Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens).

Characterization of interactions within a host-associated microbiome can help elucidate the mechanisms of microbial community formation on hosts and can be used to identify potential probiotics that protect hosts from pathogens. Microbes employ various modes of antagonism when interacting with other members of the community. The formation of biofilm by some strains can be a defense against antimicrobial compounds produced by other taxa. We characterized the magnitude of antagonistic interactions and biofilm formation of 25 phylogenetically diverse taxa that are representative of isolates obtained from egg surfaces of the threatened fish species lake sturgeon (Acipenser fulvescens) at two ecologically relevant temperature regimes. Eight isolates exhibited aggression to at least one other isolate. Pseudomonas sp. C22 was found to be the most aggressive strain, while Flavobacterium spp. were found to be one of the least aggressive and the most susceptible genera. Temperature affected the prevalence and intensity of antagonism. The aggressive strains identified also inhibited growth of known fish pathogens. Biofilm formations were observed for nine isolates and were dependent on temperature and growth medium. The most aggressive of the isolates disrupted biofilm formation of two well-characterized isolates but enhanced biofilm formation of a fish pathogen. Our results revealed the complex nature of interactions among members of an egg associated microbial community yet underscored the potential of specific microbial populations as host probiotics.

Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams.

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = -0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.

Environmental and lunar cues are predictive of the timing of river entry and spawning-site arrival in lake sturgeon Acipenser fulvescens.

The associations were quantified between daily and interannual variation in the timing of a closed population of lake sturgeon Acipenser fulvescens migration and arrival at spawning sites with stream environmental and lunar covariates. Spawning data were gathered from 1262 fish in Black Lake, Michigan 2001 to 2008 and by video monitoring 2000 to 2002. Sex-specific variation in responses to external cues was also tested. Results showed that a greater number of individuals initiated migration from lake to riverine habitats at dawn and dusk relative to other times of the day. Current and lagged effects of water temperature and river discharge, and periods in the lunar cycle were important variables in models quantifying movements into the river and timing of adult arrival at spawning sites. Different suites of covariates were predictive of A. fulverscens responses during different periods of the spawning season. The timing of initiation of migration and spawning, and the importance of covariates to the timing of these events, did not differ between sexes. Stream flow and temperature covaried with other variables including day length and the lunar cycle. Anthropogenic disruption of relationships among variables may mean that environmental cues may no longer reliably convey information for Acipenseriformes and other migratory fishes.

Patterns of invasion and colonization of the sea lamprey (Petromyzon marinus) in North America as revealed by microsatellite genotypes.

Invasions by exotic organisms have had devastating affects on aquatic ecosystems, both ecologically and economically. One striking example of a successful invader that has dramatically affected fish community structure in freshwater lakes of North America is the sea lamprey (Petromyzon marinus). We used eight microsatellite loci and multiple analytical techniques to examine competing hypotheses concerning the origins and colonization history of sea lamprey (n = 741). Analyses were based on replicated invasive populations from Lakes Erie, Huron, Michigan, and Superior, populations of unknown origins from Lakes Ontario, Champlain, and Cayuga, and populations of anadromous putative progenitor populations in North America and Europe. Populations in recently colonized lakes were each established by few colonists through a series of genetic bottlenecks which resulted in lower allelic diversity in more recently established populations. The spatial genetic structure of invasive populations differed from that of native populations on the Atlantic coast, reflecting founder events and connectivity of invaded habitats. Anadromous populations were found to be panmictic (theta(P) = 0.002; 95% CI = -0.003-0.006; P > 0.05). In contrast, there was significant genetic differentiation between populations in the lower and upper Great Lakes (theta(P) = 0.007; P < 0.05; 95% CI = 0.003-0.009). Populations in Lakes Ontario, Champlain, and Cayuga are native. Alternative models that describe different routes and timing of colonization of freshwater habitats were examined using coalescent-based analyses, and demonstrated that populations likely originated from natural migrations via the St Lawrence River.

Genetic variation over space and time: analyses of extinct and remnant lake trout populations in the Upper Great Lakes.

Lake trout (Salvelinus namaycush) in the upper Laurentian Great Lakes of North America experienced striking reductions in abundance and distribution during the mid-twentieth century. Complete collapse of populations was documented for Lake Michigan, and a few remnant populations remained only in lakes Huron and Superior. Using DNA obtained from historical scale collections, we analysed patterns of genetic diversity at five microsatellite loci from archived historical samples representing 15 populations (range 1940-1959) and from three contemporary remnant populations across lakes Huron and Superior (total n = 893). Demographic declines in abundance and the extirpation of native lake trout populations during the past 40 years have resulted in the loss of genetic diversity between lakes owing to extirpation of Lake Michigan populations and a temporal trend for reduction in allelic richness in the populations of lakes Superior and Huron. Naturally reproducing populations in Lake Superior, which had been considered to be remnants of historical populations, and which were believed to be responsible for the resurgence of lake trout numbers and distribution, have probably been affected by hatchery supplementation.

Comparisons of likelihood and machine learning methods of individual classification.

Classification methods used in machine learning (e.g., artificial neural networks, decision trees, and k-nearest neighbor clustering) are rarely used with population genetic data. We compare different nonparametric machine learning techniques with parametric likelihood estimations commonly employed in population genetics for purposes of assigning individuals to their population of origin ("assignment tests"). Classifier accuracy was compared across simulated data sets representing different levels of population differentiation (low and high F(ST)), number of loci surveyed (5 and 10), and allelic diversity (average of three or eight alleles per locus). Empirical data for the lake trout (Salvelinus namaycush) exhibiting levels of population differentiation comparable to those used in simulations were examined to further evaluate and compare classification methods. Classification error rates associated with artificial neural networks and likelihood estimators were lower for simulated data sets compared to k-nearest neighbor and decision tree classifiers over the entire range of parameters considered. Artificial neural networks only marginally outperformed the likelihood method for simulated data (0-2.8% lower error rates). The relative performance of each machine learning classifier improved relative likelihood estimators for empirical data sets, suggesting an ability to "learn" and utilize properties of empirical genotypic arrays intrinsic to each population. Likelihood-based estimation methods provide a more accessible option for reliable assignment of individuals to the population of origin due to the intricacies in development and evaluation of artificial neural networks.

Group-structured genetic models in analyses of the population and behavioral ecology of poikilothermic vertebrates.

Estimates of gene correlations among individuals within and among populations are frequently derived from statistical analyses of genetic data (e.g., F statistics). These measures can be important tools in molecular ecology and conservation, and offer important insights into population breeding structure. Using recently derived theory developed for group-structured populations, we show that fixation indices, when combined with basic population ecological and demographic data can be used to investigate population mating systems and to predict dispersal rates, trajectories and asymptotic levels of fixation indices, and effective population size. Four case studies of poikilothermic vertebrates are used to demonstrate the broad utility of evolutionary and ecological inferences afforded by group-structured models.

Sex-biased gene flow in spectacled eiders (Anatidae): inferences from molecular markers with contrasting modes of inheritance.

Genetic markers that differ in mode of inheritance and rate of evolution (a sex-linked Z-specific microsatellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro- and microgeographic scales, among breeding regions and local nesting populations within each region, respectively, for a migratory sea duck species, the spectacled eider (Somateria fisheri). Disjunct and declining breeding populations coupled with sex-specific differences in seasonal migratory patterns and life history provide a series of hypotheses regarding rates and directionality of gene flow among breeding populations from the Indigirka River Delta, Russia, and the North Slope and Yukon-Kuskokwim Delta, Alaska. The degree of differentiation in mtDNA haplotype frequency among breeding regions and populations within regions was high (phiCT = 0.189, P < 0.01; phiSC = 0.059, P < 0.01, respectively). Eleven of 17 mtDNA haplotypes were restricted to a single breeding region. Genetic differences among regions were considerably lower for nuclear DNA loci (sex-linked: phiST = 0.001, P > 0.05; biparentally inherited microsatellites: mean theta = 0.001, P > 0.05) than was observed for mtDNA. Using models explicitly designed for uniparental and biparentally inherited genes, estimates of spatial divergence based on nuclear and mtDNA data together with elements of the species' breeding ecology were used to estimate effective population size and degree of male and female gene flow. Differences in the magnitude and spatial patterns of gene correlations for maternally inherited and nuclear genes revealed that females exhibit greater natal philopatry than do males. Estimates of generational female and male rates of gene flow among breeding regions differed markedly (3.67 x 10(-4) and 1.28 x 10(-2), respectively). Effective population size for mtDNA was estimated to be at least three times lower than that for biparental genes (30,671 and 101,528, respectively). Large disparities in population sizes among breeding areas greatly reduces the proportion of total genetic variance captured by dispersal, which may accelerate rates of inbreeding (i.e., promote higher coancestries) within populations due to nonrandom pairing of males with females from the same breeding population.

Effective number of breeding adults in Bufo bufo estimated from age-specific variation at minisatellite loci.

Estimates of the effective number of breeding adults were derived for three semi-isolated populations of the common toad Bufo bufo based on temporal (i.e. adult-progeny) variance in allele frequency for three highly polymorphic minisatellite loci. Estimates of spatial variance in allele frequency among populations and of age-specific measures of genetic variability are also described. Each population was characterized by a low effective adult breeding number (Nb) based on a large age-specific variance in minisatellite allele frequency. Estimates of Nb (range 21-46 for population means across three loci) were approximately 55-230-fold lower than estimates of total adult census size. The implications of low effective breeding numbers for long-term maintenance of genetic variability and population viability are discussed relative to the species' reproductive ecology, current land-use practices, and present and historical habitat modification and loss. The utility of indirect measures of population parameters such as Nb and Ne based on time-series data of minisatellite allele frequencies is discussed relative to similar measures estimated from commonly used genetic markers such as protein allozymes.

Lekking without a paradox in the buff-breasted sandpiper.

Females in lek-breeding species appear to copulate with a small subset of the available males. Such strong directional selection is predicted to decrease additive genetic variance in the preferred male traits, yet females continue to mate selectively, thus generating the lek paradox. In a study of buff-breasted sandpipers (Tryngites subruficollis), we combine detailed behavioral observations with paternity analyses using single-locus minisatellite DNA probes to provide the first evidence from a lek-breeding species that the variance in male reproductive success is much lower than expected. In 17 and 30 broods sampled in two consecutive years, a minimum of 20 and 39 males, respectively, sired offspring. This low variance in male reproductive success resulted from effective use of alternative reproductive tactics by males, females mating with solitary males off leks, and multiple mating by females. Thus, the results of this study suggests that sexual selection through female choice is weak in buff-breasted sandpipers. The behavior of other lek-breeding birds is sufficiently similar to that of buff-breasted sandpipers that paternity studies of those species should be conducted to determine whether leks generally are less paradoxical than they appear.

Comparative analysis of intra- and interpopulation genetic diversity in Bufo bufo, using allozyme, single-locus microsatellite, minisatellite, and multilocus minisatellite data.

Estimates of genetic diversity within, and of variation among, semi-isolated populations of the common toad (Bufo bufo) were derived and compared across four classes of nuclear genetic markers, including allozymes, microsatellites, and single and multilocus minisatellites. Estimates of multilocus heterozygosity and the number of alleles per locus derived from allozymes were lower than for each class of variable number of tandem repeat (VNTR) markers. The degree of interpopulation genetic divergence as determined by genetic distance was generally concordant across all markers, although interpopulation variance in allozyme allele frequency (as measure by F-statistics) was greater than that documented for each VNTR locus. For both classes of VNTR loci, migration appeared to have less influence than mutation on the extent of interpopulation divergence. Analyses suggest that singly and multiply detected VNTR loci may be highly informative for population-level analyses addressing questions concerning population subdivision and breeding structure.

Cytonuclear genetics of experimental fish hybrid zones inside Biosphere 2.

Two species of mosquitofish (family Poeciliidae) known to hybridize in nature were introduced into freshwater habitats inside Biosphere 2, and their population genetics were monitored after 2 years. Within four to six generations, nuclear and cytoplasmic markers characteristic of Gambusia holbrooki had risen greatly in frequency, although some Gambusia affinis alleles and haplotypes were retained primarily in recombinant genotypes, indicative of introgressive hybridization. The temporal cytonuclear dynamics proved similar to population genetic changes observed in replicated experimental hybrid populations outside of Biosphere 2, thus indicating strong directional selection favoring G. holbrooki genotypes across the range of environments monitored. When interpreted in the context of species-specific population demographies observed previously, results suggest that the extremely rapid evolution in these zones of secondary contact is attributable primarily to species differences in life-history traits.

Genetic differentiation among cottontails from isolated playa basins.

Protein variation in 182 Sylvilagus floridanus from 19 playa basins in Castro Co., Texas was examined using starch-gel electrophoresis. Heterozygote deficiencies were noted for all populations. This heterozygote deficiency may be due to differential selection against heterozygous individuals over the winter months. Results of F-statistics indicated a significant degree of population differentiation at six loci. Nei's genetic distance between populations ranged from 0.20 to 0.388 and a significant association between genetic distance and linear geographic distance among playas was found. These results suggest that genetic exchange and long-distance dispersal may be hindered by expanses of unsuitable habitat.