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Data from: Benefits of turbid river plume habitat for Lake Erie yellow perch (Perca flavescens) recruitment determined by juvenile to larval genotype assignment
Carreon-Martinez, Lucia B.; Walter, Ryan P.; Johnson, Timothy B.; Ludsin, Stuart A.; Heath, Daniel D. — 2016-04-09 Nutrient-rich, turbid river plumes that are common to large lakes and coastal marine ecosystems have been hypothesized to benefit survival of fish during early life stages by increasing food availability and (or) reducing vulnerability to visual predators. However, evidence that river plumes truly benefit the recruitment process remains meager for both freshwater and marine fishes. Here, we use genotype assignment between juvenile and larval yellow perch (Perca flavescens) from western Lake Erie to estimate and compare recruitment to the age-0 juvenile stage for larvae residing inside the highly turbid, south-shore Maumee River plume versus those occupying the less turbid, more northerly Detroit River plume. Bayesian genotype assignment of a mixed assemblage of juvenile (age-0) yellow perch to putative larval source populations established that recruitment of larvae was higher from the turbid Maumee River plume than for the less turbid Detroit River plume during 2006 and 2007, but not in 2008. Our findings add to the growing evidence that turbid river plumes can indeed enhance survival of fish larvae to recruited life stages, and also demonstrate how novel population genetic analyses of early life stages can contribute to determining critical early life stage processes in the fish recruitment process.
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Data from: Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries
Balasingham, Katherine D.; Walter, Ryan P.; Mandrak, Nicholas E.; Heath, Daniel D. — 2017-10-26 The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designed group-specific primer set and next-generation sequencing for the detection of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada; the Grand River and the Sydenham River. Out of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.
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Data from: Parallel evolutionary forces influence the evolution of male and female songs in a tropical songbird
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Graham, Brendan A.; Heath, Daniel D.; Walter, Ryan P.; Mark, Melissa M.; Mennill, Daniel J. — 2018-04-04 Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics it is commonplace for both sexes to produce complex acoustic signals. Therefore tropical birds offer the opportunity to compare the sexes and provide a more comprehensive understanding of the evolution of animal signals. In this study we quantified patterns of acoustic variation in Rufous-and-white Wrens (Thryophilus rufalbus) from five populations in Central America. We quantified similarities and differences between male and female song by comparing the role that acoustic adaptation, cultural isolation, and neutral genetic divergence have played in shaping acoustic divergence. We found that males and females showed considerable acoustic variation across populations, although females exhibited greater population divergence than males. Redundancy analysis and partial-redundancy analysis revealed significant relationships between acoustic variation and ecological variables, genetic distance, and geographic distance. Both ambient background noise and geographic distance explained a high proportion of variance for both males and females, suggesting that both acoustic adaptation and cultural isolation influence song. Overall, our results indicate that parallel evolutionary forces act on male and female acoustic signals and highlight the important role that cultural drift and selection play in the evolution of both male and female songs.
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Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)
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Ginson, Robert; Walter, Ryan P.; Mandrak, Nicholas E.; Beneteau, Courtney L.; Heath, Daniel D. — 2016-01-08 Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within-river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among-drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat-specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.
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Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)
Walter, Ryan P.; Cena, Christopher J.; Morgan, George C.; Heath, Daniel D. — 2015-08-20 Populations existing in formerly glaciated areas often display composite historical and contemporary patterns of genetic structure. For Canadian freshwater fishes, population genetic structure is largely reflective of dispersal from glacial refugia and isolation within drainage basins across a range of scales. Enhancement of sport fisheries via hatchery stocking programs and other means has the potential to alter signatures of natural evolutionary processes. Using 11 microsatellite loci genotyped from 2182 individuals, we analyzed the genetic structure of 46 inland lake walleye (Sander vitreus) populations spanning five major drainage basins within the province of Ontario, Canada. Population genetic analyses coupled with genotype assignment allowed us to; 1) characterize broad and fine scale genetic structure among Ontario walleye populations; and 2) determine if the observed population divergence is primarily due to natural / historical processes or recent anthropogenic events. The partitioning of genetic variation revealed higher genetic divergence among lakes than among drainage basins or proposed ancestries—indicative of relatively high isolation among lakes, study-wide. Walleye genotypes were clustered into three major groups, likely reflective of Missourian, Mississippian, and Atlantic glacial refugial ancestry. Despite detectable genetic signatures indicative of anthropogenic influences, province-wide spatial genetic structure remains consistent with the hypothesis of dispersal from distinct glacial refugia and subsequent isolation of lakes within primary drainage basins. Our results provide a novel example of minimal impacts from fishery enhancement to the broad-scale genetic structure of inland fish populations.
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Data from: Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem
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Balasingham, Katherine D.; Walter, Ryan P.; Heath, Daniel D. — 2016-09-12 Several studies have demonstrated that environmental DNA (eDNA) can be used to detect the presence of aquatic species, days to weeks after the target species has been removed. However, most studies used eDNA analysis in lentic systems (ponds or lakes), or in controlled laboratory experiments. While eDNA degrades rapidly in all aquatic systems, it also undergoes dilution effects and physical destruction in flowing systems, complicating detection in rivers. However, some eDNA (i.e. residual eDNA) can be retained in aquatic systems, even those subject to high flow regimes. Our goal was to determine residual eDNA detection sensitivity using quantitative real-time polymerase chain reaction (qRT-PCR), in a flowing, uncontrolled river after the eDNA source was removed from the system; we repeated the experiment over two years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 hours after eDNA source removal. Residual eDNA signal strength decreased as sampling distance downstream from the eDNA source site increased, and was no longer detectable at the source site 48 hours after the eDNA source water was exhausted in both experiments. This experiment shows that residual eDNA sampled in surface water can be mapped quantitatively using qRT-PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species.

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(auteur : Walter, Ryan P.)

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