Carol A Stepien

Smithsonian Institution National Museum of Natural History

The Third U.S. National Marine Environmental DNA Workshop on June 2–5, 2024 brought together researchers, practitioners, and policymakers to overview and discuss: (1) environmental (e)DNA – defined as “DNA in the environment” – as a strategic U.S. national priority, (2) eDNA tool readiness and approaches to support decision-making, (3) emerging eDN...

The Third U.S. National Marine Environmental DNA Workshop on June 2–5, 2024 brought together researchers, practitioners, and policymakers to overview and discuss: (1) environmental (e)DNA – defined as “DNA in the environment” – as a strategic U.S. national priority, (2) eDNA tool readiness and approaches to support decision-making, (3) emerging eDN...

Paetulunio fabalis (formerly Villosa fabalis) has experienced a significant reduction in its range and is listed as endangered in both the USA and Canada. Little life history or demographic information exists for the species, but such data are critical for effective conservation. We sampled four streams in the Lake Erie and Ohio River systems of th...

Walleye is an important sportfish across eastern North America, is commercially fished in the Laurentian Great Lakes region, and has been introduced outside its native range. Thirty-eight Walleye populations within six watersheds across the Eastern Highlands and other portions of the native range were screened at eight microsatellite DNA loci to be...

Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time-consuming, require taxonomic expertise, and are hampered by a lack of diagnostic characters, particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison...

Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time consuming, require taxonomic expertise, and are hampered by lack of diagnostic characters –particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison t...

Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time consuming, require taxonomic expertise, and are hampered by lack of diagnostic characters –particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison t...

The 6th annual Environmental DNA (eDNA) Technical Exchange Workshop was a virtual workshop hosted and coordinated by the Government eDNA Working Group (GEDWG) on January 24–26, 2023. GEDWG is a no‐cost consortium that focuses on bringing together stakeholders associated with federal, state, provincial, municipal, and other government and non‐govern...

Otoliths (ear stones) of the inner ears of teleost fishes, which develop independently from the skeleton and are functionally associated with hearing and the sense of equilibrium, have significantly contributed to contemporary understanding of teleost fish systematics and evolutionary diversity. The sagittal otolith is of particular interest, since...

Background Aquatic invertebrate species that have broad salinity tolerances may be pre-adapted for invasion success and biogeographic distributional range expansions, facilitated by human-mediated dispersal (HMD), leading to a trend to become neocosmopolitan across many regions of the world. This pattern appears to characterize many Ponto-Caspian (...

The Second National Workshop on Environmental DNA was held on September 12–15, 2022, at the Southern California Coastal Water Research Project (SCCWRP) in Southern California and was focused on transitioning eDNA from research to management applications. The Workshop was attended by 150 people in‐person and an additional 200 more online. Workshop a...

An evidence-based annotated checklist of gobiid species (Teleostei: Gobiidae) inhabiting the South Caspian Sea and its catchment area (i.e., the South Caspian Sea sub-basin) is compiled. The South Caspian Sea sub-basin gobiofauna currently comprises 38 confirmed species in 11 genera (i.e., 88.4% of the Caspian gobiofauna); the most diverse genus is...

The taxonomic status and phylogenetic relationships of the Deepwater Goby, Ponticola bathybius, an endemic species in the southern Caspian Sea, which were previously unknown, are examined here. Deepwater Goby samples were collected from three southern Caspian Sea localities (southwest, mid-south, and southeast), and phylogenetic analyses were condu...

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 inte...

Genogroup -IVb of the generalist Piscine novirhabdovirus, viral haemorrhagic septicaemia virus (VHSV), resulted in fatalities of >32 fish species in the Great Lakes since its appearance in 2003. The largest mortality outbreaks occurred in 2005 and 2006, followed by periods of apparent dormancy and with punctuated smaller and more geographically-res...

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 geographic...

Traditional taxonomic analysis of zooplankton is time consuming, expensive, and unable to resolve the true species diversity of a community due to a lack of diagnostic morphological characters for many taxa. This is especially true for early life stages, undescribed, and cryptic species. This limitation has led to a dramatic under-estimation of the...

Genetic compositions and comparative diversity of zebra (Dreissena polymorpha) and quagga (D. rostriformis) mussel populations are compared across their three decade-long histories as invasive species in the Hudson River and Lake Erie of North America. We analyze 15 nuclear DNA microsatellite loci for the zebra mussel and 10 for the quagga mussel....

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 inte...

Evaporation (E) 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 E 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 Lak...

This book contains topics on the role of climatic factors on the epidemiology, prevalence, distribution, prevention and control of fish diseases. The 25 chapters that are divided into three main parts that discuss freshwater ecosystems and biological sequestrations of atmospheric carbon dioxide; microbial diseases (viral, bacterial and fungal infec...

Piscine novirhabdovirus = 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 teste...

Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are pr...

Species compositions and diversity levels of aquatic macroinvertebrate communities provide important indicators of ecosystem health. However, such community analyses typically are limited by time and effort of sampling, sorting, and identifications, as well as morphological character uncertainty for some taxa, especially at early life stages. Our o...

Bait and pond stores comprise potential, yet poorly understood, vectors for aquatic invasive species (AIS). We tested for AIS and illegal native species in 51 bait and 21 pond stores from the central Great Lakes (Lake Erie, Ohio and Lake St. Clair, Michigan) and the adjacent Wabash River (Indiana) using environmental DNA (eDNA) metabarcode assays o...

Viral Hemorrhagic Septicemia Virus (VHSV) (Piscine novirhabdovirus) appeared in the Laurentian Great Lakes in 2005, constituting a unique and highly virulent genogroup (IVb), which killed >32 fish species in large 2005 and 2006. Periods of apparent dormancy punctuated smaller outbreaks in 2007, 2008, and 2017. We conducted the first whole genome an...

Walleye (Sander vitreus) is a popular sportfish threatened by overexploitation, habitat destruction, and loss of genetic integrity due to non-native walleye stocking. Previous studies have identified a genetically distinct lineage of walleye in the Mobile River Basin, but further work is needed to assess population structure and introgression among...

This paper uses metabarcode assays to detect and identify cryptic invasive species that are accidentally being sold as bait or by pond stores.

The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human acti...

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...

Additional samples, GenBank Accession numbers, species, population locations, gene regions, and haplotypes (Hap) included in our mtDNA sequence analyses. (DOCX)

S7 nuclear ribosomal protein gene, intron 1, partial sequence haplotypes of silver carp. Nucleotide (nt) positions and substitutions, based on alignment to GenBank Accession AY325777 S7-“1” reference sequence, with dots indicating congruence with S7-“1”. Dashes denote sequence deletion (indels). Variants are GenBank Accessions MH938813–43. (DOCX)

MtDNA sequence alignment of the invasive carp HTS assay region. Alignment shows silver carp (SVC) haplotypes “A–H”, and two “novel” haplotypes “N1” and “N2” recovered with the targeted HTS assay (GenBank Accessions: MK205185–6), bighead carp (BHC), and other invasive cyprinid sequences. Nucleotide positions (above sequence) are based on the complet...

Summary of targeted assay high throughput sequencing run output for targeted invasive carp HTS assay from 48 bait shops in the Lake Erie, Lake St. Clair, and Wabash River watersheds. Raw sequence reads, trimmed reads (had both primers and were the correct length), the number and percent that DADA2 successfully merged for all samples and those havin...

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 devel...

This protocol describes the data collection and analysis performed in "Invasion genetics of the silver carp (Hypophthalmichthys molitrix) across North America: Differentiation of fronts, introgression, and eDNA detection". Published in PLOS One, 2018. The invasive silver carp Hypophthalmichthys molitrix escaped from southern U.S. aquaculture during...

Few investigations have examined whether population genetic changes occur over the course of nonindigenous species invasions, which would facilitate understanding their trajectories and ecological successes. The Eurasian ruffe fish Gymnocephalus cernua unintentionally was introduced from ballast water released into western Lake Superior of the Nort...

The invasive silver carp Hypophthalmichthys molitrix escaped from southern U.S. aquaculture during the 1970s to spread throughout the Mississippi River basin and steadily moved northward, now reaching the threshold of the Laurentian Great Lakes. The silver carp is native to eastern Asia and is a large, prolific filter-feeder that decreases food ava...

Spawning site philopatry may lead to genetic differentiation among reproductive populations, despite their locations being in close proximity in single bodies of water. Identifying and maintaining locally differentiated spawning groups of Walleye Sander vitreus constitute an agency management priority of the multi‐agency Walleye Task Group advisory...

Landmark-based geometric morphometric and meristic characters were used to explore morphological variation among three population samples of deepwater goby, Ponticola bathybius, (Family Gobiidae) along the southern Caspian Sea in Iran. Morphological differences were studied using the geometric morphometric method of thin-plate splines and multivari...

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 in finfish. Using real-time PCR, the expression of three cortisol-responsive genes (GR: glucocorticoid receptor, IGF-1: insulin-lik...

Few investigations have examined whether population genetic changes occur over the course of nonindigenous species invasions, which would facilitate understanding their trajectories and ecological successes. The Eurasian ruffe fish Gymnocephalus cernua unintentionally was introduced from ballast water released into western Lake Superior of the Nort...

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...

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 ea...

For more than a decade the Laurentian Great Lakes region of North America has hosted a unique Viral Hemorrhagic Septicemia virus (VHSV) genotype -IVb. Mortality outbreaks affected up to 32 fish species between 2005-2009, when several new haplotypes emerged approximating a “quasi-species” distribution pattern. Thirty-seven sites were investigated be...

Viral Hemorrhagic Septicemia virus (VHSV) first appeared in the Great Lakes basin as a novel strain (IVb) in 2003, killing ~32 fish species in outbreaks between 2005-09. After the initial outbreaks, many new haplotypes have evolved approximating a “quasi-species” evolutionary pattern. Thirty-seven sites were surveyed in 2015-16, from which 2561 ind...

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 li...

List of targeted species for the Sphaeriidae SPH16S assay. * indicates invasive species whose extractions were used to test primers in vitro. Ŧ indicates native or non-invasive species also used to test primers. Parentheses indicate unique OTUs for the SPH16S amplicon, the number inside the parentheses represents the number of sequences belonging t...

Collection information for each of the samples used for the mock communities and primer design. (DOCX)

Number of reads, merged reads and exact match trimmed reads of the mock community samples. (DOCX)

Number of reads per OTU identified below 97% similarity via BLAST search of aquaria samples. (DOCX)

Excel file of the Ohio EPA Maumee River sample data. (XLSX)

Number of reads per OTU identified below 97% similarity via BLAST search of Maumee River samples. (DOCX)

Collection information for additional samples used for primer design. (DOCX)

Number of reads, merged reads and processed reads of the eDNA samples. (DOCX)

Genetic diversity and divergence patterns of smallmouth bass Micropterus dolomieu spawning groups are analysed across its northern native range with mtDNA cytochrome b gene sequences and eight unlinked nuclear DNA microsatellite loci. Results reveal high levels of genetic variability and significant differences in allelic representation among popul...

Lakes are important components for regulating carbon cycling within landscapes. Most lakes are regarded as CO 2 sources to the atmosphere, except for a few eutrophic ones. Algal blooms are common phenomena in many eutrophic lakes and can cause many environmental stresses, yet their effects on the net exchange of CO 2 (F CO2) at large spatial scales...

University field stations are located off site from the main campuses and frequently in a natural setting, providing opportunity for students, faculty, and the public to engage with-and appreciate-local ecosystems. Their missions usually encompass the three cornerstones of environmental research, education, and outreach/community engagement, which...

Analyses of genetic variability and allelic composition in a species exhibiting reproductive fidelity to natal sites may provide important ecological indication of temporal population dynamics, facilitating understanding responses to past disturbances and future climate change. The walleye is an ecologically and economically valuable species, whose...

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...

The present study analyzed the distribution routes of the invasive Chinese sleeper (Perccottus glenii Dybowski, 1877) and its parasites, focusing on the Carpathian region of Europe. The invasive Chinese sleeper was sampled using beach seines from two rivers in Ukraine, then assessed for parasites. Published data about its parasites in Central and E...

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 k...

The parasitic fauna in the lower Volga River basin was investigated for four gobiid species: the nonindigenous monkey goby Neogobius fluviatilis (Pallas, 1814), the round goby N. melanostomus (Pallas, 1814), the Caspian bighead goby Ponticola gorlap (Iljin, 1949), and the tubenose goby Proterorhinus cf. semipellucidus (Kessler, 1877). In total, 19...