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Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes

Snyder, Matthew Robert
http://orcid.org/0000-0001-8057-8475
http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507

Abstract Details

2019, Doctor of Philosophy, University of Toledo, Biology (Ecology).
Invasive species are one of the top threats to native biodiversity. Their population genetics and genomics can be useful in control and management of invasive species and can be regarded as accidental evolutionary experiments. Here, in a temporal study of the high impact invasive round goby Neogobius melanostomus in the Laurentian Great Lakes, the ability of invasion genetics to track sources and temporal changes in population structure was demonstrated. We tested for three possible alternative temporal patterns in population genetic diversity over time – termed the `genetic stasis’, `supplementation’, and `replacement’ hypotheses. `Genetic stasis’ or no change in allelic composition over time could be caused by a large number of introduced propagules that possibly possess all (or most) of the diversity present in the native source, or by a density dependent process circumventing the establishment of later arrivals. Alternatively, there may be `genetic supplementation’ in which populations that experienced an initial founder effect then gain diversity over time. Finally, `replacement’ of all or some of the initial founding genetic diversity could result when the early arrivals are the best dispersers, followed by those that are better competitors. Results showed that near the site of initial establishment (the invasion core), high genetic diversity due to a large number of introduced individuals precluded significant changes in allelic composition over time. Further from the invasion core, some slight changes in genetic diversity occurred soon after population establishment. Results supported `genetic stasis’ and the founder takes all hypothesis. Due to the territoriality of adult round gobies, it is possible that a density dependent process circumvented establishment of later arrivals. Additional introductions from separate native sources were implicated in some areas of the invasion. Detection of newly introduced species before they can become established and characterizing native community composition are top concerns of management agencies. Metabarcode environmental (e)DNA assays are non-invasive sampling tools for detecting species. Targeted and general metabarcode assays and an associated custom library preparation and bioinformatic pipeline that reduce error were designed and tested. This protocol discerned 100% of species present in electrofishing surveys in the Maumee River from just six water samples. Four 1L water samples in the Maumee River were sufficient to identify 88% of species present in concomitant electrofishing surveys and 73% of those in a much larger effort (44 sampling events in 22 sites). Proportions of species-specific high-throughput sequencing reads were weakly correlated with taxa assessed using morphological surveys. Our method identified more invasive species in more samples than did morphological sampling. Haplotypic diversity discerned with metabarcode assays significantly differed from that determined with traditional population genetic data collection. The protocol increased confidence in metabarcode surveys by removing cross-contamination, index-hops (sequence to sample mis-assignment, leading to false positives), and sequencing error and achieved a high detection efficiency. To evaluate the utility of this approach, the protocol was applied to potential retail sources of invasive species in the Great Lakes, including bait and pond stores. Metabarcode assays found a much greater number of stores with illegal native and invasive species compared to morphological sampling. These included juveniles of valuable fishery species, such as walleye Sander vitreus and yellow perch Perca flavescens, and unestablished, potentially high impact invasive species, including the Eurasian ruffe Gymnocephalus cernua, Eurasian ide Leuciscus idus, and silver Hypophthalmichthys molitrix and bighead H. nobilis carps. Presence of illegal species was unrelated to retailer supply chains. Surveys showed that bait dumping is common among anglers in the Great Lakes. There appears to be serious risk of introduction of non-native species via this vector.
Carol Stepien (Committee Chair)
Jonathan Bossenbroek (Committee Member)
Kerry Naish (Committee Member)
Matthew Neilson (Committee Member)
Von Sigler William (Committee Member)
276 p.
Bioinformatics; Biology; Ecology; Genetics; Organismal Biology
eDNA assays; metabarcoding; HTS; high-throughput sequencing; invasive species; native species; community diversity and structure; population structure; retail vector; bait and pond trade; bioinformatics

Recommended Citations

Citations

  • Snyder, M. R. (2019). Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes [Doctoral dissertation, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507

    APA Style (7th edition)

  • Snyder, Matthew. Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes. 2019. University of Toledo, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507.

    MLA Style (8th edition)

  • Snyder, Matthew. "Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes." Doctoral dissertation, University of Toledo, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507

    Chicago Manual of Style (17th edition)

toledo1564680483342507
383
© 2019, some rights reserved.Creative Commons License Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes by Matthew Robert Snyder is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by University of Toledo and OhioLINK.