originally isolated from other aphids but cross‐priming with A. pisum showed polymorphism as well. Allele size ranged from three to 9 and observed heterozygosity from 0.43 to 0.84. Overall, we present 23 microsatellite loci that can be used to reveal polymorphism in pea aphids.     

Microsatellite variation in colonizing populations of yellow‐legged Asian hornet,Vespa velutina nigrithorax,in South Korea

Introduction of exotic species poses a tremendous challenge to the preservation of original biodiversity and productivity in natural ecosystems. The yellow‐legged Asian hornet Vespa velutina nigrithorax, which is native to tropical/subtropical areas in Indo‐China, was identified in 2003 for the first time in South Korea and has established itself in a short period of time. Population genetic study of invasive species may provide exceptional opportunities to test evolutionary theory as well as patterns of colonization from the beginning of the process. Here, the genetic variability of this invasive hornet was examined using seven microsatellites to estimate the propagule pressure and to expect the spreading pathway of this invasive hornet across its range. Overall, there was a significant loss of genetic diversity in its invaded ranges compared to its native range, suggesting that this invasive hornet was introduced via a very small number of propagules. Our results also support that this invasive hornet has experienced a severe bottleneck, as a large reduction was mainly observed in the number of alleles but not in heterozygosity. No significant genetic structuring among populations was found. This study provides baseline information about the current demographic status of the invaded populations, which will help governing agencies prevent further invasions and manage native ecosystems.     

Microsatellite DNA markers for Australian geckos

Nine highly polymorphic microsatellite markers were developed for Gehyra variegata from an enriched library screened for tetranucleotide repeats. An average of 19.44 alleles per locus and an average observed heterozygosity of 0.86 were found in 81 samples from fragmented populations in the Western Australian wheatbelt. Different gecko species exhibit varying rates of extinction in fragmented landscapes and the genetic markers were developed to test whether these difference are due to different rates of dispersal. The loci were tested for their ability to cross amplify in 12 species of Australian Gekkonidae and Pygopodidae, in an attempt to identify species which might be amenable to population genetic analysis using these microsatellite markers.     

Microsatellite DNA markers for genetic mapping in Oreochromis niloticus

The isolation of seven tri-, and 133 di-nucleotide microsatellite markers from a tilapia, Oreochromis niloticus , is described. An efficient methodology for isolating large numbers of such markers and their potential applications in applied aquaculture and evolutionary genetics are discussed.     

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship,population structure,and mixed‐fishery analyses

Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise F_ST, 0.12, was highly significant. These findings are consistent with patterns of continental‐level differentiation observed previously using an alternate suite of microsatellite loci. Locus‐by‐locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.     

Microsatellite DNA primers for the endangered vermilion darter,Etheostoma chermocki,and cross‐species amplification in other darters (Percidae: Etheostoma)

The endangered vermilion darter (Etheostoma chermocki) is endemic to the Black Warrior River system in the Mobile Basin in Alabama. Restoration and conservation of this species require an understanding of its population genetic structure, which can be characterized using microsatellite DNA. Nine microsatellite loci were developed; eight loci were polymorphic. Although observed heterozygosity was lower than expected heterozygosity in most polymorphic loci, only one locus showed significant deviation from Hardy–Weinberg equilibrium. These nine markers were tested in an additional 24 species of Etheostoma and appear to have sufficient allelic variation to be useful in studies of population genetic structure.     

Identification and characterization of microsatellite DNA markers developed in an endangered cyprinid of the Mekong River,the seven‐line barb (Probarbus jullieni Sauvage, 1880)

Microsatellite markers for an endangered cyprinid species of the Mekong River, the seven‐line barb (Probarbus jullieni Sauvage, 1880) were developed from the wild caught samples using (GT)₁₅ probe. The number of alleles per locus ranged from seven to 16. The expected heterozygosities ranged from 0.47 to 0.91. Also, these primers were successfully amplified in the two closely related species, P. labeamajor and P. labeaminor. These markers have proven to be very useful for the population genetic structure study in this species and other related cyprinids.     

Microsatellite markers for the endangered European mink (Mustela lutreola) and closely related mustelids

The European mink (Mustela lutreola L., 1761) is an endangered carnivore species whose populations suffered a severe decline during the last century. The genotyping of eight polymorphic microsatellite loci revealed a relatively low number of alleles per locus (two to eight), as well as low levels of polymorphism (observed and expected heterozygosity values per locus were 0.49 and 0.54, respectively). Cross‐specific polymerase chain reaction amplifications were successful in seven closely related mustelid species suggesting that these loci may be useful not only for assessing genetic variability in European mink populations but also for determining potential hybridization events between M. lutreola and other mustelid species.     

Microsatellite markers for the whelk Buccinum undatum

Five microsatellite loci are described for the commercially exploited marine gastropod, Buccinum undatum. Levels of polymorphism were variable with three to 19 alleles per locus and expected heterozygosities of 0.26–0.94 in 60 individuals of the population from which the loci were isolated. Homozygote excess at two of the loci might be attributable to null alleles, and these loci should not be used in, for example, parentage analysis. Nevertheless, because null allele frequencies can be estimated and their effects partitioned, all are useful markers for studies of population differentiation.     

Microsatellite markers for assessing DNA polymorphism of Emericella nidulans in nature

Based on genome sequence of Emericella nidulans, primers for 25 microsatellites were designed, of which, seven were chosen as polymorphic markers (five to 12 alleles). Simple sequence repeat (SSR) polymorphism was tested in 44 isolates from extremely arid soils of the southern Negev desert, Israel and some related species of Aspergillus. The SSR marker set appears suitable for population studies in diverse ecological conditions.