Ninh V. Vu

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross‐tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analyses.

We tested the hypothesis that sex‐biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (≥ 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent–offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite‐sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite‐sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two‐fold difference in density. However, the sex bias in dispersal was less pronounced in the lower‐density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male‐biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns.

Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss)

We describe 12 diagnostic single nucleotide polymorphism (SNP) assays for use in species identification among rainbow and cutthroat trout: five of these loci have alleles unique to rainbow trout (Oncorhynchus mykiss), three unique to westslope cutthroat trout (O. clarkii lewisi) and four unique to Yellowstone cutthroat trout (O. clarkii bouvieri). These diagnostic assays were identified using a total of 489 individuals from 26 populations and five fish hatchery strains.

Twelve microsatellite loci for lake trout (Salvelinus namaycush)

We describe 12 microsatellite loci isolated from lake trout (Salvelinus namaycush). The number of alleles at these loci ranged from two to 11 with an average of 5.3 alleles per locus. The expected heterozygosity ranged from 0.29 to 0.76, with an average of 0.68. Accidental (or illegal) introductions of lake trout into watersheds are decimating native trout populations in the northern Rocky Mountains, and these loci will be useful for identifying the source of these introductions and for estimating the number of founding individuals.

Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: implications for conservation

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.

Microsatellites indicate minimal barriers to mule deer Odocoileus hemionus dispersal across Montana, USA

To better understand the future spread of chronic wasting disease, we conducted a genetic assessment of mule deer Odocoileus hemionus population structure across the state of Montana, USA. Individual based analyses were used to test for population structure in the absence of a priori designations of population membership across the sampling area. Samples from the states of Wyoming, Colorado and Utah were also included in the analysis to provide a geographic context to the levels of population structure observed within Montana. Results showed that mule deer across our entire study region were characterized by weak isolation by distance and a lack of spatial autocorrelation at distances > 10 km. We found evidence for contemporary male bias in dispersal, with female mule deer exhibiting higher mean individual pairwise genetic distance than males. We tested for potential homogenizing effects of past translocations within Montana, but were unable to detect a genetic signature of these events. Our results indicate high levels of connectivity among mule deer populations in Montana and suggest few, if any, detectable barriers to mule deer gene flow or chronic wasting disease transmission.

Twelve tetranucleotide microsatellite loci for westslope cutthroat trout Oncorhynchusclarkilewisi (Salmonidae)

We isolated 12 tetra-nucleotide microsatellite loci from westslope cutthroat trout (Oncorhynchusclarkilewisi). These loci were tested against 58 individuals from a single creek for polymorphism. The number of alleles ranged from 2 to 8, with an average of 4.3. The expected heterozygosity ranged from 0.12 to 0.79, with an average of 0.52. Ten of the twelve loci conformed to Hardy–Weinberg expectations. These microsatellite loci will be useful for describing population structure in westslope cutthroat trout.

Taxonomic identity of the endangered Snake River physa, Physa natricina (Pulmonata: Physidae) combining traditional and molecular techniques

The conservation of some imperiled species has been impaired by taxonomic uncertainty. The Snake River physa, Physa natricina Taylor 1988, is an endangered gastropod to the middle Snake River that has rarely been collected live. The rarity of P. natricina and the lack of live specimens have fueled debate regarding the validity of the species. Our objectives were to: determine if P. natricina existed in a suspected population area; if found, to compare shell morphology to the holotype and soft tissue to the original description; review available museum specimens to determine species range; and phylogenetically compare suspect P. natricina with confamilial and other known Physidae. Sampling yielded suspect P. natricina with shell morphology matching the holotype and dissections revealed that the soft tissue was within the purview of the original description and not overlapping the characters of other Physidae. Review of museum Physidae collected from the Snake River revealed suspect P. natricina as far downstream as RK 592. Physella gyrina was the only confamilial species found during sampling and during review of museum collections. Phylogenetic analyses (maximum parsimony, maximum likelihood, Bayesian inference, and UPGMA) of cytochrome c oxidase subunit I and ribosomal subunit 16S markers strongly supported P. natricina as a reciprocal monophyletic group and a distinct evolutionary significant unit. Our results confirm the original description of P. natricina as a distinct species and expand the extant distribution highlighting the importance of combining traditional methods of taxonomic description with modern molecular tools when working with species of conservation concern.