- Fisheries, Marine Ecology, Phylogeography, Phylogenetics, Molecular Ecology (Ecology), Speciation, and 17 moreGene Flow, Mutation (Evolutionary Biology), Population Genetics, Evolutionary genetics, Biological Sciences, Next generation sequencing, Marine Protected Areas, Population genetics (Biology), Mitochondrial DNA, Mate Choice, Olfaction (Biology), Marine Reserves, Olfaction, Variability, Larval Dispersal, Euphausiacea, and Krilledit
Members of the Anisakidae are known to infect over 200 pelagic fish species and have been frequently used as biological tags to identify fish populations. Despite information on the global distribution of Anisakis species, there is little... more
Members of the Anisakidae are known to infect over 200 pelagic fish species and have been frequently used as biological tags to identify fish populations. Despite information on the global distribution of Anisakis species, there is little information on the genetic diversity and population structure of this genus, which could be useful in assessing the stock structure of their fish hosts. From 2005 through 2008, 148 larval anisakids were recovered from Pacific sardine (Sardinops sagax) in the California Current upwelling zone and were genetically sequenced. Sardines were captured off Vancouver Island, British Columbia in the north to San Diego, California in the south. Three species, Anisakis pegreffii, Anisakis simplex 'C', and Anisakis simplex s.s., were identified with the use of sequences from the internal transcribed spacers (ITS1 and ITS2) and the 5.8s subunit of the nuclear ribosomal DNA. The degree of nematode population structure was assessed with the use of the cytochrome c oxidase 2 (cox2) mitochondrial DNA gene. All 3 Anisakis species were distributed throughout the study region from 32°N to 50°N latitude. There was no association between sardine length and either nematode infection intensity or Anisakis species recovered. Larval Anisakis species and mitochondrial haplotype distributions from both parsimony networks and analyses of molecular variance revealed a panmictic distribution of these parasites, which infect sardines throughout the California Current ecosystem. Panmictic distribution of the larval Anisakis spp. populations may be a result of the presumed migratory pathways of the intermediate host (the Pacific sardine), moving into the northern portion of the California Current in summer and returning to the southern portion to overwinter and spawn in spring. However, the wider geographic range of paratenic (large piscine predators), and final hosts (cetaceans) can also explain the observed distribution pattern. As a result, the recovery of 3 Anisakis species and a panmictic distribution of their haplotypes could not be used to confirm or deny the presence of population subdivision of Pacific sardines in the California Current system.
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The use and importance of reintroduction as a conservation tool to return a species to its historical range where it has become extirpated will only increase as climate change and human development accelerate habitat loss and population... more
The use and importance of reintroduction as a conservation tool to return a species to its historical range where it has become extirpated will only increase as climate change and human development accelerate habitat loss and population extinctions. Although the number of reintroduction attempts has rapidly increased over the past two decades, the success rate is generally low. As a result of population differences in fitness-related traits and divergent responses to environmental stresses, there is a high likelihood for differential performance among potential source populations upon reintroduction. It is well known that population performance upon reintroduction is highly variable and it is generally agreed that selecting an appropriate source population is a critical component of a successful reintroduction. Conservation Genomics is an emerging field that addresses long-standing challenges in conservation biology, and the potential for using novel molecular genetic approaches to ...
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Phenotypic plasticity allows genotypes to produce alternate phenotypes that enhance survivability and reproductive ability in different environments, creating altered selective pressures, which act on genotypes governing traits such as... more
Phenotypic plasticity allows genotypes to produce alternate phenotypes that enhance survivability and reproductive ability in different environments, creating altered selective pressures, which act on genotypes governing traits such as growth rate, development, and reproductive strategies. The giant kelp, Macrocystis, is able to dramatically reduce sexual reproduction normally utilized by the subtidal morph (M. pyrifera), to asexual growth in the intertidal morph (M. integrifolia). To test for genetic isolation caused by ecological divergence in the intertidal, we performed fine scale spatial sampling and molecular analysis of parapatric, M. pyrifera and M. integrifolia, populations in Central California. Using seven microsatellite markers, we compared genetic differentiation between morphs in the same site and among morphs across different sites. Additionally, we identified the presence of clonal replicates in intertidal populations. Preliminary results from two study sites suggest...
Research Interests: Genetics, Geography, Gene Flow, Marine Protected Areas, Marine Reserves, and 15 moreMolecular Ecology, Biological Sciences, California, Copper, Ichthyoplankton, Animals, Fishes, Larval Dispersal, Ecosystem, Analysis of Variance, Marine Protected Area, Marine Reserve, Genetic variation, Microsatellite DNA, and Isolation by distance
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Research Interests: Population Genetics, Population genetics (Biology), Mitochondrial DNA, Variability, Animals, and 11 moreMalacostraca, Mitochondrial Genome, Mitogenome, Control Region Sequences, Krill, Euphausiacea, Genetic variation, Base Sequence, Biochemistry and cell biology, Molecular Biology Reports, and Molecular Sequence Data
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Research Interests: Genetics, Mate Choice, Molecular Evolution, Biology, Medicine, and 15 moreGene expression, Heredity, Olfaction, Phylogeny, Animals, Vomeronasal Organ, Fishes, Molecular Phylogenetics and Evolution, Protein Sequence Analysis, Pheromone Receptor Gene, Sebastes, Species Specificity, Amino Acid Sequence, Molecular Sequence Data, and conserved sequence
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the... more
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the Northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate if they could be explained by oceanographic transport and other environmental drivers. We then modeled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, Central California, continental Santa Barbara...
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The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was... more
The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was suggested based on internal transcribed spacer 1 (ITS1) sequences from samples collected in Svalbard, Norway. Another species, Beroe ovata, was introduced to Europe from North America, initially in the Black Sea and subsequently (and possibly secondarily) into the Mediterranean and Baltic Seas. In areas where ctenophores have been introduced, they have often had significant detrimental ecological effects. The potential for other cryptic and/or undescribed Beroe species and history of spread of some species in the genus give reason for additional study. When alive, morphological hallmarks may be challenging to spot and photograph owing to the animals' transparency and near-constant motion. We sampled and analyzed 109 putative Beroe specimens from Eur...
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The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls... more
The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure. We identified three clusters, corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie plus eastern Lake Ontario, along with three highly divergent populations. Bottleneck analysis identified founder effects in two divergent populations. Regression analyses of isolation by distance and allelic richness vs. distance from the initial invasion site were consistent with limited migration. However, some populations in eastern Lake Erie and Lake ...
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Inbreeding depression is the loss of fitness resulting from the mating of genetically-related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, though recent research has identified DNA methylation... more
Inbreeding depression is the loss of fitness resulting from the mating of genetically-related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, though recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here we use a targeted, multi-gene approach to assess methylation at 22 growth, metabolic, immune, and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS, and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, though methylation decreased with age in five genes, CK-1, IFNɣ, HNRNP, hsc71, and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on aging, environment and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically-based inbreeding depression in vertebrates. This article is protected by copyright. All rights reserved.
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Patterns of spatial genetic structure (SGS), typically estimated by genotyping adults, integrate migration over multiple generations and measure the effective gene flow of populations. SGS results can be compared with direct ecological... more
Patterns of spatial genetic structure (SGS), typically estimated by genotyping adults, integrate migration over multiple generations and measure the effective gene flow of populations. SGS results can be compared with direct ecological studies of dispersal or mating system to gain additional insights. When mismatches occur, simulations can be used to illuminate the causes of these mismatches. Here, we report a SGS and simulation-based study of self-fertilization in Macrocystis pyrifera, the giant kelp. We found that SGS is weaker than expected in M. pyrifera and used computer simulations to identify selfing and early mortality rates for which the individual heterozygosity distribution fits that of the observed data. Only one (of three) population showed both elevated kinship in the smallest distance class and a significant negative slope between kinship and geographical distance. All simulations had poor fit to the observed data unless mortality due to inbreeding depression was imposed. This mortality could only be imposed for selfing, as these were the only simulations to show an excess of homozygous individuals relative to the observed data. Thus, the expected data consistently achieved nonsignificant differences from the observed data only under models of selfing with mortality, with best fits between 32% and 42% selfing. Inbreeding depression ranged from 0.70 to 0.73. The results suggest that density-dependent mortality of early life stages is a significant force in structuring Macrocystis populations, with few highly homozygous individuals surviving. The success of these results should help to validate simulation approaches even in data-poor systems, as a means to estimate otherwise difficult-to-measure life cycle parameters.
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ABSTRACT: Rockfish species of the genus Sebastes are notable for being numerous and diverse. Rockfishes are unusual among fish because they fertilize their eggs internally and release live, swimming larvae. They undergo complex courting... more
ABSTRACT: Rockfish species of the genus Sebastes are notable for being numerous and diverse. Rockfishes are unusual among fish because they fertilize their eggs internally and release live, swimming larvae. They undergo complex courting behaviors, which may allow females to be selective about their mates. The major histocompatibility complex (MHC) is implicated as having an important influence on mate selection in other fishes, especially in sticklebacks and salmonids. Research suggests that females choose mates that optimize the MHC genotypes of their offspring. Previous research on rockfishes indicates that multiple functional MHC sequences may be found in each species, and that multiple mating is common in the genus, possibly as a bet-hedging strategy against uncertain or incomplete mate-selection information. In this project, we characterized the MHC genotypes of copper (S. caurinus) and quillback (S. maliger) rockfish parents, assessed parentage of 14 larval broods, and assessed the MHC genotypes of the parents to determine if MHC-mediated mate choice was occurring. As in previous studies, we found that rockfishes possess multiple, highly variable MHC genes, and that females may mate with multiple males. We also found evidence of female preference for particular males. However, we found no strong evidence of selection based on MHC genotype. Females were not consistently selective based on relatedness, allele count, proportion of shared alleles, or minimum, mean, or maximum DNA or amino acid genetic distance. Instead, it appears that females were selective based on other measures of mate quality not considered in this study, with some hedging of bets through multiple mating also occurring.
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The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with... more
The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly–spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (~2200 km), significant population subdivision (FST = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (~450 km, FST = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (Nem) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.
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V1r-like Ora genes express putative chemoreceptors that may function as pheromone receptors in fishes. We used a candidate gene approach to test whether V1r-like Ora2 genes show evidence of positive selection that could suggest a role in... more
V1r-like Ora genes express putative chemoreceptors that may function as pheromone receptors in fishes. We used a candidate gene approach to test whether V1r-like Ora2 genes show evidence of positive selection that could suggest a role in mate recognition and the avoidance of hybridization between closely related rockfishes. We amplified a 492-bp fragment of a single V1r-like Ora2 gene from each of 5 species of rockfish. Despite separation of up to 7.8 My, the sequence of V1r-like Ora2 is highly conserved. Genetic distances are small, and all our study species shared at least one sequence with another species. Sequence comparisons suggested that, although most amino acids were subject to purifying selection, 9 amino acids showed evidence of positive selection. Because many of these amino acids were not associated with the areas of the protein suggested to be involved in ligand binding based on structural similarity to other olfactory receptors, this signal may reflect an echo of the relaxation of selection associated with the speciation events that separate these species. Strong sequence conservation suggests that this gene is of functional significance. However, because of shared alleles among species, the V1r-like Ora2 gene, in isolation, would be unlikely to differentiate species during mating season.
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Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics... more
Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 ? base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 ? bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.
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The conference Next Generation Genome Analysis in Non-Model Organisms was an American Genetic Association special event hosted by the University of Connecticut at Storrs from 11 to 13 June 2009. Organized by Drs Linda Strausbaugh and... more
The conference Next Generation Genome Analysis in Non-Model Organisms was an American Genetic Association special event hosted by the University of Connecticut at Storrs from 11 to 13 June 2009. Organized by Drs Linda Strausbaugh and Rachel O'Neill, the conference was a 2-day survey of recent research and future possibilities using next generation sequencing technologies. Talks covered diverse topics, from model organisms such as C. elegans through wallabies and planarians to sequencing technologies and bioinformatics. Despite the theme of . . .
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Most marine fishes disperse as planktonic larvae, and because the distance and direction of dispersal are often poorly understood, the contributions of different portions of the population to overall population genetic structure are also... more
Most marine fishes disperse as planktonic larvae, and because the distance and direction of dispersal are often poorly understood, the contributions of different portions of the population to overall population genetic structure are also poorly understood. At the extremes of their geographic ranges, many species are traditionally thought to “recruit”(settle as benthic juveniles) only under favorable conditions, in essence producing a net transport of larvae outward from the center of the range (Cowen 1985, Pringle 1986).
The 100 North Pacific rockfish species in the genus Sebastes are highly diverse. Rockfishes fertilize their eggs internally and release swimming larvae. Complex courting behaviors may allow female rockfish to be selective about their... more
The 100 North Pacific rockfish species in the genus Sebastes are highly diverse. Rockfishes fertilize their eggs internally and release swimming larvae. Complex courting behaviors may allow female rockfish to be selective about their mates and may promote and maintain speciation. In this study, I applied genetic techniques to survey the factors that structure rockfish populations and have potential to affect speciation.