Ryan P. Walter

Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada

Temporal instability in population genetic structure has significant implications for management and conservation decisions. Here, we evaluate temporal stability in five populations of Chinook salmon (Oncorhynchus tshawytscha) from the Upper Fraser River, British Columbia, Canada, based on estimates of temporal allelic variance and effective population size (Ne) at 11 microsatellite loci. Significant temporal variation in allele frequencies was found within individual populations sampled at 5- to 12-year intervals. Removal of migrant fish or correcting for migrants resulted in higher allelic variance or reduced Ne. Populations with higher levels of temporally consistent gene flow show reduced temporal allelic variance (i.e., reduced genetic drift) and higher Ne. This study is an important empirical example of the effect of gene flow on genetic stability and Ne. In salmonids, low straying levels may have evolved to favor local adaptation; however, we show that even such low levels of gene flow can elevate ...

First record of living Manta alfredi × Manta birostris hybrid

Following a recent taxonomic revision, two manta species (Manta alfredi and Manta birostris ) have been advocated based on meristic and morphological characteristics (Marshall et al. 2009). Subsequent genetic analyses of the two species using mitochondrial and nuclear markers confirmed two distinguishable genetic groups (Kashiwagi et al. 2012). Using the above taxonomic and genetic criteria, we provide evidence for the first record of a living Manta alfredi ×Manta birostris hybrid. The Manta individual (Fig. 1a, b) was non-lethally sampled from a known manta aggregation site in Dunganab Bay, Sudan, Red Sea, in October 2012. The individual was identified in the field as Manta alfredi based on distinguishing morphological criteria: dorsoventral colouration/spot patterns, mouth and pectoral fin colouration, and absence of remnant spine (Fig. 1b; Marshall et al. 2009). DNA was recovered from a fin clip using standard molecular genetic protocols. The mitochondrial gene ND5 (1,154 bp) and nuclear gene RAG1 (646 bp) were amplified following Kashiwagi et al. (2012), and sequenced. Recovered sequences (GenBank accession nos. KF574269-KF574270) were aligned with those previously reported (Kashiwagi et al. 2012) and a haplotype network was constructed in TCS 1.21 (Clement et al. 2000). TheManta specimen was confirmed to carry a newManta alfredi mtDNA haplotype (red in Fig. 1). However, the RAG1 sequence indicates that this individual is an interspecific hybrid. The twoManta species are reciprocally monophyletic at the RAG1 locus, which contains two species-specific single nucleotide polymorphisms (SNPs): at position 73 (M . alfredi : G; M . birostris : A) and position 507 (M . alfredi : A; M . birostris : C) following Kashiwagi et al. (2012). The hybrid individual is heterozygous at both SNPs (see inset chromatograms). Heterozygosity was confirmed by sequencing this individual in triplicate in both forward and reverse directions at RAG1 . Our finding indicates that reproductive isolation among M . alfredi and M . birostris may be less complete than previously thought, or alternatively, that species-specific taxonomic and genetic differentiation is not as unambiguous as currently suggested. Given the designation of the two discrete species as vulnerable on the IUCN Red List and their recent listing on CITES appendix II following concern over increasing global R. P. Walter (*) : S. T. Kessel :A. T. Fisk :D. D. Heath : N. E. Hussey University of Windsor – GLIER, Windsor, Canada e-mail: rwalter@uwindsor.ca

Hybrid ‘superswarm’ leads to rapid divergence and establishment of populations during a biological invasion

Understanding the genetic background of invading species can be crucial information clarifying why they become invasive. Intraspecific genetic admixture among lineages separated in the native ranges may promote the rate and extent of an invasion by substantially increasing standing genetic variation. Here, we examined the genetic relationships among threespine stickleback that recently colonized Switzerland. This invasion results from several distinct genetic lineages that colonized multiple locations and have since undergone range expansions, where they coexist and admix in parts of their range. Using 17 microsatellites genotyped for 634 individuals collected from 17 Swiss and two non‐Swiss European sites, we reconstruct the invasion of stickleback and investigate the potential and extent of admixture and hybridization among the colonizing lineages from a population genetic perspective. Specifically, we test for an increase in standing genetic variation in populations where multiple lineages coexist. We find strong evidence of massive hybridization early on, followed by what appears to be recent increased genetic isolation and the formation of several new genetically distinguishable populations, consistent with a hybrid ‘superswarm’. This massive hybridization and population formation event(s) occurred over approximately 140 years and likely fuelled the successful invasion of a diverse range of habitats. The implications are that multiple colonizations coupled with hybridization can lead to the formation of new stable genetic populations potentially kick‐starting speciation and adaptive radiation over a very short timescale.

Dispersal and population genetic structure of Telmatherina antoniae, an endemic freshwater Sailfin silverside from Sulawesi, Indonesia.

Population genetic structure in the presence of substantial dispersal provides a unique perspective on the evolution of reproductive isolation. We sampled Telmatherina antoniae, an endemic fish species, at 10 sites in Lake Matano, Indonesia. Significant genetic structure (FST = 0.03) was found, despite a migration rate of 10.2% and a mean dispersal distance of 13.6 km, estimated by genotype assignment. Neither dispersal distance nor direction differed from random expectations, indicative of no dispersal barrier in Lake Matano. However, Bayesian genotype cluster assignment identified a population structure consisting of four to six clusters that did not coincide with sample site distribution, but explained two to three times more genetic variance than sample site. The mechanism for continued isolation of those genetic clusters is unknown, but assortative mating and temporal isolation are obvious candidates. Our results resolve the apparent paradox of population genetic structure coupled with frequent dispersal, and highlight the importance of considering cryptic genetic structure.

Comparison of Walleye Habitat Suitability Index (HSI) Information with Habitat Features of a Walleye Spawning Stream

Abstract The objective of our study was to determine habitat conditions in a stream where walleye successfully produce fry and to compare these conditions with the nationally-applicable Habitat Suitability Index (HSI) model for walleye. During 17–20 d migration periods in April of 1996, 1997 and 2000, walleye were observed spawning; eggs were collected primarily in April and fry primarily in May. Water depths, velocities, and temperatures where walleyes spawned were at the lower end of or below the optimum ranges specified in the HSI for spawning walleye. However, random sampling indicated that optimum HSI conditions for these parameters generally did not exist in the stream. Substrate, dissolved oxygen, and pH were optimal according to the HSI. Our results indicate that predictions using the HSI alone are not sufficient to identify regional tributaries where walleye can successfully establish viable populations.

Isolation and differentiation of Rivulus hartii across Trinidad and neighboring islands

Diversification of freshwater fishes on islands is considered unlikely because the traits that enable successful colonization—specifically, broad salinity tolerances and the potential for oceanic dispersal—may also constrain post‐colonization genetic differentiation. Some secondary freshwater fish, however, exhibit pronounced genetic differentiation and geographic structure on islands, whereas others do not. It is unclear what conditions give rise to contrasting patterns of differentiation because few comparative reconstructions of population history have been carried out for insular freshwater fishes. In this study, we examined the phylogeography of Hart’s killifish (Rivulus hartii) across Trinidad, with reference to neighboring islands and northern South America, to test hypotheses of colonization and differentiation derived from comparable work on co‐occurring guppies (Poecilia reticulata). Geographic patterns of mitochondrial DNA haplotype variation and microsatellite genotype variation provide evidence of genetic differentiation of R. hartii among islands and across Trinidad. Our findings are largely consistent with patterns of geographically structured ancestry and admixture found in Trinidadian guppies, which suggests that both species share a history of colonization and differentiation and that post‐colonization diversification may be more common among members of insular freshwater fish assemblages than has been previously thought.

Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem.

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 2 years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 h 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 h 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.

Range expansion by invasion: genetic characterization of invasion of the greenside darter (Etheostoma blennioides) at the northern edge of its distribution

Species introductions in freshwater ecosystems are often complex processes, yet an understanding of the nature of the introduction can inform management and conservation actions. The greenside darter (Etheostoma blennioides), until recently a species of special concern, expanded its Canadian range and is now common and widespread in the Grand River watershed (GRW). This is despite there being no evidence of greenside darter in the GRW prior to 1990. The goal of this study was to genetically characterize the GRW greenside darter introduction. Greenside darter were sampled in the GRW, the three known native watersheds in Canada, and one site from Ohio. We measured genetic diversity and population structure, and tested for population bottlenecks using eight microsatellite loci. Genotype assignment was used to identify possible introduction sources. Populations in the GRW showed similar genetic diversity to native watershed populations with no evidence for recent or historical population bottlenecks. Genotype assignment showed that one of the Canadian watersheds and the Ohio site were not potential sources of the GRW greenside darter, whereas the Thames River watershed was the most likely source. Substantial population genetic structure exists among the sample sites in the GRW. Clearly, the current widespread and abundant distribution of the greenside darter in the GRW is not the result of recent expansion of an existing native population, but rather multiple introductions into at least three sites in the GRW, followed by rapid population growth. Although the GRW E. blennioides is introduced, it harbours considerable genetic diversity and represents an important northern range extension for this species.

Hierarchical analysis of genetic structure in the habitat‐specialist Eastern Sand Darter (Ammocrypta pellucida)

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.

No barriers to gene flow among sympatric polychromatic ‘small’Telmatherina antoniae from Lake Matano, Indonesia

Genetic divergence, assortative courtship and intermale aggression were assessed between sympatric colour morphs of the sailfin silverside Telmatherina antoniae, endemic to Lake Matano, Indonesia. Genetic analysis using microsatellite markers showed no barriers to gene flow among T. antoniae primary colour morphs (blue and yellow) within sampling sites, sympatric populations or at the lake-wide level. Low but significant genetic differentiation was found between yellow morphs and mixed (blue-yellow) morphs. Behavioural surveys indicated assortative courtship does occur along primary colour lines; however, intermale aggression among paired and intruding male morphs appeared equal with respect to male colour. These observations support the hypothesis that males view other males as threats to their courtship regardless of their colour. This study supports recent work suggesting that assortative mating is present in T. antoniae despite a lack of reproductive isolation among colour morphs.