Eric Taylor

Hybrid zones, where diverged lineages meet and interbreed, are often exploited to study natural mechanisms associated with varying stages of speciation. My thesis focuses on the western North American Arctic char (Salvelinus alpinus), bull trout (Salvelinus confluentus), and Dolly Varden (Salvelinus malma), described as a “species complex” due to their close inter-relationships, variable morphology, and tendency to hybridize. These aspects have caused debate over their taxonomic and physical identification. Furthermore, a recent subspecies contact zone between northern Dolly Varden (Salvelinus malma malma, NDV) and southern Dolly Varden (Salvelinus malma lordi, SDV), including an admixed population in the Chignik Lake watershed of southwestern Alaska, was recently described. Little is known about the hybrid composition, the effects of ecological selection on proportion of ancestry, and the resulting genomic landscape of this population. In my first chapter, I developed TaqMan assays for efficient, cost-effective, and accurate genotyping of sympatric char species and their hybrids for research, conservation, and management purposes. In my second chapter, I created a genotyping-by-sequencing library to investigate the Chignik Lake watershed population in the context of a NDV and SDV contact zone. My results show that the Chignik Lake watershed population is admixed between NDV and SDV, genetically diverse, and likely the result of historical introgression. I found associations between sampled habitat, distance from the estuary, compared with the proportion of the genome that was NDV (QNDV). In addition, the number of seaward migrations significantly correlated with QNDV, suggesting divergent selection on life history traits resulting from admixture, consistent with findings in other salmonids. Finally, Bayesian genomic cline analysis revealed outlier loci associated with excess ancestry for NDV, and I identified several putative biological processes associated with those outlier loci. My findings suggest that: (i) NDV and SDV show weak reproductive isolation from each other resulting in extensive admixture in the Chignik Lake watershed, and (ii) divergence seen within the watershed may be shaped by diverse habitats and historical gene flow. Future work should take advantage of replicate populations within this contact zone to assess the generality of my results.

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Anadromous freshwater fishes are among the most threatened vertebrates in North America. Population declines and collapses due to overfishing, habitat loss, and climate change have long been documented for socioeconomically important salmonids such as Pacific salmon (Oncorhynchus spp), but the conservation status of other species such as Dolly Varden char (Salvelinus malma) remains largely unknown. Even without the pressures of direct commercial harvest, many anadromous salmonids may still be vulnerable to the other threats faced by commercially-harvested species, but conservation efforts continue to be hampered by a lack of basic life history and demographic information. While the Northern Dolly Varden (S. m. malma) has been assessed as “Special Concern” by the Committee on the Status of Endangered Wildlife in Canada, the Southern Dolly Varden (S. m. lordi) has received little conservation attention despite near ubiquity in coastal watersheds from Alaska to Washington, partly due to a lack of data throughout the broad coastal range. I conducted surveys on a population of Southern Dolly Varden in a lake-headed coastal watershed on the mid coast of British Columbia to identify key spawning, rearing, and foraging habitat, to characterize seasonal patterns in their iteroparous anadromous migratory life history, and to assess the extent of migratory coupling among Pacific salmon and Dolly Varden throughout the year. I found that Dolly Varden used a wide range of habitats distributed throughout the entire watershed, and that there were distinct seasonal movements that were temporally associated with Pacific salmon migrations. My observations indicate that this population of Southern Dolly Varden requires the entire extent of the watershed, from lake tributaries to the estuarine river mouth, for individuals to express their complete migratory life history, and that this population is vulnerable to any disturbance leading to the degradation or loss of access to key habitats for spawning, rearing, and foraging. This population could serve as a baseline for understanding the conservation status of Southern Dolly Varden throughout the rest of the range, and can be used as a rare model for studying predator-prey migratory coupling as it relates to socioeconomically important species of Pacific salmon.

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The Salish sucker (Catostomus sp. cf. catostomus) is a federally Threatened species under Canada’s Species at Risk Act and is restricted to 11 watersheds in British Columbia (lower Fraser River Valley) and six in Washington State. Agricultural development has been historically prominent in these areas, and hypoxia and the physical destruction of habitat have been identified as the most important threats to this species. Synergistic effects of reduced streamflow, nutrient inputs, and high temperatures are likely large determinants of seasonal hypoxia. The effects of stream flow on temperature and dissolved oxygen in Salish sucker critical habitat, and corresponding changes in habitat use, distribution, and growth of Salish sucker were studied. As salmonids are even more sensitive to impaired water quality than suckers, and maintaining salmonid populations is an additional major conservation concern in the lower Fraser Valley, the biological response of juvenile coho salmon was also studied as they co-occur in Salish sucker habitats. Through various flow manipulation and enclosure experiments I found that severely reducing flow in off-channel ponds resulted in low levels of dissolved oxygen (
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This research investigated a population of lake chub (Couesius plumbeus) inhabiting a geothermal spring complex south of the community of Atlin, in the far northwest of British Columbia. These lake chub live in thermal isolation in 13-26°C water year round, while the only neighbouring water body, glacier-fed Atlin Lake, remains below 6°C year round and has no known population of lake chub. Through mark-recapture sampling I estimated the population size of this isolated and physiologically distinct population to be on the order of 1,000 to 2,000 mature individuals. I measured its area of occupancy as 3,602m². As such, the population is small in both habitat extent and population size, as well as being physically isolated from other populations of this widespread species. Tagging of fish in individual sections of the warm springs showed a general lack of movement among different sites. Size-frequency histograms for individual sites and points in time illustrated the presence of distinct cohorts suggesting lifespans of three to four years, with outliers living a year or two longer. I also studied the invasive cherry shrimp (Neocaridina davidi var. red), performing experiments to observe survivorship and behaviour under different temperature regimes. I found no significant decrease in mortality in adults when water was cooled to 5°C, but a significant reduction in their ability to react to stimuli below 15°C. I also observed 100% mortality in juveniles at water temperatures of 10°C or lower within two days. Based on these data, barring future adaptation to considerably colder conditions, is unlikely that cherry shrimp will be able to expand their range further into the Yukon River basin. Overall, my study provides a baseline of understanding about the population and life history of an isolated warm-springs population of lake chub, and provides observations of the early stages and probable outcomes of an exotic species invading an isolated location.

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Resource polymorphism and natural hybridization are evolutionary phenomena that play an important role in the development of reproductive isolation during speciation. The Arctic char (Salmonidae: Salvelinus alpinus) exhibits substantial phenotypic and genetic diversity across its Holarctic range, making it an ideal species to examine the role of intraspecific trophic polymorphism in driving reproductive isolation and the interactions between hybridizing species in sympatry. In one southwestern post-glacial lake previously analyzed for resource polymorphism (Lower Tazimina Lake), I found evidence for two genetic groups of char and for significant differences in the distribution of microsatellite variability among at least two of the three previously described body-size morphotypes (‘large’, ‘medium’, and ‘small’–bodied char; maximum FST = 0.09). I also found significant associations between genetic type and gill raker counts among body-size morphs (r = -0.73, P
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Natural selection and local adaptation influence fish abundances and distributions on both short and long-term time scales: first, by influencing recruitment dynamics and second, by affecting long-term population persistence in fluctuating environmental conditions. Little is known, however, about the significance of adaptive population divergence in the marine environment. In this study, I utilized an FST outlier approach to detect putatively selected loci from an Amplified Fragment Length Polymorphism (AFLP) marker dataset of yelloweye rockfish (Sebastes ruberrimus) collected from southeast Alaska south to Oregon. During the data analysis phase, a plate bias was detected and efforts to eliminate this effect were unsuccessful. Therefore, each PCR plate was analyzed separately, resulting in seven independent analyses. A total of 966-1580 AFLP loci were identified for the seven plates, and 0-10 loci (0-0.79%) per plate were identified as FST outliers by program, BAYESCAN. Based on results from the outlier analyses, datasets composed of neutral loci (those with no support for being under selection) and outlier loci (those exceeding a minimum posterior threshold of 0.7, corresponding to a moderate amount of support for being under selection) were established for each plate. Global FST values are approximately five times greater for the outlier datasets (mean FST=0.56) than for putatively neutral loci (mean FST=0.10). The genetic clustering program, STRUCTURE, identified similar patterns of population structure both for the neutral and outlier datasets. The outlier datasets, however, lead to overall higher assignment probabilities of individual fish to genetic groups than observed with the neutral datasets. In addition, several similar clustering patterns (e.g. southern vs. northern genetic clusters, presence of isolated clusters) were observed across several plates, providing independent evidence for regionally restricted gene flow. Overall, my results suggest that population structure driven by neutral processes may be reinforced by natural selection, which has implications for the management of yelloweye rockfish fishery stocks and the scale of connectivity within the Rockfish Conservation Area marine reserve network.

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Brassy minnow, Hybognathus hankinsoni, is a little-studied cyprinid fish with highly disjunct distributions in western Canada. Phylogeographic scenarios on the origins of brassy minnow in British Columbia (BC) were explored using two mitochondrial loci (cyt b and ND4) that were sequenced for up to 32 localities. This revealed an approximate ‘east-west’ geographic split, suggesting that BC populations are likely post-glacial colonists from the Mississippi-Missouri refugium. However, certain ‘eastern’ populations exhibited incongruences between gene and species trees, suggesting complex evolutionary histories in brassy minnow. Sampling brassy minnow within BC revealed highest catch rates in the Interior of the province, and a year-long survey conducted in the Lower Mainland (n = 60 sites), revealed that brassy minnow abundances were highest at Westham Island. A logistic-regression habitat model was performed incorporating seven physical habitat parameters over 37 sites, identifying conductivity as a near significant parameter for predicting brassy minnow presence. Additionally, in the Lower Mainland, eight invasive species constituted 28 % of the relative abundance of species sampled. Compared to historical records from the University of BC Fish Museum, sites exhibited a significant decline in the number of cypriniform species, including brassy minnow, but showed no significant change in the number of invasive species present. A detrended correspondence analysis (DCA) of species abundance across sites suggested brassy minnow overlapped most closely with two invasive species: bullfrogs, Lithobates catesbieanus, and brown bullhead, Ameiurus nebulosus. To explore the impact of brown bullhead on brassy minnow, pools with and without adult brown bullhead were compared at Tamboline Slough, Westham Island, and showed significant differences in the native fish species abundances across pools, including brassy minnow. Additionally, growth experiments were conducted over 90 days with brassy minnow, young-of-year brown bullhead, and redside shiner, Richardsonius balteatus, kept in all possible combinations for a total of four treatments per species. Treatments showed that brassy minnow were the only species to exhibit weight loss and mortality when with other species. In addition to providing insights into the biogeography, ecology, and conservation implications of brassy minnow, my thesis provides a quantitative baseline for invasive species found within the Lower Mainland.

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The Cultus pygmy sculpin (Cottus aleuticus) is endemic to Cultus Lake, southwestern BC, and is listed as threatened under the federal Species at Risk Act (SARA). The Cultus pygmy sculpin was first discovered by Ricker in the 1930’s (Ricker 1960) and was described as a dwarf coastrange sculpin (C. aleuticus). It matures at a smaller size than the “normal” C. aleuticus; has a lacustrine rather than a fluvial life history; and appears to undertake diurnal feeding migrations into the water column to feed on the abundance of Daphnia. The Cultus pygmy sculpin also has different morphological features, including larger cephalic pores, shorter pelvic fins, and a greater number of pectoral fin rays, which may be advantageous for an open-water, planktivorous lifestyle. Little else, however, is known of the biology of this fish. I used mtDNA and microsatellite analyses to determine whether there is any genetic distinction between the pygmy sculpin and the coastrange sculpin. Potential behavioural differences between the two forms were also examined by comparing vertical depth selection in the laboratory, with and without Cottus asper, a benthic predator found in Cultus Lake. Results from combined microsatellite and mtDNA analyses indicate that there is no clear phylogeographic separation between pygmy and coastrange sculpin, but that there is genetic differentiation at the population level. Pelagic sculpin from Lake Washington were compared with the Cultus pygmy sculpin and showed divergence from it, which suggests that the pelagic life history has evolved independently in each lake. The Cultus pygmy sculpin was found significantly higher in experimental depth selection tanks than the stream forms of C. aleuticus, but only when C. asper was also present in the tanks. Taken together, molecular and behavioural results indicate that the Cultus pygmy sculpin is discrete from the coastrange sculpin, and validate its recognition as a conservation unit distinct from “typical” C.aleuticus. The presence of abundant planktonic prey within the water column of Cultus Lake, combined with the presence of predators on the lake’s bottom, may be important features of the lake that have promoted the evolution of pelagic behaviour by the Cultus pygmy sculpin.

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Southwestern British Columbia is unique in that it is apparently the only place on Earth with sympatric species pairs of threespine stickleback (Gasterosteus aculeatus). As such, these species pairs are listed as endangered and are protected under Canada’s Species at Risk Act. Historically these species pairs inhabited seven known lakes but their distribution is currently limited to five lakes in three watersheds. Within these lakes stickleback are found in two forms: benthic and limnetic. These species pairs are thought to have originated through a double-invasion process followed by character displacement. While this hypothesis is supported by morphology and genetics it does not take into account the environmental factors needed to support threespine stickleback in two separate microhabitats, which may be essential for their continued persistence. It is conceivable that the divergence and persistence of the threespine stickleback species pairs may be due in part to unique environmental characteristics of the lakes they inhabit, including physical lake characteristics, water chemistry, or biological productivity. Alternatively, divergence and persistence could be due to specific attributes of fish community structure or random colonization events unrelated to lake attributes. To establish this, I measured a number of abiotic (water chemistry, physical lake parameters) and biotic (food resources, macrophyte abundance) variables from both species pair and non-species pair threespine stickleback lakes in order to identify any factors that may discriminate species pair lakes from non-species pair lakes, thereby leading to a clearer understanding of their critical habitat. While I did not find any clear environmental differences between species pair and non-species pair lakes, my study suggests that a major determinant of the existence of stickleback species pairs is the community of fish present in the lakes and that nesting habitat heterogeneity and its influence on pre-mating reproductive barriers may be important to the persistence of these species pairs. My study provides a baseline to monitor the environments for all known species pair lakes and suggests that the fish assemblage in stickleback lakes may affect resource availability as strongly as the limnological attributes of the lakes themselves although predation may also be an important factor in the evolution of these species pairs.

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Biodiversity is of critical importance to the quality of life on Earth. In light of rapidly increasing extinction rates in recent years, understanding threats to biodiversity such as habitat destruction, over-exploitation, and the introduction of invasive species is of utmost importance to conservation efforts. Invasive species, in particular, are a threat of great concern in aquatic environments, due, in part, to their potential role in facilitating introgressive hybridization between closely related species. In recent decades, such a case of hybridization has led to genomic extinction in a benthic-limnetic species pair of threespine stickleback (Gasterosteus aculeatus) in Enos Lake, British Columbia, following the appearance of invasive American signal crayfish (Pacifastacus leniusculus) in this waterbody. In an effort to shed light on the potential role of these crayfish in this loss of diversity, research was conducted using an intact species pair from Paxton Lake, BC to determine if crayfish exert meaningful impacts on sticklebacks through the disruption of i) male stickleback reproductive behaviours and/or ii) juvenile stickleback growth rates. The results of reproductive behaviour trials demonstrated that limnetic male reproductive behaviour frequency was suppressed to a greater degree than that of benthic males in the presence of crayfish. This result suggests that crayfish disruptions may reduce conspecific mating opportunities for limnetic females, thus leading to increases in introgressive hybridization between benthic males and limnetic females. The results of the juvenile growth rate trial, on the other hand, demonstrated that crayfish do not disrupt growth rates of juveniles; however, significantly higher stickleback mortality levels were detected in the presence of crayfish. I conclude that invasive American signal crayfish have likely facilitated introgressive hybridization between the Enos Lake species pair, but other factors may have contributed to this loss of biodiversity. My study highlights the sensitivity of recently differentiated species to disruption by invasive species. By identifying important sources of ecological disruption and significant threats to biodiversity, such studies are critical for guiding conservation efforts in Canada and worldwide.

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