Population genetic structure and comparative diversity of smallmouth bass Micropterus dolomieu: congruent patterns from two genomes.

Genetic diversity and divergence patterns of smallmouth bass Micropterus dolomieu spawning groups are analysed across its northern native range with mtDNA cytochrome b gene sequences and eight unlinked nuclear DNA microsatellite loci. Results reveal high levels of genetic variability and significant differences in allelic representation among populations (mtDNA: mean ± s.e., HD = 0·50 ± 0·06, mean ± s.e., θST = 0·41 ± 0·02 and microsatellites: mean ± s.e. HO = 0·46 ± 0·03, mean ± s.e. θST = 0·25 ± 0·01). The distributions of 28 variant mtDNA haplotypes, which differ by an average of 3·94 nucleotides (range = 1-8), denote divergent representation among geographic areas. Microsatellite data support nine primary population groups, whose high self-assignment probabilities likewise display marked divergence. Genetic patterns demonstrate: (1) high genetic diversity in both genomes, (2) significant divergence among populations, probably resulting from natal site homing and low lifetime migration, (3) support for three post-glacial refugia that variously contributed to the current northern populations, which remain evident today despite waterway connectivity and (4) a weak yet significant genetic isolation by geographic distance pattern, indicating that other processes affect the differences among populations, such as territoriality and site fidelity.

Genetic and morphometric differences demonstrate fine-scale population substructure of the yellow perch Perca flavescens: need for redefined management units.

Whole-body morphometrics and 15 nuclear DNA microsatellite loci were analysed for 158 Perca flavescens collected during the spawning season from four spawning locations in central Lake Erie, two along the northern shore and two along the southern shore, to evaluate fine-scale variation (spanning 17-94 km). Results showed significant morphological and genetic differences among P. flavescens from the four locations. The magnitudes of differences were unrelated to geographic distance, demonstrating spatially heterogeneous levels of genetic divergence. These results linked morphometric and genetic variation, showing a discontinuity of scale between currently defined management units and population structure of P. flavescens in Lake Erie, and support that P. flavescens might exist as one or more metapopulations. Findings demonstrate the value of using complementary techniques for evaluating population structure.

Signatures of vicariance, postglacial dispersal and spawning philopatry: population genetics of the walleye Sander vitreus.

Population genetic relationships reveal the signatures of current processes such as reproductive behaviour and migration, as well as historic events including vicariance and climate change. We analyse population structure of native walleye Sander vitreus across North America, encompassing 10 nuclear DNA microsatellite loci, 26 spawning sites and 921 samples from watersheds across the Great Lakes, Lake Winnipeg, upper Mississippi River, Ohio River and Mobile Bay of the Gulf Coast. Geographical patterning is assessed using phylogenetic trees, pairwise F(ST) analogues, hierarchical partitioning, Mantel regression, Bayesian assignment and Monmonier geographical networks. Results reveal congruent divergences among population groups, corresponding to historic isolation in glacial refugia, dispersal patterns and basin divisions. Broad-scale relationships show genetic isolation with geographical distance, but reproductive groups within basins do not -- with some having pronounced differences. Greatest divergence distinguishes outlying Gulf Coastal and northwest populations, the latter tracing to dispersal from the Missourian refugium to former glacial Lake Agassiz, and basin isolation approximately 7000 ya. Genetic barriers in the Great Lakes separate groups in Lakes Superior, Huron's Georgian Bay, Erie and Ontario, reflecting contributions from Mississippian and Atlantic refugia, and changes in connectivity patterns. Walleye genetic patterns thus reflect vicariance among watersheds and glacial refugia, followed by re-colonization pathways and changing drainage connections that established modern-day northern populations, whose separations are maintained through spawning site fidelity. Conservation management practices should preserve genetic identity and unique characters among these divergent walleye populations.

Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites.

Catchment population structure and divergence patterns of the rainbow darter Etheostoma caeruleum (Percidae: Teleostei), an eastern North American benthic fish, are tested using a landscape genetics approach. Allelic variation at eight nuclear DNA microsatellite loci and two mitochondrial DNA regions [cytochrome (cyt) b gene and control region; 2056 aligned base pairs (bp)] is analysed from 89 individuals and six sites in the Lake Erie catchment (Blanchard, Chagrin, Cuyahoga and Grand Rivers) v. the Ohio River catchment (Big Darby Creek and Little Miami River). Genetic and geographic patterning is assessed using phylogenetic trees, pair-wise F(ST) analogues, AMOVA partitioning, Mantel regression, Bayesian assignment, 3D factorial correspondence and barrier analyses. Results identify 34 cyt b haplotypes, 22 control region haplotypes and 137 microsatellite alleles whose distributions demonstrate marked genetic divergence between populations from the Lake Erie and Ohio River catchments. Etheostoma caeruleum populations in the Lake Erie and Ohio River catchments diverged c. 1.6 mya during the Pleistocene glaciations. Greater genetic separations characterize the Ohio River populations, reflecting their older habitat age and less recent connectivity. Divergence levels within the Lake Erie catchment denote more recent post-glacial origins. Notably, the western Lake Erie Blanchard River population markedly differs from the three central basin tributary samples, which are each genetically distinguishable using microsatellites. Overall relationships among the Lake Erie sites refute a genetic isolation by geographic distance hypothesis. Etheostoma caeruleum populations thus exchange few genes and have low migration among tributaries and catchments.

Phylogeography of the spotted sand bass, Paralabrax maculatofasciatus: divergence of Gulf of California and Pacific Coast populations.

Have the warm tropical waters and currents of the southern Gulf of California, Mexico (also known as the Sea of Cortez), formed a barrier to gene flow, resulting in disjunct populations in the upper gulf that are isolated from the outer Pacific Coast? Phylogeographic and genetic divergences of the spotted sand bass, Paralabrax maculatofasciatus, from three Gulf of California and two outer Pacific coastal locations were tested using mitochondrial DNA (mtDNA) control region sequences. Sequence data from two congeners that are sympatrically distributed along the outer Pacific Coast, the barred sand bass, P. nebulifer, and the kelp bass, P. clathratus, were used to gauge the levels of genetic divergences. Differences among the three species and between the northern gulf and outer Pacific coastal populations of P. maculatofasciatus also were analyzed using 40 allozymic presumptive gene loci. Allozyme and mtDNA analyses each revealed many fixed differences among the species. Three significant allozymic frequency differences and two fixed mtDNA substitutions differentiated the gulf and outer Pacific coastal populations of P. maculatofasciatus. Three unique mtDNA haplotypes and three unique allozyme alleles were identified from the outer Pacific coastal population. The gulf sites contained four unique mtDNA haplotypes and six unique allozyme alleles. Partitioning of the mtDNA variation revealed that 72% of the variance occurred between the gulf and outer Pacific Coast, 20% between sampling sites in the two regions, and 8% within the sites. There appears to be little gene flow across the waters of the southern Baja Penninsula, producing divergence estimated as 120,000 to 600,000 years between the outer Pacific coastal and the Gulf of California populations. This separation level may date to a hypothesized seaway closure near La Paz, Mexico, during the mid-Pleistocene, and characterizes other fish populations. A second pattern of deeper allopatric species-level divergences in some other fishes may date to a Pliocene closure of a mid Baja Penninsular seaway. Significant differences also were discerned in P. maculatofasciatus between the San Diego and central Baja California coastal sites and between the upper/central and the lower gulf locations. Variation between locations in the two regions may be indicative of larval retention and low adult migration, which needs to be tested further.

Genetic diversity and evolutionary relationships of the troglodytic "living fossil" Congeria kusceri (Bivalvia: Dreissenidae).

Population genetic theory predicts that long-term isolation of "living fossils" in relic habitats might reduce genetic variability due to small population sizes and inbreeding. The recent description of a troglodytic "living fossil" Congeria kusceri--the only known subterranean bivalve mollusc--from a genus thought to be extinct since the Miocene, offers a unique opportunity to examine this hypothesis. Here, we use DNA sequences from two mitochondrial genes to compare levels of genetic variability and to test phylogenetic relationships of C. kusceri with surface-dwelling dreissenid relatives. Phylogenetic analyses of sequences from the cytochrome oxidase 1 (COI) and 16S rDNA genes reveal that Mytilopsis is the sister genus to Congeria and this clade forms the sister taxon to Dreissena. Relatively high levels of DNA diversity characterized the population of C. kusceri (haplotypic diversity= 0.50 for 16S rDNA and 0.66 in the COI gene), in contrast to no intraspecific variability in populations of Dreissenapolymorpha, D. bugensis, Mytilopsisleucophaeta, and Corbiculafluminea. Maintenance of genetic variability in C. kusceri may result from long-term population size stability, which merits further investigation. This underground species apparently was buffered from the climatic changes and resultant population bottlenecks that affected its surface-dwelling relatives during the Pliocene and Pleistocene Ice Ages.

Phylogeography of Ophioblennius: the role of ocean currents and geography in reef fish evolution.

Many tropical reef fishes are divided into Atlantic and East Pacific taxa, placing similar species in two very different biogeographic regimes. The tropical Atlantic is a closed ocean basin with relatively stable currents, whereas the East Pacific is an open basin with unstable oceanic circulation. To assess how evolutionary processes are influenced by these differences in oceanography and geography, we analyze a 630-bp region of mitochondrial cytochrome b from 171 individuals in the blenniid genus Ophioblennius. Our results demonstrate deep genetic structuring in the Atlantic species, O. atlanticus, corresponding to recognized biogeographic provinces, with divergences of d = 5.2-12.7% among the Caribbean, Brazilian, St. Helena/Ascension Island, Gulf of Guinea, and Azores/Cape Verde regions. The Atlantic phylogeny is consistent with Pliocene dispersal from the western to eastern Atlantic, and the depth of these separations (along with prior morphological comparisons) may indicate previously unrecognized species. The eastern Pacific species, O. steindachneri, is characterized by markedly less structure than O. atlanticus, with shallow mitochondrial DNA lineages (dmax = 2.7%) and haplotype frequency shifts between locations in the Sea of Cortez, Pacific Panama, Clipperton Island, and the Galapagos Islands. No concordance between genetic structure and biogeographic provinces was found for O. steincdachneri. We attribute the phylogeographic pattern in O. atlanticus to dispersal during the reorganization of Atlantic circulation patterns that accompanied the shoaling of the Isthmus of Panama. The low degree of structure in the eastern Pacific is probably due to unstable circulation and linkage to the larger Pacific Ocean basin. The contrast in genetic signatures between Atlantic and eastern Pacific blennies demonstrates how differences in geology and oceanography have influenced evolutionary radiations within each region.

Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA.

Diagnostic genetic markers from 486 aligned nucleotide sequences of mitochondrial 16S ribosomal DNA were developed for the four closely related species of dreissenoid and corbiculoid bivalves that have invaded North America; the zebra mussel Dreissena polymorpha, the quagga mussel D. bugensis, and the dark false mussel Mytilopsis leucophaeata of the superfamily Dreissenoidea, and the Asian clam Corbicula fluminea of the sister superfamily Corbiculoidea. Evolutionary relationships were examined among the four genera and comparisons were made with native Eurasian populations of D. polymorpha and D. bugensis. Tests were conducted for gender-specific mitochondrial lineages, which occur in some other bivalves. Genetic variability and divergence rates were tested between stem (paired) and loop (unpaired) regions of secondary structure. There were 251 variable nucleotide sites, of which 99 were phylogenetically informative. Overall transition to transversion ratio was 0.76:1.00 and both accumulated linearly in stem and loop regions, suggesting appropriate phylogenetic signal. Genetic distance calibration with the fossil record estimated the pairwise sequence divergence as 0. 0057 +/- 0.0004 per million years. Mytilopsis and Dreissena appear to have diverged about 20.7 +/- 2.7 million years ago. D. bugensis and D. polymorpha appear separated by about 13.2 +/- 2.2 million years. No intraspecific variation was found, including between Eurasian and North American populations, among shallow and deep morphotypes of D. bugensis and between the sexes. Restriction endonuclease markers were developed to distinguish among the species at all life history stages, allowing rapid identification in areas of sympatric distribution.

Phylogeographical structure of the Dover sole Microstomus pacificus: the larval retention hypothesis and genetic divergence along the deep continental slope of the northeastern Pacific Ocean.

Population genetic variability and phylogeographical structure of the Dover sole, Microstomus pacificus (Teleostei: Pleuronectidae), were examined along the continental slope of the north-eastern Pacific Ocean using sequences of the left domain of the mitochondrial DNA (mtDNA) control region. Six sites were sampled in three primary biogeographical provinces (based on surface water temperatures), ranging from the subarctic to the warm temperate zones. Many haplotypes were discerned, totalling 90 for 110 individuals. Neighbour joining and parsimony analyses of the entire data set showed that some groups of haplotypes of adult Dover sole were widely distributed, suggesting either panmixia or homoplasy and reversals. However, a substantial number of groups of related haplotypes were geographically circumscribed, and there were significant differences among sites in the distribution of restricted haplotypes (based on a reduced number of characters), supporting geographical structure. Geographical differentiation of populations appeared to be consistent with the member-vagrant hypothesis for retention of the pelagic larvae in currents and recruitment to adult habitats, reducing long-distance dispersal. Results of this study indicate phylogeographical structure among some populations, despite extended pelagic larval periods, and apparent environmental homogeneity in the adult habitats along the continental slope.

Population genetic structure, phylogeography and spawning philopatry in walleye (Stizostedion vitreum) from mitochondrial DNA control region sequences.

Mitochondrial (mt) DNA control region sequences were used to test the genetic and phylogeographic structure of walleye Stizostedion vitreum populations at different geographical scales: among spawning sites, lake basins, lakes, and putative glacial refugia in the Great Lakes region. Sequencing 199 walleye revealed nucleotide substitutions and tandemly repeated sequences that varied in copy number, as well as in sequence composition, in approximately 1200 bp of the mtDNA control region. Variable numbers of copies of an 11-bp tandem repeat showed no geographical patterning and were not used in further analyses. Substitutions in the other areas of the control region yielded 19 haplotypes, revealing phylogeographic structure and significant differences among glacial refugia, lakes, basins and some spawning sites. Differences among spawning populations were consistent with reduced gene flow, philopatry and possible natal homing. Analysis of spawning populations showed consistency of genotypic frequencies among years and between males and females, supporting philopatry in both sexes. The unglaciated plateau in southern Ohio, USA housed a very different haplotype that diverged prior to the Missouri, Mississippi and Atlantic glacial refugia types. Haplotypes from the three refugia colonized the Great Lakes after retreat of the Wisconsin glaciers, and their present distribution reflects the geography of their prior isolation and differential colonization. Populations that became associated with spawning localities appear to have diverged further due to philopatry, resulting in fine-scale phylogeographic structuring.

Tandemly repeated sequences in the mitochondrial DNA control region and phylogeography of the Pike-Perches Stizostedion.

DNA sequences from the mitochondrial DNA control region are used to test the phylogeographic relationships among the pike-perches, Stizostedion (Teleostei: Percidae) and to examine patterns of variation. Sequences reveal two types of variability: single nucleotide polymorphisms and 6 to 14 copies of 10- to 11-base-pair tandemly repeated sequences. Numbers of copies of the tandem repeats are found to evolve too rapidly to detect phylogenetic signal at any taxonomic level, even among populations. Sequence similarities of the tandem repeats among Stizostedion and other percids suggest concerted evolutionary processes. Predicted folding of the tandem repeats and their proximity to termination-associated sequences indicate that secondary structure mediates slipped-strand mispairing among the d-loop, heavy, and light strands. Neighbor-joining and maximum parsimony analyses of sequences indicate that the genus is divided into clades on the continents of North America and Eurasia. Calibrating genetic distances with divergence times supports the hypothesis that Stizostedion dispersed from Eurasia to North America across a North Pacific Beringial land bridge approximately 4 million years before present, near the beginning of the Pliocene Epoch. The North American S. vitreum and S. canadense appear separated by about 2.75 million years, and the Eurasian S. lucioperca and S. volgensis are diverged by about 1.8 million years, suggesting that speciation occurred during the late Pliocene Epoch.