SFS Annual Meeting

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

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

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

Abstract: Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA may also hold great potential to uncover population genetic information from water samples. In this study, we sequenced a panel of multiallelic microsatellite markers from eDNA and tissue samples to characterize intraspecific diversity of the round goby (Neogobius melanostomus) at 15 locations across their invaded range. We tested the similarity between eDNA-based and individual genotype-based estimates of allele frequencies and demonstrate a novel approach to estimate genetic diversity and differentiation from eDNA samples. eDNA approaches detected alleles at similar frequencies to genotyped tissues, with correlations of up to r = 0.89 between the relative frequencies of eDNA sequences and the relative frequencies of alleles in sampled individuals. Genetic variability within and between populations was also detected from eDNA in patterns that were consistent with individual tissue-based estimates of genetic diversity and differentiation. Our study demonstrates the potential for eDNA-based population genetics to characterize key population parameters required to effectively monitor, manage, and sustain aquatic species.

Jesus Antonio Rocamontes-Morales (Primary Presenter/Author)
Universidad Autonoma de Zacatecas, rocamontes.morales@gmail.com;

Carla Gutiérrez-Rodríguez (Co-Presenter/Co-Author)
Instituto de Ecología, A.C, carla.gutierrez@inecol.mx;

Oscar Rios-Cardenas (Co-Presenter/Co-Author)
Instituto de Ecología, A.C, oscar.rios@inecol.mx;

Pablo Cesar Hernandez-Romero (Co-Presenter/Co-Author)
Universidad Nacional Autonoma de México, pablohernandez@conbiodes.com;

Abstract: Patterns of genetic variation among populations of species are influenced by geographic and historical factors, which can promote population diverge by isolating populations. In freshwater systems, the structure of the basins, geographic distance, and climatic fluctuations of the Pleistocene are important drivers of population divergence. Xiphophorus hellerii is a fish widely distributed in the basins of the Gulf of Mexico slope. We used mitochondrial DNA sequences and ecological niche modeling to investigate the roles of geographic and historical factors in the population divergence of X. hellerii. We found strong genetic structure conforming to the Stream Hierarchy and isolation by distance models. Demographic tests and ecological niche modeling suggested that the niche and populations of the species underwent contractions and expansions during the Pleistocene. Our study suggests that X. hellerii from different basins and hydrological regions followed independent evolutionary routes and that geographical and historical factors played an important role in population divergence.

Halle M. Nienhaus (Primary Presenter/Author)
Western Michigan University , halle.m.nienhaus@wmich.edu;

Devin Bloom (Co-Presenter/Co-Author)
Western Michigan University, devin.bloom@wmich.edu;

Sarah W. Fitzpatrick (Co-Presenter/Co-Author)
Western Michigan University, sfitz@msu.edu;

Tiffany Schriever (Co-Presenter/Co-Author)
Western Michigan University, tiffany.schriever@wmich.edu;

Abstract: Nested within Lake Michigan’s coastal dune ecosystem are interdunal wetlands, a unique and naturally fragmented habitat, occurring along a latitudinal gradient. We investigated whether differences in dispersal ability or environmental conditions along the Lake Michigan coastline determine population genetic structure of three aquatic insect species which have high (Anax junius), intermediate (Notonecta undulata), and low (Caenis amica) dispersal ability. We hypothesized that all insect populations experienced isolation-by-distance along the coastline, while the strength of this pattern increases with decreasing dispersal ability. We confirmed species identification using COI barcoding, and used RADseq to generate SNP data for population genetic analyses. We found that A. junius displays a significant isolation-by-distance relationship while N. undulata does not, and that both species display K=2 genetic clusters along the coastline with significant increases in genetic diversity with increasing latitude. The COI data revealed our Caenis samples included two different, but closely related species with a remarkably strong north-south species break along the coastline. Our results indicate that all three species occupying the same naturally fragmented habitat are subject to resistance to gene flow despite dispersal ability.

Maslin Osathanunkula (Co-Presenter/Co-Author)
Research Centre in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Thailand, maslin.cmu@gmail.com;

Jeanine Brantschen (Co-Presenter/Co-Author)
Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland , Jeanine.Brantschen@eawag.ch;

Cristina Di Muri (Co-Presenter/Co-Author)
Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, United Kingdom, C.Di-Muri-2016@hull.ac.uk;

Lynsey Harper (Co-Presenter/Co-Author)
School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom, lynsey.harper2@gmail.com;

Bernd Hänfling (Co-Presenter/Co-Author)
Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, United Kingdom, B.Haenfling@hull.ac.uk;

Florian Altermatt (Co-Presenter/Co-Author)
Eawag, Swiss Federal Institute of Aquatic Science and Technology, florian.altermatt@eawag.ch;

Rosetta Blackman (Primary Presenter/Author)
Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland, rosiecblackman@gmail.com;

Elvira Mächler (Co-Presenter/Co-Author)
Eawag, Swiss Federal Institute of Aquatic Science and Technology, elvira.maechler@eawag.ch;

Abstract: Tropical and subtropical freshwater habitats are among the most biodiverse ecosystems, containing characteristic fauna and high numbers of endemic species. However, exploitation of organisms, global climate change, pollution and introduction of invasive species severely threaten this diversity. Implementation of appropriate conservation and protection measures in tropical freshwater systems depends on comprehensive knowledge of state and change in biodiversity, which however, has been barely feasible due to logistic, technical and taxonomic challenges in tropical and subtropical ecosystems. Here we use a single environmental DNA sampling campaign in the Chao Phraya river basin, Thailand, to provide key information on freshwater fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network with respect to alpha- and beta-diversity patterns. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. Mapping these clusters over the catchment not only accurately matched the topology of the river network, but also revealed distinct groups of sites which should each be considered of high conservation value. Our study demonstrates a key application of large-scale eDNA monitoring to identify distinct areas for conservation.

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

Abstract: 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. Zooplankton samples are collected three times per year (spring, summer, and fall) at all 7 NEON lake sites. Zooplankton samples are collected for analysis using vertical tow nets or Schindler traps during mid-summer, with additional samples collected in spring and fall to be archived in bulk. Metabarcode samples are homogenized prior to DNA extraction, and two fragments of the COI gene are PCR-amplified and Illumina-sequenced. Data are processed through a bioinformatics pipeline. Both processed bioinformatics data as well as raw sequence data are publicly available and hosted on the NEON data portal. DNA extracts and bulk samples from spring and fall sampling 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.

Tatsuya Saito (Primary Presenter/Author)
University of Hyogo, tatwoeight630@icloud.com;

Hideyuki Doi (Co-Presenter/Co-Author)
University of Hyogo, hideyuki.doi@icloud.com;

Abstract: Environmental DNA (eDNA) methods have been developed to detect organisms’ distributions abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation, while, the dynamics and mechanisms of eDNA degradation are largely unknown. We conducted the degradation experiments using freshwater and sea water and a meta-analysis. Firstly, we experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA (IPC), free cells from Oncorhynchus kisutch, and the resident fish species of pond and sea. Our results showed that eDNA derived from both cells and IPC decreased exponentially in the both pond and sea water samples. The degradation of eDNA from the resident fish species showed similar behavior to the cell-derived eDNA. As a meta-analysis, we complied the degradation rates of eDNA from 28 studies. We also collected the related factors. Our results suggested that water temperature and PCR amplicon lengths of the measured DNA. were significantly related to the degradation rate of eDNA using 95% quantile models. From the simulation based on the 95% quantile model, we predicted the maximum degradation rate of eDNA in various combinations of water temperature and PCR amplicon length.

John Olson (Co-Presenter/Co-Author)
Dept of Applied Environmental Science, California State University Monterey Bay, CA, USA, joolson@csumb.edu;

Emma Teall (Primary Presenter/Author)
California State University Monterey Bay, eteall@csumb.edu;

Abstract: Environmental DNA (eDNA) is DNA shed into the environment by an organism. Isolating eDNA from environmental samples allows researchers to identify what organisms have been present in the area. But quantification of eDNA amounts is complicated by variation in degradation rates, which makes estimating organism abundance or how long ago the animal shed the DNA difficult. Recent studies suggest the rate of eDNA degradation may be most heavily influenced by bacteria. Bacteria and other microorganisms consume eDNA as a source of phosphorus and nitrogen, and may shorten how long an eDNA fragment remains detectable from four weeks to less than a day. To investigate this, we measured degradation rate of eDNA under different levels of bacteria concentrations. Clarifying the degree to which bacteria impact eDNA degradation will inform future eDNA studies and improve the accuracy of estimations of species presence and abundance based on eDNA.

Sakiko Yaegashi (Primary Presenter/Author)
University of Yamanashi, sakikoy@yamanashi.ac.jp;

Hiroya Aruga (Co-Presenter/Co-Author)
University of Yamanashi, t16ce062@yamanashi.ac.jp;

Hidehiro Kaneko (Co-Presenter/Co-Author)
University of Yamanashi, kaneko@yamanashi.ac.jp;

Abstract: Environmental DNA (eDNA) has been paid attention to as a new biological monitoring method on the aquatic ecosystem. The eDNA meta-barcoding analysis is currently employed to investigate the community composition of various aquatic organisms such as fishes, amphibians, mammals, and insects. This study examined aquatic insect communities in the river fragmented by a dam (Shiokawa River) and non-fragmented river (Kamanashi River) in Yamanashi, Japan, using eDNA meta-barcoding. Water-samplings were performed between Nov 2018 and Nov 2020. This basin was disturbed by heavy typhoon Hagibis in 2019. We collected 500ml of river-water and filtered it by a mixed cellulose membrane filter (pore size 0.2µm). The eDNA was extracted by the phenol-chloroform method or DNeasy Blood and Tissue kit (Qiagen). The Cytochrome Oxidase I region was amplified by PCR and sequenced using Illumina sequencer. The obtained reads were filtered by sequence quality and searched its origin organisms by BLAST.

Erik Pilgrim (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, pilgrim.erik@epa.gov;

Christopher Nietch (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, nietch.christopher@epa.gov;

Lester Yuan (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, yuan.lester@epa.gov;

John Darling (Co-Presenter/Co-Author)
U.S Environmental Protection Agency, darling.john@epa.gov;

Huiyun Wu (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, wu.huiyun@epa.gov;

Marirosa Molina (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, molina.marirosa@epa.gov;

John Martinson (Co-Presenter/Co-Author)
U.S Environmental Protection Agency, martinson.john@epa.gov;

Brent Johnson (Co-Presenter/Co-Author)
U.S. Environmental Protection Agency, johnson.brent@epa.gov;

Nathan Smucker (Primary Presenter/Author)
U.S. Environmental Protection Agency, smucker.nathan@epa.gov;

Abstract: Interest in developing diatom and microbial indicators of nutrients continues to grow because their relationships with nutrient concentrations can help inform the assessment, conservation, and management of stream ecosystems. Here, we used metabarcoding of diatoms and bacteria to examine their potential use as nutrient indicators based on their relationships with total phosphorus (TP) and total nitrogen (TN) concentrations. From July to October, we sampled 25 sites in a watershed (1293 square kilometers) 12-14 times (typically weekly) to investigate how temporal variation in nutrients and biota affected interpretations of monitoring data. Regressions showed that diatom and bacterial assemblages were more strongly associated with summer mean TP or TN concentrations than with same week concentrations. Nutrients and assemblages were variable, but relationships remained strong for most weeks except for two high flow events temporarily weakening diatom- and bacteria-nutrient relationships. Assemblages recovered from these disturbances within two weeks. TN concentrations decreased over time along with high nitrogen diatom relative abundances, whereas low nitrogen diatom relative abundances increased. These results highlight the potential for using diatom and bacterial metabarcoding to develop indicators that can be used in monitoring programs.

Hideyuki Doi (Primary Presenter/Author)
University of Hyogo, hideyuki.doi@icloud.com;

Takeshi Watanabe (Co-Presenter/Co-Author)
Pacific Consultants Co., Ltd, takeshi3.watanabe@os.pacific.co.jp;

Naofumi Nishizawa (Co-Presenter/Co-Author)
GO!FOTON INC. , Nash.nishizawa@gofoton.com;

Tatsuya Saito (Co-Presenter/Co-Author)
University of Hyogo, tatwoeight630@icloud.com;

Hisao Nagata (Co-Presenter/Co-Author)
GO!FOTON INC. , hisao.nagata@gofoton.com;

Yuichi Kameda (Co-Presenter/Co-Author)
GO!FOTON INC. , Yuichi.Kameda@gofoton.com;

Nobutaka Maki (Co-Presenter/Co-Author)
Pacific Consultants Co., Ltd, nobutaka.maki@ss.pacific.co.jp;

Kousuke Ikeda (Co-Presenter/Co-Author)
Pacific Consultants Co., Ltd, kousuke.ikeda@ss.pacific.co.jp;

Takashi Fukuzawa (Co-Presenter/Co-Author)
GO!FOTON INC. , takashi.fukuzawa@gofoton.com;

Abstract: Environmental DNA method has been developed for biomonitoring in aquatic habitats. Recently, the eDNA methods were applied to fish distribution analysis in freshwater ecosystems. However, the eDNA collection/measurement will take a time, e..g., 5-6 hours. We recently developed a on-site/rapid method for the field processing of eDNA samples and measurements using an ultra-rapid mobile PCR (hereafter, mobile PCR) to reduce the measurement time to 30 min and maintain high detectability of aquatic organisms. We firstly tested the ability and performance of the on-site/rapid method with comparing to the laboratory experiment using standard DNA. Further, we demonstrated its on-site use to detect the distribution of silver carp, Hypophthalmichthys molitrix, an invasive fish in Japanese rivers and lakes. We compared the on-site eDNA measurement to the laboratory extraction and detection using a benchtop qPCR platform and the national survey to confirm the performance. Our on-site method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to the national observation surveys and laboratory eDNA method. We summarized that our on-site/rapid eDNA method could be immediately applied to various taxa and environments in freshwater habitats.