Conservation genetic studies of the endangered Cape Fear Shiner, Notropis mekistocholas (Teleostei: Cyprinidae)

Genetic variation at ten microsatellite lociand one anonymous-nuclear locus was assayed for three geographic samples of the criticallyendangered North American cyprinid Notropis mekistocholas (Cape Fear shiner). Despite low abundance of this species, there was little suggestion of small population effects; allele diversity and heterozygosity were relatively high, F_IS values within samples were non-significant, and genotypes were distributed in frequencies according to Hardy-Weinberg expectations. Genetic divergence among samples was minimal despite the presence of dams, constructed in the early1900s, that separate the sample sites. This suggests that recent gene flow has been sufficient to inhibit genetic divergence or that gene flow has been reduced but there has been insufficient time for genetic divergence to develop. Tests of heterozygosity excess were non-significant, suggesting that N.mekistocholas in the localities sampled have not undergone recent reductions ineffective population size. Future studies employing larger sample sizes to provide more robust tests of population structure and temporally separated samples to estimate contemporaneous N_e are warranted.

Low allozyme variation in snapper, Pagrus auratus, in Victoria, Australia

The population genetic structure of snapper, Pagrus auratus (Bloch and Schneider), in Victoria was investigated using six polymorphic allozyme loci. Fish were sampled from four sites in Victoria and single locations in South Australia, Western Australia and New Zealand. Although there were distinct genetic differences between the snapper populations from each of the Australian states and New Zealand, only minor and largely insignificant differences were detected among Victorian populations. The results are consistent with previous genetic and tagging studies that indicate no mixing between snapper stocks in Victoria and Spencer Gulf in South Australia. This justifies separate management of the snapper fisheries in these regions. The low levels of polymorphism and heterozygosity in Victorian snapper suggest an isolation by distance model of population structure rather than one of discrete subpopulations.

Microsatellite DNA analysis of southeast Australian Haliotis laevigata (Donovan) populations - implications for ranching in Port Phillip Bay

The genetic composition of greenlip abalone (Haliotis laevigata) from Point Cook in Port Phillip Bay was examined prior to the aggregation of individuals from this site for ranching. The very thinly distributed natural population at Point Cook was believed to be of low genetic diversity, because the animals all originated from a single spawning event 5 y previously. Animals from Point Cook were compared with other H. laevigata from two sampling sites within Port Phillip Bay, and two sites outside the Bay in Bass Strait, to examine their genetic diversity and origin. Variation was assessed at five microsatellite loci. Deviations from Hardy-Weinberg equilibrium (HWE) were observed at some loci in various populations, but the Point Cook population was in HWE at all five loci. Mean heterozygosity and number of alleles was similar in all populations. Hierarchical analysis of molecular variance indicated significant genetic variation among populations, but did not differentiate Port Phillip Bay from Bass Strait populations. Pairwise comparisons of multilocus F_STand R_ST indicated significant genetic differences between Point Cook and some populations, as well as between other populations, but no consistent spatial pattern of differentiation was observed. There was no significant correlation between genetic and geographic distance. The level of genetic variation observed in the Point Cook individuals was similar to that in individuals from the other four sites, and sufficient to support a ranching program. However, this variation should be monitored to maximize genetic potential, and avoid commercially undesirable effects of inbreeding. Implications of this study in relation to the management of a ranching population in Port Phillip Bay are discussed.

Isolation and characterization of microsatellite loci to DNA fingerprint the powerful owl (Ninox Strenua)

An enriched microsatellite library was constructed for the Powerful Owl (Aves; Strigiformes: Ninox strenua) from which 14 polymorphic microsatellite markers were characterized. Forty individuals (32 unrelated and four pairs of siblings) were genotyped to determine the application of these markers for genetic profiling. The mean observed and expected heterozygosity for unrelated individuals was 0.53 and 0.59, respectively. We demonstrate that this suite of markers is sufficient to unequivocally identify individuals and will be beneficial in assessing the population genetics and reproductive ecology of this species.

Microsatellites revealed no genetic differentiation between hatchery and contemporary wild populations of striped catfish, Pangasianodon hypophthalmus (Sauvage 1878) in Vietnam

Aquaculture of the striped catfish, Pangasianodon hypophthalmus (Sauvage 1878), in Vietnam has become one of the fastest growing primary food production sectors in the world. Although a demand on quantity of fingerlings is currently reached, it is likely that the long term quality of the stocks may be uncertain due to lacking of genetic broodstock management measures. The present study employed five microsatellite loci to investigate levels of genetic variation of the stripped catfish of the current wild stocks as well as of the selected hatcheries in Vietnam. The study included four hatchery populations and two wild populations spawned in 2005 in the Mekong and Bassac Rivers, and one wild population (spawned in 2006) in the Bassac River. The results showed no genetic differentiation among populations as revealed by F_ST and a model-based clustering method. AMOVA also showed no genetic differentiation between pooled wild and pooled hatchery populations while variation within groups was significant. Genetic variation of wild (mean number of alleles per locus, A = 4.80–6.20; allelic richness, A_r = 4.54–5.06; mean effective number of alleles per locus, A_e = 2.86–3.20; observed heterozygosity, H_o = 0.62–0.65; expected heterozygosity, H_e = 0.62–0.64) and hatchery populations (A = 4.60–5.20; A^_r = 4.10–4.83; A_e = 2.80–3.11; H_o = 0.61–0.66; H_e = 0.61–0.64) were not statistically different. There were no evidences for recent genetic bottleneck in all populations. Therefore it is implied that the hatchery stocks of striped catfish in Vietnam were founded from sufficient numbers of brooders and current population size is large. The domestication process is in an early stage.

Genetic status of an endemic marine mammal, the Australian fur seal, following historical harvesting

Genetic variation, and the way in which it is partitioned among populations, has implications for a species’ survival and evolutionary potential. Such information is particularly important for the successful conservation and management of species that have experienced past human impacts and potential losses of genetic diversity. Overharvesting of the Australian fur seal Arctocephalus pusillus doriferus in the 18th and 19th centuries resulted in severe population reductions and elimination of an estimated 17 of 26 colonies. Currently, the subspecies is recovering and c. 20 000 pups are produced annually at 13 colony sites, most of which are situated in Bass Strait in south-eastern Australia. Genetic analysis of samples collected from pups captured at nine colonies revealed no difference in allelic diversity or heterozygosity at five microsatellite loci and no differences in haplotype diversity within a 344 bp region of the mitochondrial DNA control region. There was some evidence for isolation by distance but the program STRUCTURE predicted a single cluster of individuals. Gene flow among colonies appears to be substantial at present, indicating that the Australian fur seal is currently a single, panmictic unit.

The development of 20 microsatellite loci for the Australian marine mollusk, Donax deltoides, through next generation DNA sequencing

 Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean number of alleles per locus = 7.3; mean heterozygosity = 0.633) with only a single locus (Ddel32) displaying significant deviation from Hardy–Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, however two loci were found to be influenced by null alleles. The 10 viable markers characterized in the present study provide a valuable resource for future population genetic assessments and fisheries management of D. deltoides in Australia.

Development of novel microsatellite markers for the invasive Northern Pacific seastar, Asterias amurensis

The Northern Pacific seastar, Asterias amurensis, is a benthic marine predator, which has recently established several invasive populations in Australian waters. To investigate population structure, diversity and patterns of connectivity, we isolated and characterised 27 microsatellite loci and tested their polymorphism based on 46 individuals from two invasive populations. The mean allelic richness was 4.33; observed heterozygosity was 0.42, while the percentage of polymorphic loci was 92.6%. The polymorphic markers will prove useful in the assessment of population genetic parameters, in both invasive and native A. amurensis populations.

Characterisation of 22 polymorphic microsatellite loci for the Broadbill Swordfish, Xiphias gladius

The Broadbill Swordfish is harvested by fisheries throughout the world. In order to devise more effective management strategies, we need a clear understanding of the population structure of the species. From a library of 29 tetranucleotide repeats, 22 microsatellite markers were characterised for 94 swordfish samples captured from eastern and western Australia. The number of alleles ranged from 2 to 26 and observed heterozygosity from 0.066 to 0.923. We have identified 18 microsatellites that will be valuable in the examination of swordfish population structure.

Development of twenty-four novel microsatellite markers for the freshwater crayfish, Geocharax gracilis, using next generation sequencing

The crayfish Geocharax gracilis is an important inhabitant of natural and agricultural drainage systems in south-eastern Australia. To investigate population structure, genetic diversity and patterns of connectivity in natural and human-altered ecosystems, we isolated and characterised 24 microsatellite loci using next generation sequencing. Loci were initially tested for levels of variation based on 12 individuals from across the species’ geographical range. A further 33 individuals from a single population were used to test for departures from Hardy–Weinberg equilibrium and linkage disequilibrium. We detected high to moderate levels of genetic variation across most loci with a mean allelic richness of 8.42 and observed heterozygosity of 0.629 (all samples combined). We found no evidence for linkage disequilibrium between any loci and only three loci (Geo01, Geo24 and Geo47) showed significant deviations from Hardy–Weinberg expectations. These same three loci, plus two additional loci (Geo06 and Geo28), also showed the presence of null alleles. These 24 variable markers will provide an important tool for future population genetic assessments in natural and human altered environments.

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

Characterization of nine polymorphic microsatellite loci in the dyeing poison frog Dendrobates tinctorius (Dendrobatidae), and their cross-species utility in two other dendrobatoid species

While field and laboratory based studies have provided significant insights into the parental care and courtship behaviour of dendrobatoid frogs, a comprehensive assessment of their genetic mating systems and population genetic parameters has been precluded because ofthe lack of highly variable DNA markers. Here we document the development of nine novel polymorphic microsatellite markers for the dyeing poison frog Dendrobates tinct or ius (Dendrobatidae ). We found between three and 16 alleles per locus in 60 individuals (30 males, 30 females) from the field site Saut Parare, French Guiana, with an average observed heterozygosity of 0. 75. None of the loci deviated significantly from Hardy-Weinberg equilibrium or showed linkage disequilibrium. We also report successful cross-species amplification of the nine markers in two other dendrobatoid species (Allobates femora/is and Oophaga pumilio). These markers have the potential to aid in determining the genetic structure of local populations, identifying small-scale phylogenies such as parent-offspring relationships and will allow for cross-species comparisons within dendrobatoid species. Therefore, these markers can be applied to a wide range of scientific fields, such as conservation, behavioural ecology and evolutionary biology.

Microsatellite variation in the yellowhammer Emberiza citrinella : population structure of a declining farmland bird

In recent years, there has been much concern in the UK about population declines of widespread species in agricultural habitats. Conservation-orientated research on declining birds has focused on vital rates of survival and productivity. However, the environmental factors which may influence movements between populations of widespread species is poorly understood. Population genetic structure is an indirect description of dispersal between groups of individuals. To attempt to develop an understanding of genetic structuring in a widespread, but declining, farmland bird, we therefore investigated the yellowhammer, Emberiza citrinella, population in England and Wales using microsatellite data. Our first aim was to investigate whether there was genetic substructuring in the population. A second aim was to investigate if there was a relationship between genetic distances and various environmental variables. Finally, we analysed the microsatellite data for evidence of loss of genetic variation due to population decline. Our data showed a slight but significant structure within the yellowhammer population. This therefore cannot be considered a panmictic population. Our example from South Cumbria implies that high-altitude barriers may have a slight influence on population structure. However, on the whole, genetic distances between sample sites were not significantly correlated with geographical distances, degrees of population connectivity, high altitudes, or differences in precipitation between sites. Finally, we detected departures from mutation-drift equilibrium (excess heterozygosity), which is indicative of a loss of genetic variation through recent decline.

Expected shannon entropy and shannon differentiation between subpopulations for neutral genes under the finite island model

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Genetic structure and sex-biased dispersal of a declining cooperative-breeder, the Grey-crowned Babbler, Pomatostomus temporalis, at the southern edge of its range

Loss and fragmentation of habitat can disrupt genetic exchange between populations, which is reflected in changes to the genetic structure of populations. The Grey-crowned Babbler (Pomatostomus temporalis) is a cooperatively breeding woodland bird, once common and widespread in south-eastern Australia. The species has suffered population declines of >90% across its southern distribution as a result of loss and fragmentation of habitat. We investigated patterns of genetic diversity and population structure of Grey-crowned Babblers in fragmented habitats at the southernmost extent of its range. We sampled blood from 135 individual Babblers from 39 groups stratified into six subpopulations in three regions. Genotypic data were used to estimate genetic diversity, population substructure, local relatedness and dispersal patterns. Individuals showed high heterozygosity within regions, and varying numbers of private alleles among regions suggested differences in levels of connectivity between regions. Four genetic clusters revealed population substructure consistent with treeless landscapes acting as strong barriers to gene flow. In contrast to previous studies,we identified a male-biased dispersal pattern and significant isolation-by-distance patterns for females at fine spatial scales. We recommend that conservation plans for this species incorporate opportunities to increase and enhance corridor areas to facilitate genetic exchange among subpopulations.