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SFS Annual Meeting

Wednesday, May 22, 2019
09:00 - 10:30

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09:15 - 09:30: / 254 B NOVEL ENVIRONMENTAL DNA METHODS FOR MONITORING POPULATION GENETICS OF AN INVASIVE SPECIES

5/22/2019  |   09:15 - 09:30   |  254 B

NOVEL ENVIRONMENTAL DNA METHODS FOR MONITORING POPULATION GENETICS OF AN INVASIVE SPECIES Environmental DNA (eDNA) methods are well established for detecting species presence and biodiversity, yet little research has been conducted using these methods to obtain population-level genetic information on aquatic species. In this study, we developed an approach using eDNA methods to detect intraspecific diversity at multiple nuclear microsatellite markers in an invasive species and compared these methods to traditional tissue-derived genetic estimates in mesocosm experiments and field collections. Microsatellite allele frequencies from eDNA accurately reflected allele frequencies from genotyped round goby tissue samples, indicating population genetic parameters can be reliably estimated with eDNA methods. This study is the first to document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information from environmental samples. Such an approach has the potential to revolutionize our ability to characterize populations where conventional sampling strategies may be biased or cost-prohibitive, and broadens the application of eDNA methodologies to inform population-level management objectives.

Suresh Sethi (Co-Presenter/Co-Author), Cornell University, suresh.sethi@cornell.edu;


David Lodge (Co-Presenter/Co-Author), Cornell University, dml356@cornell.edu;


Jose Andres (Co-Presenter/Co-Author), Cornell University, jaa53@cornell.edu;


Kara Andres (Primary Presenter/Author), Cornell University, kja68@cornell.edu;


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09:30 - 09:45: / 254 B PHYLOGEOGRAPHY AND POPULATION GENETICS OF A HEADWATER SPECIALIST, CAMBARUS PRISTINUS (DECAPODA: CAMBARIDAE) FROM THE CUMBERLAND PLATEAU IN TENNESSEE

5/22/2019  |   09:30 - 09:45   |  254 B

PHYLOGEOGRAPHY AND POPULATION GENETICS OF A HEADWATER SPECIALIST, CAMBARUS PRISTINUS (DECAPODA: CAMBARIDAE) FROM THE CUMBERLAND PLATEAU IN TENNESSEE Habitat loss and fragmentation represent significant threats to North American crayfish diversity. Understanding genetic diversity can aid conservation decisions by assessing impacts from habitat fragmentation and identifying historical and contemporary factors contributing to geographic structure. Our objective is to examine variation in mitochondrial DNA (COI) and alleles (microsatellites) to provide estimates of phylogeographic relationships and contemporary levels of genetic structure within Cambarus pristinus, a species of conservation concern and habitat specialist endemic to the Cumberland Plateau in Tennessee. We detected 12 haplotypes and recovered two independent haplotype networks that differed by 11 mutations. One network included the nominal form of C. pristinus; the second included the long-recognized, but undescribed “Sequatchie” form. These were recovered as separate, well-supported clades, indicating long-standing isolation between the forms and supporting recognition of the “Sequatchie” form as a distinct taxon. Lack of definable geographic structure within the nominal form suggests historic connectivity of those populations. An ongoing assessment of genotypic data will examine contemporary connectivity and diversity in the nominal form. Using historical and contemporary perspectives will provide a robust baseline for effective conservation actions.

John Johansen (Co-Presenter/Co-Author), Austin Peay State University, johansenj@apsu.edu;


Rebecca Blanton Johansen (Co-Presenter/Co-Author), Austin Peay State University, Center of Excellence in Field Biology, Clarksville, TN, johansenr@apsu.edu;


Brooke Grubb (Primary Presenter/Author), Austin Peay State University, Center of Excellence in Field Biology, Clarksville, TN, bgrubb@my.apsu.edu;


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09:45 - 10:00: / 254 B BENTHIC MACROINVERTEBRATE COMMUNITIES ACROSS THE NEON OBSERVATORY: USING METABARCODE AND MORPHOLOGICAL TAXONOMY DATA TO ASSESS TRENDS

5/22/2019  |   09:45 - 10:00   |  254 B

BENTHIC MACROINVERTEBRATE COMMUNITIES ACROSS THE NEON OBSERVATORY: USING METABARCODE AND MORPHOLOGICAL TAXONOMY DATA TO ASSESS TRENDS The National Ecological Observatory Network (NEON) is research platform designed to assess the effects of ecological change on ecosystems across North America. NEON’s aquatic program includes of a suite of instrument and observational data collected at 34 sites: 24 wadeable streams, 7 lakes, and 3 large rivers ranging from Puerto Rico to Alaska. Benthic macroinvertebrate samples are collected three times per year (spring, summer, and fall) at all NEON aquatic sites. Benthic macroinvertebrate samples are collected using quantitative methods for morphological taxonomic analysis, while a second set of samples are collected at the same time and location for metabarcode analysis. Morphological taxonomy samples are processed and identified to the lowest practical taxonomic level. Metabarcode samples are homogenized prior to DNA extraction, and two fragments of the COI gene are PCR-amplified and Illumina sequenced. NEON morphological taxonomy data are publically available and hosted on the NEON data portal, while sequence data are hosted on MG-RAST. DNA extracts are stored at the NEON bioarchive facility for further use by the community. These data and archived samples are a novel resource that will enable analyses over large spatial and temporal scales.

Stephanie Parker (Primary Presenter/Author), NEON/Battelle, sparker@battelleecology.org;


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10:00 - 10:15: / 254 B ONE FISH, TWO FISH: EDNA AS A QUANTITATIVE TOOL

5/22/2019  |   10:00 - 10:15   |  254 B

ONE FISH, TWO FISH: eDNA AS A QUANTITATIVE TOOL Environmental DNA (eDNA) is an emerging tool for the detection of rare and elusive aquatic species with accelerating application in invasive species management and conservation of endangered species. The next step for this emerging tool is quantitative: relating copy numbers of DNA recovered from the environment to abundance or biomass of a target species. Here, we test the quantitative utility of a single-species eDNA assay for an inland fishery in northern Wisconsin (USA). Real-Time quantitative PCR (qPCR) results reveal significant positive relationships between traditional estimates of walleye (Sander vitreus) density and eDNA copy number across 25 lakes. This study supports eDNA’s potential as a quantitative tool, demonstrates the molecular method’s ecological relevance beyond questions of presence/absence, and could inform broader active management of this important walleye fishery.

Holly Embke (Co-Presenter/Co-Author), University of Wisconsin Madison, Center for Limnology, hembke@wisc.edu;


Patrick Krysan (Co-Presenter/Co-Author), University of Wisconsin Madison, Genome Center, pjkrysan@wisc.edu;


Jake M. Vander Zanden (Co-Presenter/Co-Author), University of Wisconsin Madison, Center for Limnology, mjvanderzand@wisc.edu;


Michael Spear (Primary Presenter/Author), University of Wisconsin Madison, Center for Limnology, mspear2@wisc.edu;


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10:15 - 10:30: / 254 B HIGHLY ACCURATE FRESHWATER MACROZOOBENTHOS METABARCODING WITH NANOPORE MINION

5/22/2019  |   10:15 - 10:30   |  254 B

HIGHLY ACCURATE FRESHWATER MACROZOOBENTHOS METABARCODING WITH NANOPORE MINION DNA barcoding coupled with High-Throughput Sequencing (HTS), commonly known as metabarcoding, has compelling advantage over traditional approaches for obtaining species distribution data. Although it has become a more commonly used tool complementing routine biomonitoring techniques, it is often difficult to detect all species diversity in a bulk sample. This can – in parts – be attributed to shorter read lengths most HTS instruments generate. Moreover, most HTS platforms are not portable, making in situ field-based sequencing infeasible. Oxford Nanopore sequencing platforms (ONT), such as MinION, are an exception. They are also known to provide longer reads albeit limited by rather high error rates (~12-15%). We used a freshwater mock community of 50 OTUs to test the capacity of ONT MinION coupled with rolling circle amplification (RCA) to provide long read metabarcoding results and estimated its diversity with >99% average sequence accuracy for 1D2 sequencing. Our DNA metabarcoding workflow of freshwater organisms using Nanopore sequencing shows that high error rates of long-read single-molecule sequencing can be mitigated using RCA. It appears that cost-effective field-based DNA metabarcoding is possible and future bioassessment programs will benefit from portable, accurate, species-level metabarcoding.

Bilgenur Baloglu (Primary Presenter/Author), Centre for Biodiversity Genomics (University of Guelph), bbaloglu@uoguelph.ca;


Vasco Elbrecht (Co-Presenter/Co-Author), Centre for Biodiversity Genomics (University of Guelph), elbrecht@uoguelph.ca;


Thomas Braukmann (Co-Presenter/Co-Author), Centre for Biodiversity Genomics (University of Guelph), tbraukma@uoguelph.ca;


Shanna MacDonald (Co-Presenter/Co-Author), Centre for Biodiversity Genomics (University of Guelph), smacdo25@uoguelph.ca;


Dirk Steinke (Co-Presenter/Co-Author), Centre for Biodiversity Genomics (University of Guelph), dsteinke@uoguelph.ca;


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