Tim L. King

Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): conservation implications of range discontinuity

A nucleotide sequence analysis of the first internal transcribed spacer region (ITS‐1) between the 5.8S and 18S ribosomal DNA genes (640 bp) and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (mtDNA) (576 bp) was conducted for the freshwater bivalve Lasmigona subviridis and three congeners to determine the utility of these regions in identifying phylogeographic and phylogenetic structure. Sequence analysis of the ITS‐1 region indicated a zone of discontinuity in the genetic population structure between a group of L. subviridis populations inhabiting the Susquehanna and Potomac Rivers and more southern populations. Moreover, haplotype patterns resulting from variation in the COI region suggested an absence of gene exchange between tributaries within two different river drainages, as well as between adjacent rivers systems. The authors recommend that the northern and southern populations, which are reproductively isolated and constitute evolutionarily significant lineages, be managed as separate conservation units. Results from the COI region suggest that, in some cases, unionid relocations should be avoided between tributaries of the same drainage because these populations may have been reproductively isolated for thousands of generations. Therefore, unionid bivalves distributed among discontinuous habitats (e.g. Atlantic slope drainages) potentially should be considered evolutionarily distinct. The DNA sequence divergences observed in the nuclear and mtDNA regions among the Lasmigona species were congruent, although the level of divergence in the COI region was up to three times greater. The genus Lasmigona, as represented by the four species surveyed in this study, may not be monophyletic.

Regional Differentiation and Sex-Biased Dispersal among Populations of the Horseshoe Crab Limulus polyphemus

Abstract Fourteen microsatellite DNA loci were surveyed in 892 horseshoe crabs Limulus polyphemus collected from 21 sites ranging from Franklin, Maine, to the Yucatan Peninsula, Mexico. This rangewide survey revealed a high degree of genetic diversity (up to 50 alleles per locus) and heterozygosity (up to 97.2%). There appears to be substantial gene flow between each population and its nearest neighbors. The correlation of genetic distance and geographic distance supports isolation by distance as a mechanism underlying the structure of L. polyphemus along the Atlantic coast of North America. Two statistical descriptors, mean assignment percentage and assignment variance, suggested the presence of male-biased dispersal throughout the study area. Within the continuum of isolation by distance and in the presence of male-biased dispersal, the clustering of specific collections on a tree of genetic distances and hierarchical gene diversity analyses demonstrate discrete regional units. These results suggest def...

Stock Origin of Migratory Atlantic Sturgeon in Minas Basin, Inner Bay of Fundy, Canada, Determined by Microsatellite and Mitochondrial DNA Analyses

Abstract Five distinct population segments of Atlantic sturgeon Acipenser oxyrinchus were recently listed (April 2012) as endangered or threatened under the U.S. Endangered Species Act. Atlantic sturgeon are anadromous, spawning occurs in rivers from the St. Lawrence River, Quebec, to the Satilla River, Georgia, and subadults and adults undertake extensive coastal migrations. Bycatch of Atlantic sturgeon in coastal fisheries may have resulted in the slowed or failed rebuilding of many populations despite the imposition of a U.S. federal moratorium on their harvest in 1998. Canadas Bay of Fundy hosts weir and trawl fisheries which bycatch Atlantic sturgeon of unknown origin. Additionally, tidal power development projects for the Bay of Fundy have been proposed which could detrimentally impact migratory sturgeon. We hypothesized that the Atlantic sturgeon that occur in Minas Basin in the Bay of Fundy are of local Saint John River, New Brunswick, origin with little or no U.S. contribution. We used microsate...

Tools for the management and conservation of genetic diversity in brook trout (Salvelinus fontinalis): tri- and tetranucleotide microsatellite markers for the assessment of genetic diversity, phylogeography, and historical demographics

We document isolation and characterization of 13 tri- and tetranucleotide microsatellite DNA markers in brook trout (Salvelinus fontinalis). These markers displayed moderate to high levels of allelic diversity (averaging 20.5 alleles/locus) and heterozygosity (averaging 53.5%) in a range-wide survey of more than 13,000 fish. A comparison of two geographically proximal populations located on opposite sides of the eastern continental divide in Maryland, USA, found no deviations from Hardy–Weinberg equilibrium and minimal linkage disequilibrium. Microsatellite markers developed for S. fontinalis yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate phylogeographic structure; and (3) provide unique demographic perspectives of population sizes and historical demographics. This suite of markers also provided considerable cross-species amplification utility among related salmonids.

Population dynamics of American horseshoe crabs—historic climatic events and recent anthropogenic pressures

Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent‐based methods. The analysis showed strong declines in population sizes throughout the species’ distribution except in the geographically isolated southern‐most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics—a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest.

Targeted stock identification using multilocus genotype ‘familyprinting’

Abstract We present an approach to stock identification of small, targeted populations that uses multilocus microsatellite genotypes of individual mating adults to uniquely identify first- and second-generation offspring in a mixture. We call the approach ‘familyprinting’; unlike DNA fingerprinting where tissue samples of individuals are matched, offspring from various families are assigned to pairs of parents or sets of four grandparents with known genotypes. The basic unit of identification is the family, but families can be nested within a variety of stock units ranging from naturally reproducing groups of fish in a small tributary or pond from which mating adults can be sampled to large or small collections of families produced in hatcheries and stocked in specific locations. We show that, with as few as seven alleles per locus using four loci without error, first-generation offspring can be uniquely assigned to the correct family. For second-generation applications in a hatchery more alleles per locus (10) and loci (10) are required for correct assignment of all offspring to the correct set of grandparents. Using microsatellite DNA variation from an Atlantic salmon (Salmo solar) restoration river (Connecticut River, USA), we also show that this population contains sufficient genetic diversity in sea-run returns for 100% correct first-generation assignment and 97% correct second-generation assignment using 14 loci. We are currently using first- and second-generation familyprinting in this population with the ultimate goal of identifying stocking tributary. In addition to within-river familyprinting, there also appears to be sufficient genetic diversity within and between Atlantic salmon populations for identification of ‘familyprinted’ fish in a mixture of multiple populations. We also suggest that second-generation familyprinting with multiple populations may also provide a tool for examining stock structure. Familyprinting with microsatellite DNA markers is a viable method for identification of offspring of randomly mating adults from small, targeted stocks and should provide a useful addition to current mixed stock analyses with genetic markers.

Special Issue on Gene Conservation: Identification and Management of Genetic Diversity

Effective programmes for conserving threatened spe-cies require the identification of unambiguous units ofmanagement that reflect evolutionarily important line-ages (Avise 1994). Heritable genetic information offers anobjective means to delineate conservation units, andprovides an evolutionary framework from which to developand evaluate conservation priorities. The value of molecularmarkers in delineating breeding structures and evolu-tionarily important lineages is well established (Avise1994; Hillis

Phylogeographic analyses suggest multiple lineages of Crystallaria asprella (Percidae: Etheostominae)

The crystal darter, Crystallaria asprella, exists in geographically isolated populations that may be glacial relicts from its former, wide distribution in the Eastern U.S. An initial phylogeographic survey of C. asprella based upon the mitochondrial cytochrome b (cyt b) gene indicated that there were at least four distinct populations within the species: Ohio River basin, Upper Mississippi River, Gulf coast, and lower Mississippi River. In particular, the most divergent population was the most recently discovered, from the Elk River, WV, in the Ohio River basin, and it was postulated that this population represents an undescribed, potentially threatened species. However, differentiation observed at a single gene region is generally not considered sufficient evidence to establish taxonomic status. In the present study, nucleotide variation at the mitochondrial control region and a nuclear S7 ribosomal gene intron were compared to provide independent verification of phylogeographic results between individuals collected from the same five disjunct populations previously surveyed. Variation between populations at the control region was substantial (except between Gulf drainages) and was concordant with patterns of sequence divergence from cyt b. Only the Elk River population was resolved as monophyletic based upon nuclear S7, but significant differences based upon ΦST statistics were observed between most populations. Morphometric data were consistent with molecular data regarding the distinctiveness of the Elk River population. It is proposed that populations of C. asprella consist of at least four distinct population segments, and that the Elk River group likely constitutes a distinct species.

Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix

We document the isolation and characterization of novel tetranucleotide microsatellite DNA markers for the invasive silver carp Hypophthalmichthys molitrix and provide the results of cross-species amplification for three additional invasive carp species: bighead (H. nobilis), grass (Ctenopharyngodon idella) and black (Mylopharyngodon piceus). In the target species these markers yielded levels of allelic diversity (average 4.4 alleles/locus) and heterozygosity (average 54.7%) sufficient to: (1) provide unique multilocus genotypes; (2) delineate kinship relationships; (3) differentiate populations/species; (4) estimate effective population sizes; and (5) provide unique demographic perspectives for control or eradication. Currently these markers are being utilized to determine the degree of introgressive hybridization between H. molitrix and H. nobilis, to quantify gene flow between different sub-basins established in the central United States, and to assess the demographic status of sub-basin groups. This information will be critically important in the management/control of these invasive species.

Characterization of 13 microsatellite loci for the deep-sea coral, Lophelia pertusa (Linnaeus 1758), from the western North Atlantic Ocean and Gulf of Mexico

A suite of 13 polymorphic tri‐ and tetranucleotide microsatellite loci were isolated from the ahermatypic deep‐sea coral, Lophelia pertusa. Among 51 individuals collected from three disjunct oceanic regions, allelic diversity ranged from six to 38 alleles and averaged 9.1 alleles per locus. Observed heterozygosity ranged from 9.1 to 96.8% and averaged 62.3% in the Gulf of Mexico population. For some loci, amplification success varied among collections, suggesting regional variation in priming site sequences. Four loci showed departures from Hardy–Weinberg equilibrium in certain collections which may reflect nonrandom mating.