Publications by authors named "Carol A Stepien"

26 Publications

  • Page 1 of 1

Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool.

Manag Biol Invasion 2021 Jul;12(3):747-775

US Department of Agriculture Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E Beckwith Ave, Missoula, MT 59801, USA.

Invasive species surveillance programs can utilize environmental DNA sampling and analysis to provide information on the presence of invasive species. Wider utilization of eDNA techniques for invasive species surveillance may be warranted. This paper covers topics directed towards invasive species managers and eDNA practitioners working at the intersection of eDNA techniques and invasive species surveillance. It provides background information on the utility of eDNA for invasive species management and points to various examples of its use across federal and international programs. It provides information on 1) why an invasive species manager should consider using eDNA, 2) deciding if eDNA can help with the manager's surveillance needs, 3) important components to operational implementation, and 4) a high-level overview of the technical steps necessary for eDNA analysis. The goal of this paper is to assist invasive species managers in deciding if, when, and how to use eDNA for surveillance. If eDNA use is elected, the paper provides guidance on steps to ensure a clear understanding of the strengths and limitation of the methods and how results can be best utilized in the context of invasive species surveillance.
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http://dx.doi.org/10.3391/mbi.2021.12.3.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8958948PMC
July 2021

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes.

PLoS One 2021 28;16(5):e0232923. Epub 2021 May 28.

Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America.

A unique and highly virulent subgenogroup (-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary changes from 48 isolates in relation to immunogenicity in cell culture. Our investigation compares genomic and genetic variation, selection, and rates of sequence changes in VHSV-IVb, in relation to other VHSV genogroups (VHSV-I, VHSV-II, VHSV-III, and VHSV-IVa) and with other Novirhabdoviruses. Results show that the VHSV-IVb isolates we sequenced contain 253 SNPs (2.3% of the total 11,158 nucleotides) across their entire genomes, with 85 (33.6%) of them being non-synonymous. The most substitutions occurred in the non-coding region (NCDS; 4.3%), followed by the Nv- (3.8%), and M- (2.8%) genes. Proportionally more M-gene substitutions encoded amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHSV genogroups and subgenogroups, VHSV-IVa from the northeastern Pacific Ocean has shown the fastest substitution rate (2.01x10-3), followed by VHSV-IVb (6.64x10-5) and by the VHSV-I, -II and-III genogroups from Europe (4.09x10-5). A 2016 gizzard shad (Dorosoma cepedianum) from Lake Erie possessed the most divergent VHSV-IVb sequence. The in vitro immunogenicity analysis of that sample displayed reduced virulence (as did the other samples from 2016), in comparison to the original VHSV-IVb isolate (which had been traced back to 2003, as an origin date). The 2016 isolates that we tested induced milder impacts on fish host cell innate antiviral responses, suggesting altered phenotypic effects. In conclusion, our overall findings indicate that VHSV-IVb has undergone continued sequence change and a trend to lower virulence over its evolutionary history (2003 through present-day), which may facilitate its long-term persistence in fish host populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232923PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8162641PMC
October 2021

Intra-Annual and Interannual Dynamics of Evaporation Over Western Lake Erie.

Earth Space Sci 2020 Nov 23;7(11):e2020EA001091. Epub 2020 Nov 23.

Center for Global Change and Earth Observations Michigan State University East Lansing MI USA.

Evaporation () is a critical component of the water and energy budget in lake systems yet is challenging to quantify directly and continuously. We examined the magnitude and changes of and its drivers over Lake Erie-the shallowest and most southern lake of the Laurentian Great Lakes. We deployed two eddy-covariance tower sites in the western Lake Erie Basin-one located nearshore (CB) and one offshore (LI)-from September 2011 through May 2016. Monthly varied from 5 to 120 mm, with maximum occurring in August-October. The annual was 635 ± 42 (±SD) mm at CB and 604 ± 32 mm at LI. Mean winter (October-March) was 189 ± 61 mm at CB and 178 ± 25 mm at LI, accounting for 29.8% and 29.4% of annual . Mean daily was 1.8 mm during the coldest month (January) and 7.4 mm in the warmest month (July). Monthly exhibited a strong positive linear relationship to the product of wind speed and vapor pressure deficit. Pronounced seasonal patterns in surface energy fluxes were observed with a 2-month lag in from , due to the lake's heat storage. This lag was shorter than reports regarding other Great Lakes. Difference in between the offshore and nearshore sites reflected within-lake spatial heterogeneity, likely attributable to climatic and bathymetric differences between them. These findings suggest that predictive models need to consider lake-specific heat storage and spatial heterogeneity in order to accurately simulate lake and its seasonal dynamics.
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http://dx.doi.org/10.1029/2020EA001091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757182PMC
November 2020

Evolutionary trajectory of fish (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification.

Ecol Evol 2020 Sep 2;10(18):9740-9775. Epub 2020 Sep 2.

Genetics and Genomics Group (G3), Department of Environmental Sciences University of Toledo Toledo OH USA.

 = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb ( = 184 individual fish isolates) diversified into 36 -gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). -gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the -gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
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http://dx.doi.org/10.1002/ece3.6611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520192PMC
September 2020

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels.

Ecol Evol 2019 Mar 4;9(6):3515-3538. Epub 2019 Mar 4.

Genetics and Genomics Group NOAA Pacific Marine Environmental Laboratory Seattle, Washington.

Identifying species and population genetic compositions of biological invasions at early life stages and/or from environmental (e)DNA using targeted high-throughput sequencing (HTS) metabarcode assays offers powerful and cost-effective means for early detection, analysis of spread patterns, and evaluating population changes. The present study develops, tests, and applies this method with a targeted sequence assay designed to simultaneously identify and distinguish between the closely related invasive Eurasian zebra and quagga mussels ( and ) and their relatives and discern their respective population genetic patterns. Invasions of these dreissenid mussel species have markedly changed freshwater ecosystems throughout North America and Europe, exerting severe ecological and economic damage. Their planktonic early life stages (eggs and larvae) are morphologically indistinguishable, yet each species exerts differential ecological effects, with the quagga often outcompeting the zebra mussel as adults. Our targeted assay analyzes genetic variation from a diagnostic sequence region of the mitochondrial (mt)DNA cytochrome oxidase I (COI) gene, to assess temporal and spatial inter- and intra-specific genetic variability. The assay facilitates analysis of environmental (e)DNA from water, early life stages from thousands of individuals, and simultaneous analysis of 50-100 tagged field-collected samples. Experiments evaluated its accuracy and performance using: (a) mock laboratory communities containing known DNA quantities per taxon, (b) aquaria with mixed-species/haplotype compositions of adults, and (c) field-collected water and plankton versus traditional sampling of adult communities. Results delineated species compositions, relative abundances, and population-level diversity differences among ecosystems, habitats, time series, and life stages from two allopatric concurrent invasions in the Great Lakes (Lake Erie) and the Hudson River, which had separate founding histories. Findings demonstrate application of this targeted assay and our approach to accurately and simultaneously discern species- and population-level differences across spatial and temporal scales, facilitating early detection and ecological understanding of biological invasions.
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http://dx.doi.org/10.1002/ece3.4985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434565PMC
March 2019

Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection.

PLoS One 2019 27;14(3):e0203012. Epub 2019 Mar 27.

NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America.

In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203012PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436794PMC
December 2019

Effects of cortisol and lipopolysaccharide on expression of select growth-, stress- and immune-related genes in rainbow trout liver.

Fish Shellfish Immunol 2018 Mar 8;74:410-418. Epub 2018 Jan 8.

Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.

Many studies have shown that stress-induced cortisol levels negatively influence growth and immunity in finfish. Despite this knowledge, few studies have assessed the direct effects of cortisol on liver immune function. Using real-time PCR, the expression of three cortisol-responsive genes (GR: glucocorticoid receptor, IGF-1: insulin-like growth factor-I and SOCS-1: suppressor of cytokine signaling-I), genes involved with innate and adaptive immunity (IL-1β: interleukin-1 beta, IgM: immunoglobin-M and Lyz: lysozyme), and liver-specific antimicrobial peptides (hepcidin and LEAP-2A: liver-expressed antimicrobial peptide-2A) was studied in vitro using rainbow trout liver slices. The abundances of GR, SOCS-1 and IGF-1 mRNAs were suppressed by cortisol treatment. Abundance of IL-1β mRNA was upregulated by LPS and suppressed by cortisol treatment in a time-dependent manner. While abundance of IgM mRNA was suppressed by cortisol treatment and stimulated by LPS, there were no effects of cortisol or LPS on abundance of Lyz mRNA. Abundance of hepcidin and LEAP-2A mRNA levels were suppressed by cortisol treatment and stimulated by LPS. These results demonstrate that cortisol directly suppresses abundance of GR, IGF-1, IL-1β, IgM, hepcidin, LEAP-2A and SOCS-1 mRNA transcripts in the rainbow trout liver. We report for the first time, a suppressive effect of cortisol (within 8 h of treatment) on hepcidin and LEAP-2A mRNAs in rainbow trout liver, which suggests that acute stress may negatively affect liver immune function in rainbow trout.
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http://dx.doi.org/10.1016/j.fsi.2018.01.003DOI Listing
March 2018

Role of Viral Hemorrhagic Septicemia Virus Matrix (M) Protein in Suppressing Host Transcription.

J Virol 2017 10 12;91(19). Epub 2017 Sep 12.

Department of Biological Sciences, The University of Toledo, Toledo, Ohio, USA

Viral hemorrhagic septicemia virus (VHSV) is a pathogenic fish rhabdovirus found in discrete locales throughout the Northern Hemisphere. VHSV infection of fish cells leads to upregulation of the host's virus detection response, but the virus quickly suppresses interferon (IFN) production and antiviral gene expression. By systematically screening each of the six VHSV structural and nonstructural genes, we identified matrix protein (M) as the virus' most potent antihost protein. Only M of VHSV genotype IV sublineage b (VHSV-IVb) suppressed mitochondrial antiviral signaling protein (MAVS) and type I IFN-induced gene expression in a dose-dependent manner. M also suppressed the constitutively active simian virus 40 (SV40) promoter and globally decreased cellular RNA levels. Chromatin immunoprecipitation (ChIP) studies illustrated that M inhibited RNA polymerase II (RNAP II) recruitment to gene promoters and decreased RNAP II C-terminal domain (CTD) Ser2 phosphorylation during VHSV infection. However, transcription directed by RNAP I to III was suppressed by M. To identify regions of functional importance, M proteins from a variety of VHSV strains were tested in cell-based transcriptional inhibition assays. M of a particular VHSV-Ia strain, F1, was significantly less potent than IVb M at inhibiting SV40/luciferase (Luc) expression yet differed by just 4 amino acids. Mutation of D62 to alanine alone, or in combination with an E181-to-alanine mutation (D62A E181A), dramatically reduced the ability of IVb M to suppress host transcription. Introducing either M D62A or D62A E181A mutations into VHSV-IVb via reverse genetics resulted in viruses that replicated efficiently but exhibited less cytotoxicity and reduced antitranscriptional activities, implicating M as a primary regulator of cytopathicity and host transcriptional suppression. Viruses must suppress host antiviral responses to replicate and spread between hosts. In these studies, we identified the matrix protein of the deadly fish novirhabdovirus VHSV as a critical mediator of host suppression during infection. Our studies indicated that M alone could block cellular gene expression at very low expression levels. We identified several subtle mutations in M that were less potent at suppressing host transcription. When these mutations were engineered back into recombinant viruses, the resulting viruses replicated well but elicited less toxicity in infected cells and activated host innate immune responses more robustly. These data demonstrated that VHSV M plays an important role in mediating both virus-induced cell toxicity and viral replication. Our data suggest that its roles in these two processes can be separated to design effective attenuated viruses for vaccine candidates.
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http://dx.doi.org/10.1128/JVI.00279-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599748PMC
October 2017

Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs.

J Environ Manage 2017 Nov 22;202(Pt 1):299-310. Epub 2017 Jul 22.

U.S. Environmental Protection Agency, Great Lakes National Program Office, Chicago, IL, 60604, USA. Electronic address:

Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.
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http://dx.doi.org/10.1016/j.jenvman.2017.07.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927374PMC
November 2017

Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes.

PLoS One 2017 18;12(5):e0177643. Epub 2017 May 18.

Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, University of Toledo, Toledo, OH, United States of America.

Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05) and high coefficients of determination (R2) for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177643PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436814PMC
September 2017

Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America.

Mol Ecol 2017 Feb 27;26(4):1075-1090. Epub 2017 Jan 27.

Great Lakes Genetics/Genomics Laboratory, The Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH, 43606, USA.

Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.
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http://dx.doi.org/10.1111/mec.13997DOI Listing
February 2017

Gene Diversification of an Emerging Pathogen: A Decade of Mutation in a Novel Fish Viral Hemorrhagic Septicemia (VHS) Substrain since Its First Appearance in the Laurentian Great Lakes.

PLoS One 2015 27;10(8):e0135146. Epub 2015 Aug 27.

ARS/USDA/University of Wisconsin at Milwaukee/School of Freshwater Sciences, Milwaukee, Wisconsin, 53204, United States of America.

Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus, which causes one of the world's most serious fish diseases, infecting >80 freshwater and marine species across the Northern Hemisphere. A new, novel, and especially virulent substrain-VHSv-IVb-first appeared in the Laurentian Great Lakes about a decade ago, resulting in massive fish kills. It rapidly spread and has genetically diversified. This study analyzes temporal and spatial mutational patterns of VHSv-IVb across the Great Lakes for the novel non-virion (Nv) gene that is unique to this group of novirhabdoviruses, in relation to its glycoprotein (G), phosphoprotein (P), and matrix (M) genes. Results show that the Nv-gene has been evolving the fastest (k = 2.0 x 10-3 substitutions/site/year), with the G-gene at ~1/7 that rate (k = 2.8 x 10-4). Most (all but one) of the 12 unique Nv- haplotypes identified encode different amino acids, totaling 26 changes. Among the 12 corresponding G-gene haplotypes, seven vary in amino acids with eight total changes. The P- and M- genes are more evolutionarily conserved, evolving at just ~1/15 (k = 1.2 x 10-4) of the Nv-gene's rate. The 12 isolates contained four P-gene haplotypes with two amino acid changes, and six M-gene haplotypes with three amino acid differences. Patterns of evolutionary changes coincided among the genes for some of the isolates, but appeared independent in others. New viral variants were discovered following the large 2006 outbreak; such differentiation may have been in response to fish populations developing resistance, meriting further investigation. Two 2012 variants were isolated by us from central Lake Erie fish that lacked classic VHSv symptoms, having genetically distinctive Nv-, G-, and M-gene sequences (with one of them also differing in its P-gene); they differ from each other by a G-gene amino acid change and also differ from all other isolates by a shared Nv-gene amino acid change. Such rapid evolutionary differentiation may allow new viral variants to evade fish host recognition and immune responses, facilitating long-time persistence along with expansion to new geographic areas.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135146PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552161PMC
May 2016

A population genetic window into the past and future of the walleye Sander vitreus: relation to historic walleye and the extinct "blue pike" S. v. "glaucus".

BMC Evol Biol 2014 06 17;14:133. Epub 2014 Jun 17.

The Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43616, USA.

Background: Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant- "blue pike" S. v. "glaucus" -described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the "blue pike".

Results: Walleye populations are distinguished by considerable genetic divergence (mean FST mtDNA = 0.32 ± 0.01, μsat = 0.13 ± 0.00) and substantial diversity across their range (mean heterozygosity mtDNA = 0.53 ± 0.02, μsat = 0.68 ± 0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the Ohio/New River population that houses the oldest haplotype and has the most pronounced divergence. Northern formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA = 0.79 ± 0.00, μsat = 0.72 ± 0.01). Genetic diversity was much less in the historic Lake Erie samples from 1923-1949 (mean heterozygosity mtDNA = 0.05 ± 0.01, μsat = 0.47 ± 0.06) than today. The historic "blue pike" had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the "blue pike".

Conclusions: Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70-90 years ago significantly differed from those today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic "blue pike" is indistinguishable from walleye, indicating that taxonomic designation is not warranted.
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http://dx.doi.org/10.1186/1471-2148-14-133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229939PMC
June 2014

Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv) with a two-color fluorometric real-time PCR assay.

PLoS One 2013 20;8(8):e71851. Epub 2013 Aug 20.

Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, United States of America.

Viral Hemorrhagic Septicemia virus (VHSv) is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR) assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02) and a linear dynamic range that spans seven orders of magnitude (R(2) = 0.99), ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6) actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071851PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748128PMC
April 2014

A new StaRT-PCR approach to detect and quantify fish Viral Hemorrhagic Septicemia virus (VHSv): enhanced quality control with internal standards.

J Virol Methods 2013 Apr 30;189(1):129-42. Epub 2013 Jan 30.

Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43616, United States.

Viral Hemorrhagic Septicemia virus (VHSv) causes one of the world's most important finfish diseases, killing >80 species across Eurasia and North America. A new and especially virulent strain (IVb) emerged in the North American Great Lakes in 2003, threatening fisheries, baitfish, and aquaculture industries. Weeks-long and costly cell culture is the OIE and USDA-APHIS approved diagnostic. A new Standardized Reverse Transcriptase Polymerase Chain Reaction (StaRT-PCR) assay that uniquely incorporates internal standards to improve accuracy and prevent false negatives was developed and evaluated for its ability to detect and quantify VHSv. Results from StaRT-PCR, SYBR(®) green real time qRT-PCR, and cell culture were compared, as well as the effects of potential PCR inhibitors (EDTA and high RNA). Findings show that StaRT-PCR is sensitive, detecting a single molecule, with 100% accuracy at six molecules, and had no false negatives. In comparison, false negatives ranged from 14 to 47% in SYBR(®) green real time qRT-PCR tests, and 47-70% with cell culture. StaRT-PCR uniquely controlled for EDTA and RNA interference. Range of VHSv quantitation by StaRT-PCR was 1.0×10(0)-1.2×10(5) VHSv/10(6)actb1 molecules in wild caught fishes and 1.0×10(0)-8.4×10(5) molecules in laboratory challenged specimens. In the latter experiments, muskellunge with skin lesions had significantly more viral molecules (mean=1.9×10(4)) than those without (1.1×10(3)) (p<0.04). VHSv infection was detected earlier in injection than in immersion challenged yellow perch (two versus three days), with molecule numbers in both being comparable and relatively consistent over the remaining course of the experiment. Our results show that the StaRT-PCR test accurately and reliably detects and quantifies VHSv.
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http://dx.doi.org/10.1016/j.jviromet.2013.01.006DOI Listing
April 2013

Waterscape genetics of the yellow perch (Perca flavescens): patterns across large connected ecosystems and isolated relict populations.

Mol Ecol 2012 Dec 18;21(23):5795-826. Epub 2012 Oct 18.

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH 43616, USA.

Comparisons of a species' genetic diversity and divergence patterns across large connected populations vs. isolated relict areas provide important data for understanding potential response to global warming, habitat alterations and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns, because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and/or from contemporary anthropogenic perturbations. Our research objective is to better understand the interplay between historic influences and modern-day factors (fishery exploitation, stocking supplementation and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. We employ a modified landscape genetics approach, analysing sequences from the entire mitochondrial DNA control region and 15 nuclear DNA microsatellite loci of 664 spawning adults from 24 populations. Results support that perch from primary glacial refugium areas (Missourian, Mississippian and Atlantic) founded contemporary northern populations. Genetic diversity today is highest in southern (never glaciated) populations and also is appreciable in northern areas that were founded from multiple refugia. Divergence is greater among isolated populations, both north and south; the southern Gulf Coast relict populations are the most divergent, reflecting their long history of isolation. Understanding the influence of past and current waterway connections on the genetic structure of yellow perch populations may help us to assess the roles of ongoing climate change and habitat disruptions towards conserving aquatic biodiversity.
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http://dx.doi.org/10.1111/mec.12044DOI Listing
December 2012

Evolution and biogeography of an emerging quasispecies: diversity patterns of the fish Viral Hemorrhagic Septicemia virus (VHSv).

Mol Phylogenet Evol 2012 May 11;63(2):327-41. Epub 2012 Jan 11.

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Road, Oregon, OH 43616, USA.

Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus that causes one of the most important finfish diseases, affecting over 70 marine and freshwater species. It was discovered in European cultured fish in 1938 and since has been described across the Northern Hemisphere. Four strains and several substrains have been hypothesized, whose phylogenetic relationships and evolutionary radiation are evaluated here in light of a quasispecies model, including an in-depth analysis of the novel and especially virulent new substrain (IVb) that first appeared in the North American Laurentian Great Lakes in 2003. We analyze the evolutionary patterns, genetic diversity, and biogeography of VHSv using all available RNA sequences from the glycoprotein (G), nucleoprotein (N), and non-virion (Nv) genes, with Maximum Likelihood and bayesian approaches. Results indicate that the G gene evolves at an estimated rate of μ=2.58×10(-4) nucleotide substitutions per site per year, the N gene at μ=4.26×10(-4), and Nv fastest at μ=1.25×10(-3). Phylogenetic trees from the three genes largely are congruent, distinguishing strains I-IV as reciprocally monophyletic with high bootstrap and posterior probability support. VHSv appears to have originated from a marine ancestor in the North Atlantic Ocean, diverging into two primary clades: strain IV in North America (the Northwestern Atlantic Ocean), and strains I-III in the Northeastern Atlantic region (Europe). Strain II may comprise the basal group of the latter clade and diverged in Baltic Sea estuarine waters; strains I and III appear to be sister groups (according to the G and Nv genes), with the former mostly in European freshwaters and the latter in North Sea marine/estuarine waters. Strain IV is differentiated into three monophyletic substrains, with IVa infecting Northeastern Pacific salmonids and many marine fishes (with 44 unique G gene haplotypes), IVb endemic to the freshwater Great Lakes (11 haplotypes), and a newly-designated IVc in marine/estuarine North Atlantic waters (five haplotypes). Two separate substrains independently appeared in the Northwestern Pacific region (Asia) in 1996, with Ib originating from the west and IVa from the east. Our results depict an evolutionary history of relatively rapid population diversifications in star-like patterns, following a quasispecies model. This study provides a baseline for future tracking of VHSv spread and interpreting its evolutionary diversification pathways.
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http://dx.doi.org/10.1016/j.ympev.2011.12.024DOI Listing
May 2012

Microsatellite loci for dreissenid mussels (Mollusca: Bivalvia: Dreissenidae) and relatives: markers for assessing exotic and native populations.

Mol Ecol Resour 2011 Jul 1;11(4):725-32. Epub 2011 Apr 1.

Field Museum, 1400 S Lake Shore Dr, Chicago, IL 60605, USA.

We developed and tested 14 new polymorphic microsatellite loci for dreissenid mussels, including the two species that have invaded many freshwater habitats in Eurasia and North America, where they cause serious industrial fouling damage and ecological alterations. These new loci will aid our understanding of their genetic patterns in invasive populations as well as throughout their native Ponto-Caspian distributions. Eight new loci for the zebra mussel Dreissena polymorpha polymorpha and six for the quagga mussel D. rostriformis bugensis were compared with new results from six previously published loci to generate a robust molecular toolkit for dreissenid mussels and their relatives. Taxa tested include D. p. polymorpha, D. r. bugensis, D. r. grimmi, D. presbensis, the 'living fossil'Congeria kusceri, and the dark false mussel Mytilopsis leucophaeata (the latter also is invasive). Overall, most of the 24 zebra mussel (N = 583) and 13 quagga mussel (N = 269) population samples conformed to Hardy-Weinberg equilibrium expectations for the new loci following sequential Bonferroni correction. The 11 loci (eight new, three previously published) evaluated for D. p. polymorpha averaged 35.1 alleles and 0.72 mean observed heterozygosity per locus, and 25.3 and 0.75 for the nine loci (six new, three previously published) developed for D. r. bugensis. All but three of these loci successfully amplified the other species of Dreissena, and all but one also amplified Congeria and Mytilopsis. All species and populations tested were significantly divergent using the microsatellite data, with neighbour-joining trees reflecting their evolutionary relationships; our results reveal broad utility for resolving their biogeographic, evolutionary, population and ecological patterns.
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http://dx.doi.org/10.1111/j.1755-0998.2011.03012.xDOI Listing
July 2011

Systematics of the greenside darter Etheostoma blennioides complex: consensus from nuclear and mitochondrial DNA sequences.

Mol Phylogenet Evol 2010 Oct 1;57(1):434-47. Epub 2010 Jul 1.

Lake Erie Center and Department of Environmental Sciences, University of Toledo, Toledo, OH 43616, USA.

The phylogenetic systematic relationships of the enigmatic greenside darter Etheostoma blennioides complex are analysed using sequences from the mitochondrial (mt) DNA cytochrome b gene and nuclear S7 ribosomal protein intron 1 from putative members of the complex, close relatives, and outgroups (totaling 421 individuals). We compare results from Bayesian and maximum likelihood analysis approaches and a variety of rooting and taxon inclusion scenarios, and include all putative subspecies and intergrade taxa for a new comprehensive analysis. Results reveal that nuclear and mtDNA data congruently, under all scenarios and approaches tested, define a highly-supported restricted greenside darter complex comprising three putative subspecies: E. b. blennioides, E. b. pholidotum, and part of E. b. newmanii (excepting those from the Tennessee/Hiwassee River clade). Within this redefined E. blennioides, only a single putative subspecies -E. b. blennioides - is monophyletic in the mtDNA trees, and none are monophyletic in the nuclear DNA trees. Nuclear and mtDNA results support E. gutselli as a separate species and suggest that the Tennessee/Hiwassee River clade of "E. b. newmanii" also may constitute a separate species (provisionally "E. newmanii"), with neither being a part of our redefined E. blennioides complex. The nuclear DNA trees depict the two as highly-supported divergent clades, but the mtDNA results group them together as a single clade, indicating introgression. Future study with greater sample sizes in the southern watersheds, coupling morphological analyses with additional nuclear gene phylogenies, is recommended to further investigate the relationships within the greenside darter complex.
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http://dx.doi.org/10.1016/j.ympev.2010.06.017DOI Listing
October 2010

Escape from the Ponto-Caspian: evolution and biogeography of an endemic goby species flock (Benthophilinae: Gobiidae: Teleostei).

Mol Phylogenet Evol 2009 Jul;52(1):84-102

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Rd., Toledo, OH 43618, USA

Endemic Ponto-Caspian gobies include a flock of 24 "neogobiin" species (containing the nominal genera and subgenera Apollonia, Babka, Neogobius, Mesogobius, Ponticola, and Proterorhinus; Teleostei: Gobiidae), of which a large proportion (5 species; 21%) recently escaped to invade other freshwater Eurasian systems and the North American Great Lakes. We provide its first comprehensive phylogenetic and biogeographic analysis based on 4709 bp sequences from two mitochondrial and two nuclear genes with maximum parsimony, likelihood, and Bayesian approaches. We additionally compare its relationships with the tadpole gobies (Benthophilus and Caspiosoma), which comprise a related endemic Ponto-Caspian gobiid group; along with a variety of postulated relatives and outgroups. Results of all phylogenetic approaches are highly congruent and provide very strong support for recognizing the subfamily Benthophilinae; which encompasses both the "neogobiins" and tadpole gobies, and genetically diverges from other Gobiidae subfamilies-including (non-monophyletic) Gobiinae and Gobinellinae. Benthophilinae contains three tribes: Neogobiini (Neogobius, which is synonymized here with Apollonia; containing the type species N. fluviatilis, along with N. melanostomus and N. caspius), Ponticolini (containing the genera Mesogobius, Proterorhinus, Babka, and Ponticola-elevating the latter two from subgenera and removing them from the formerly paraphyletic Neogobius), and Benthophilini (tadpole gobies). Within Ponticolini, Proterorhinus and Mesogobius comprise the sister clade of the Ponticola and Babka clade. Further work is needed to clarify the interrelationships of the tadpole gobies. Invasiveness is widespread in freshwater and euryhaline taxa of Neogobius, Proterorhinus, Babka, and Ponticola; but not in marine species, Mesogobius, or tadpole gobies.
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http://dx.doi.org/10.1016/j.ympev.2008.12.023DOI Listing
July 2009

Microsatellite loci for Ponto-Caspian gobies: markers for assessing exotic invasions.

Mol Ecol Resour 2009 Mar 31;9(2):639-44. Epub 2009 Jan 31.

Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA Lake Erie Center and the Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA.

We developed and tested eight polymorphic microsatellite loci for Ponto-Caspian 'neogobiin' gobies, many of which are invasive in Eurasia and North America, whose study will aid understanding of the population genetics underlying their success. We tested samples from one to two locations from 12 taxa in the recently revised genera Babka, Benthophilus, Mesogobius, Neogobius = Apollonia, Ponticola and Proterorhinus; including the bighead, Caspian, knout, monkey, racer, round, tadpole and tubenose gobies; and taxa from introduced vs. native populations, those diverging between fresh and marine waters, and those differentiated between the Black and Caspian Seas. Populations conformed to Hardy-Weinberg equilibrium expectations, averaging five to 15 alleles per locus and 0.11 to 0.67 mean heterozygosity. Allelic variation significantly differentiated among all taxa and populations.
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http://dx.doi.org/10.1111/j.1755-0998.2008.02495.xDOI Listing
March 2009

Invasion genetics of the Eurasian round goby in North America: tracing sources and spread patterns.

Mol Ecol 2009 Jan;18(1):64-79

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Rd, Toledo, OH 43618, USA.

The Eurasian round goby Neogobius melanostomus (Apollonia melanostoma) invaded the North American Great Lakes in 1990 through ballast water, spread rapidly, and now is widely distributed and moving through adjacent tributaries. We analyse its genetic diversity and divergence patterns among 25 North American (N = 744) and 22 Eurasian (N = 414) locations using mitochondrial DNA cytochrome b gene sequences and seven nuclear microsatellite loci in order to: (i) identify the invasion's founding source(s), (ii) test for founder effects, (iii) evaluate whether the invasive range is genetically heterogeneous, and (iv) determine whether fringe and central areas differ in genetic diversity. Tests include F(ST) analogues, neighbour-joining trees, haplotype networks, Bayesian assignment, Monmonier barrier analysis, and three-dimensional factorial correspondence analysis. We recovered 13 cytochrome b haplotypes and 232 microsatellite alleles in North America and compared these to variation we previously described across Eurasia. Results show: (i) the southern Dnieper River population was the primary Eurasian donor source for the round goby's invasion of North America, likely supplemented by some alleles from the Dniester and Southern Bug rivers, (ii) the overall invasion has high genetic diversity and experienced no founder effect, (iii) there is significant genetic structuring across North America, and (iv) some expansion areas show reduced numbers of alleles, whereas others appear to reflect secondary colonization. Sampling sites in Lake Huron's Saginaw Bay and Lake Ontario significantly differ from all others, having unique alleles that apparently originated from separate introductions. Substantial genetic variation, multiple founding sources, large number of propagules, and population structure thus likely aided the goby's ecological success.
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http://dx.doi.org/10.1111/j.1365-294X.2008.04014.xDOI Listing
January 2009

Molecular, morphological, and biogeographic resolution of cryptic taxa in the Greenside Darter Etheostoma blennioides complex.

Mol Phylogenet Evol 2008 Oct 29;49(1):69-83. Epub 2008 Jul 29.

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA.

The systematic identity and genetic divergence of cryptic taxa and morphological subspecies in the Greenside Darter Etheostoma blennioides complex are analyzed from mitochondrial and nuclear DNA sequence data, along with morphological characters. We sequenced the mtDNA cytochrome b gene and control region and is the nuclear S7 intron 1 for 345 Greenside Darters from 19 locations across their distribution including areas of sympatry and allopatry, in comparison to putative sister species and relatives. Results provide the first genetic evidence that E. gutselli is a separate species and is the sister species of E. blennius, which together with E. rupestre comprise the sister group to the Greenside Darter complex; separating approximately 4.0 mya. MtDNA results show that the complex comprises 6 clades and supports only the morphological subspecies Etheostoma blennioides blennioides, distinguished by theta(ST)=0.94, approximately 1.7 my, scale counts, and ventral squamation. The former E. b. pholidotum and E. b. newmanii are polyphyletic and are invalid taxa, together comprising 5 differentiated clades that diverged approximately 0.90-1.7 mya. Nuclear DNA results recover some of the mtDNA clades, which are distinguished morphologically by subtle meristic count differences. Populations of E. b. blennioides genetically diverge, with diversity increasing to the southwest; attributed to restricted gene flow and genetic isolation with geographic distance. Samples of the former E. b. pholidotum from the Great Lakes/Wabash River clade are less divergent, with diversity increasing to the southwest, reflecting allopatric fragmentation and isolation by distance.
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http://dx.doi.org/10.1016/j.ympev.2008.07.013DOI Listing
October 2008

Ancient divisions, recent expansions: phylogeography and population genetics of the round goby Apollonia melanostoma.

Mol Ecol 2008 Jun 2;17(11):2598-615. Epub 2008 May 2.

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA.

During the past two decades, the round goby Apollonia melanostoma (=Neogobius melanostomus) has expanded its range via shipping transport and canals, extending north and west from the Ponto-Caspian region of Eurasia and to the North American Great Lakes. Exotic populations of the round goby have been very successful in the Baltic Sea and the Great Lakes regions, exerting significant ecological changes. Our study evaluates the population genetic and biogeographical structure of the round goby across its native and nonindigenous ranges, in light of geological history and its expansion pathways. We analyzed seven new nuclear microsatellite loci and mitochondrial DNA cytochrome b gene sequences from 432 individuals in 22 locations. Population structure was tested using F(ST)-analogs, phylogenetic trees, clustering diagrams, Bayesian assignment tests and nested clade analyses. Results show that native populations in the Black vs. the Caspian Sea basins diverge by 1.4% and c. 350,000 years, corresponding to closure of their prior connections and supporting the taxonomic separation of the Black Sea A. m. melanostoma from the Caspian Sea A. m. affinis. Their within-basin populations diverge by approximately 0.4% and 100,000 years. Nonindigenous populations in the Baltic Sea and Danube and Dnieper Rivers trace to separate northern Black Sea origins, whereas the upper Volga River system houses mixed populations of A. m. melanostoma and A. m. affinis. Native populations average twice the genetic diversity of most exotic sites; however, sites in the Volga River system have high diversity due to mixing of the two taxa. Our results highlight how vicariance and anthropogenic disturbances have shaped a rapidly expanding species' genetic heritage.
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http://dx.doi.org/10.1111/j.1365-294X.2008.03777.xDOI Listing
June 2008

Broad- to fine-scale population genetic patterning in the smallmouth bass Micropterus dolomieu across the Laurentian Great Lakes and beyond: an interplay of behaviour and geography.

Mol Ecol 2007 Apr;16(8):1605-24

Great Lakes Genetics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA.

Analysis of population genetic relationships reveals the signatures of current processes such as spawning behaviour and migration, as well as those of historical events including vicariance and climate change. This study examines these signatures through testing broad- to fine-scale genetic patterns among smallmouth bass Micropterus dolomieu spawning populations across their native Great Lakes range and outgroup areas, with fine-scale concentration in Lake Erie. Our primary hypotheses include whether genetic patterns result from behavioural and/or geographical isolation, specifically: (i) Are spawning groups in interconnected waterways genetically separable? (ii) What is the degree of isolation across and among lakes, basins, and tributaries? (iii) Do genetic divergences correspond to geographical distances? and (iv) Are historical colonization patterns from glacial refugia retained? Variation at eight nuclear microsatellite DNA loci are analysed for 666 smallmouth bass from 28 locations, including 425 individuals in Lake Erie; as well as Lakes Superior, Huron, and Ontario, and outgroups from the Mississippi, Ohio, St. Lawrence, and Hudson River drainages. Results reveal marked genetic differences among lake and river populations, as well as surprisingly high divergences among closely spaced riverine sites. Results do not fit an isolation-by-geographical-distance prediction for fine-scale genetic patterns, but show weak correspondence across large geographical scales. Genetic relationships thus are consistent with hypotheses regarding divergent origins through vicariance in glacial refugia, followed by colonization pathways establishing modern-day Great Lakes populations, and maintenance through behavioural site fidelity. Conservation management practices thus should preserve genetic identity and unique characters among smallmouth bass populations.
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http://dx.doi.org/10.1111/j.1365-294X.2006.03168.xDOI Listing
April 2007

Genetic diversity of invasive species in the Great Lakes versus their Eurasian source populations: insights for risk analysis.

Risk Anal 2005 Aug;25(4):1043-60

Lake Erie Center and Department of Earth, Ecological and Environmental Sciences, The University of Toledo, Toledo, OH 43618, USA.

Combining DNA variation data and risk assessment procedures offers important diagnostic and monitoring tools for evaluating the relative success of exotic species invasions. Risk assessment may allow us to understand how the numbers of founding individuals, genetic variants, population sources, and introduction events affect successful establishment and spread. This is particularly important in habitats that are "hotbeds" for invasive species--such as the North American Great Lakes. This study compares genetic variability and its application to risk assessment within and among three Eurasian groups and five species that successfully invaded the Great Lakes during the mid 1980s through early 1990s; including zebra and quagga mussels, round and tubenose gobies, and the ruffe. DNA sequences are compared from exotic and native populations in order to evaluate the role of genetic diversity in invasions. Close relatives are also examined, since they often invade in concert and several are saline tolerant and are likely to spread to North American estuaries. Results show that very high genetic diversity characterizes the invasions of all five species, indicating that they were founded by very large numbers of propagules and underwent no founder effects. Genetic evidence points to multiple invasion sources for both dreissenid and goby species, which appears related to especially rapid spread and widespread colonization success in a variety of habitats. In contrast, results show that the ruffe population in the Great Lakes originated from a single founding population source from the Elbe River drainage. Both the Great Lakes and the Elbe River populations of ruffe have similar genetic diversity levels--showing no founder effect, as in the other invasive species. In conclusion, high genetic variability, large numbers of founders, and multiple founding sources likely significantly contribute to the risk of an exotic species introduction's success and persistence.
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http://dx.doi.org/10.1111/j.1539-6924.2005.00655.xDOI Listing
August 2005
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