Scott M. Reid

Influence of dams and habitat condition on the distribution of redhorse ( Moxostoma ) species in the Grand River watershed, Ontario

Redhorse, Moxostoma spp., are considered to be negatively affected by dams although this assertion is untested for Canadian populations. One hundred and fifty-one sites in the Grand River watershed were sampled to identify factors influencing the distribution of redhorse species. Individual species of redhorse were captured from 3 to 32% of sites. The most widespread species were golden redhorse, M. erythrurum (30%) and greater redhorse, M. valenciennesi (32%), while river redhorse, M. carinatum, was only found along the lower Grand River. Redhorse were absent from the highly fragmented Speed River sub-watershed and upper reaches of the Conestogo River and the Grand River. Redhorse species richness was positively correlated to river fragment size and upstream drainage area. Generalized additive models (GAMs) were applied to evaluate the influence of river fragment length, connectivity and habitat on species distribution. Principal component analysis reduced habitat data to three axes representing: channel structure, substrate, and pool, riffle and run habitats (PC1); gradient and drainage area (PC2); and cover (PC3). GAMs indicate that PC2 was important for predicting black redhorse and greater redhorse site occupancy and PC1 was important for golden redhorse. River fragment length was important for predicting site occupancy for shorthead redhorse, but not other species.

Influence of riffle characteristics, surficial geology, and natural barriers on the distribution of the channel darter, Percina copelandi, in the Lake Ontario basin

SynopsisThe channel darter, Percina copelandi, is a small benthic fish with a wide but disjunct distribution across central North America. The development of conservation and recovery strategies for Canadian populations is limited by a lack of knowledge regarding ecology, population size and other factors that affect its distribution and abundance. We sampled five rivers in the Lake Ontario basin to test whether the distribution of P. copelandi reflected riffle habitat characteristics or landscape-scale factors such as surficial geology and natural barriers (waterfalls). At most sites yielding P. copelandi, riffles flowed into deep sand bottomed run or pool habitats. Despite a lack of association with local surficial geology or riffle habitat characteristics, both the upstream limits of P. copelandi occurrence and distribution of suitable habitats reflected the distribution of waterfalls, chutes and bedrock outcroppings. In contrast to P. copelandi, distributions of Etheostoma flabellare, P. caprodes and Rhinichthys cataractae reflected among site differences in riffle habitat.

Species traits influence the genetic consequences of river fragmentation on two co-occurring redhorse (Moxostoma) species

We used microsatellite DNA markers to test whether fragmentation of the Trent River (Ontario, Canada) has re- duced genetic diversity and increased genetic differentiation among populations of river redhorse (Moxostoma carinatum) and shorthead redhorse (Moxostoma macrolepidotum). Allelic richness of both species was significantly greater along the free-flowing Muskegon River (Michigan, USA) than along the fragmented Trent River. Contrary to expectations, there was no evidence of a fragment length effect on genetic diversity, recent population bottlenecks, or increased relatedness among individuals in fragmented populations. High levels of linkage disequilibrium indicate extinction-recolonization pop- ulation dynamics along the Trent River. For both species, pairwise FST tests identified weak but statistically significant population differentiation. In the Trent River, differentiation was significantly greater for river redhorse than for shorthead redhorse and, for both species, greater than in the Muskegon River. Moderate fragmentation effects likely reflect the per- meability of the dam-lock system to redhorse movement. Differences between species indicate that as a result of smaller effective population sizes, habitat specialists and species at the periphery of their geographic range are more sensitive to river fragmentation.

PCR-RFLP based diagnostic tests for Moxostoma Species in Ontario

Six Moxostoma species are found in Ontario, including two federally listed species. Knowledge of their distribution and status has been limited by incorrect field identifications, collections that report Moxosotoma or sucker species, and new site records without voucher specimens. To develop species diagnostic genetic markers, we amplified and sequenced two mitochondrial genes (ATPase subunits 6 and 8). Species-specific sequence differences were easily identified (of 830 analyzed bases, 132 substitutions were phylogenetically informative). Based on sequence differences, four restriction enzymes were identified and tested for their reliability as species diagnostic tools. Restriction digests of previously sequenced samples matched predicted species-specific patterns. Overall, 90% of samples digested matched. Disagreement between 20% of samples provided by various government agencies and species-specific digest patterns indicate a need for greater care during field identifications.

First record of Ammocrypta pellucida (Agassiz, 1863) (Actinopterygii: Perciformes) from the Lake Ontario drainage basin

The objective of this paper is to document the first occurrence of Ammocrypta pellucida in the Lake Ontario basin from samples collected in West Lake, Ontario (Canada) in 2013. Prior to this record, the known range of this imperilled species consisted of two disjunct elements in eastern North America separated by about 500 km. The new occurrence is in the middle of these two distributional elements and suggests that further inventory efforts are warranted in the intervening area.

Establishing detection thresholds for environmental DNA using receiver operator characteristic (ROC) curves

Environmental DNA (eDNA) detection is increasingly being used to assess the potential presence of aquatic species. Setting defensible thresholds for qPCR assays are necessary to differentiate “detection” from “non-detection”, but threshold rationales are rarely reported in eDNA studies. Detection thresholds for data inclusion and exclusion have implications for downstream data analysis; uncritical acceptance could result in false positive results (Type I error), whereas overly conservative thresholds could result in high false negative interpretation (Type II error). We assessed the use of the receiver operator characteristics (ROC) framework to identify a detection threshold for balancing sensitivity and specificity of eDNA data. The ROC framework was tested using empirical eDNA data from redside dace (Clinostomus elongatus), an endangered freshwater fish in southwestern Ontario. Based on negative controls, positive controls, and quality assurance guidelines, a minimum concentration of 1 copy reaction−1 was identified as the most appropriate threshold for this study. Although optimal thresholds will likely vary between studies and labs based on empirical data, the ROC framework provides a statistical method for establishing defensible thresholds for data acceptance or rejection as well as tradeoffs between the sensitivity and specificity of eDNA data.

Conservation genetics of redside dace (Clinostomus elongatus): phylogeography and contemporary spatial structure

Redside dace Clinostomus elongatus (Teleostei: Cyprinidae) is a species of conservation concern that is declining throughout its range as a result of habitat fragmentation, degradation and loss. We characterized the genetic structure and diversity of redside dace populations across the species range using mitochondrial and microsatellite data to inform conservation efforts and assess how historical and recent events have shaped genetic structure and diversity within and among populations. Phylogeographic structure among 28 redside dace populations throughout southern Ontario (Canada) and the United States was assessed by sequence analysis of the mitochondrial cytochrome b and ATPase 6 and 8 genes. Populations were also genotyped using ten microsatellite loci to examine genetic diversity within and among populations as well as contemporary spatial structuring. Mitochondrial DNA sequence data revealed three geographically distinct lineages, which were highly concordant with groupings identified by microsatellite analysis. The combined genetic data refute published glacial refugia hypotheses of a single Mississippian refugium or of two lineages associated with Mississippian and Atlantic refugia. Secondary contact between the two eastern groups was documented in the Allegheny River drainage and tributaries to Lake Ontario. With the exception of several allopatric populations within the Allegheny watershed, high genetic structuring among populations suggests their isolation, indicating that recovery efforts should be population-based.