Kyle, Chris

Effective population size (Ne) is a key concept in population genetics, evolutionary biology and conservation biology that describes an important facet of genetic diversity and the capacity of populations to respond to future evolutionary pressures. The importance of Ne in management and conservation of wild populations encouraged the development of numerous genetic estimators which rely on a variety of methods. Despite the number and diversity of available Ne methods, however, tests of estimator performance have largely relied on simulations, with relatively few tests based on empirical data. I used well-studied wild populations of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario as a model system to assess the comparative performance of multiple Ne estimation methods and programs, comparing the resultant Ne estimates against demographic population size estimates.

As a first step, the genetic diversity and ancestry of wild brook trout populations was determined using 14 microsatellite loci. Genetic structure of brook trout populations showed variable contributions from historical supplemental stocking and also identified localized gene pools within and between watersheds, reflecting variable levels of connectivity and gene flow. Once the genetic ancestry and connectivity of populations had been resolved, single sample (point) and two samples (temporal) genetic estimators were used to estimate Ne of populations with pure native ancestry. Values obtained from genetic estimators utilizing both methods were variable within as well as among populations. Single sample (point) estimators were variable within individual populations, but substantially less than was observed among the temporal methods. The ratios of Ne to the estimated demographic population size (N) in small populations were substantially higher than in larger populations. Variation among estimates obtained from the different methods reflects varying assumptions that underlay the estimation algorithms. This research further investigated the effect of sampling effort and number of microsatellite loci used on Ne values obtained using the linkage disequilibrium (LD) estimation method. Ne estimates varied substantially among values generated from subsets of loci and genotyped individuals, highlighting the necessity for proper sampling design for efforts aiming to measure Ne. Despite the variation observed among and within estimation methods, the Ne concept is a valuable for the conservation and management of both exploited and endangered species.

Author Keywords: Brook Trout, Effective population size, Genetic Diversity, Genetic Structure

Identifying the population origin of aquaculture-reared caviar is crucial for both conservation and management strategies of farmed fish but could also facilitate international trade of a CITES regulated product. Shortnose sturgeon (Acipenser brevirostrum) is the main source of caviar production in Atlantic Canada, from Breviro Caviar Inc. aquaculture facility. Shortnose sturgeon are also listed as a species-at-risk under the Species At Risk Act. Currently there is no genetic method for delineating wild from aquaculture-reared caviar. By targeting the mitochondrial genome (mitogenome) using novel long-range PCR primers and next-generation sequencing (NGS) methods we have successfully sequenced the full mitogenome of 37 shortnose sturgeon. The purpose of this study was to increase the resolution of diagnostic variation among populations and to validate Canadian aquaculture-reared stock from wild US populations.

Results provided a previously unobserved novel control region haplotype in high frequency within both the aquaculture-reared and Saint John River wild sample sets. Similar frequencies were observed with whole mitogenome haplotypes. Diagnostic mitochondrial lineage found in high frequency within the captive Breviro Caviar Inc. population has the potential to allow caviar product from Breviro Caviar Inc. to be distinguished from protected US shortnose sturgeon populations. The application of full mitogenomic characterization provides the potential to further resolve differences between aquaculture and natural Canadian shortnose sturgeon stocks, US/Canadian populations and to contribute to future conservation strategies. Future research identifying signatures of selection on the mitogenome between captive and wild populations and across latitudinal gradients found within the species range. These novel methods have produced a proof-of-concept to provide a "farm-to-fork" validation and ecobrand of Breviro Caviar Inc. product and its aquaculture origin to support importation into US caviar markets.

Author Keywords: aquaculture, mitogenome, next-generation sequencing, species-at-risk, sturgeon

Forensic epistemology is the study of knowledge as it relates to forensic science and can be broken into four sources; intuitive, authoritative, logical and empirical. In a four-phase research approach, I explored reasoning skills (logical knowledge) used by crime scene experts and methods (empirical knowledge) for forensic case-specific experimentation. First, the reasoning skills of crime scene investigators (CSI) and bloodstain pattern analysts (BPA) were tested, correlated to demographics and reasoning categories were compared. Practitioner's with graduate level education performed better on the reasoning test, however, significant differences were not found between test scores and years of experience. Similarly, there was no difference between test scores and employment status (specifically, police or civilian employees), for the CSI group nor within the BPA group. This information suggests that level of education plays the most important role in the development and use of reasoning skills, whereas experience and employment status are not as influential. Second, I investigate potential strategies in selecting data types for case-specific experimentation in pattern-interpretation disciplines within forensic science. I also examined the epistemic status of practitioner case experimentation in forensic science. Practitioners were more confident in a mixed-method approach when conducting case-specific experimentation. In addition, there is a knowledge gap in experimental design for some forensic practitioners. Third, is a reprint of the introductory section of my published book entitled The Scientific Method in Forensic Science: A Canadian Handbook that abridges knowledge gained from this dissertation with further evidence-based literature review and experiential examples. This phase summarizes the scientific method in forensic science and provides guidance for forensic science students and practitioners. The final phase merges the findings from the primary studies with a literature review; offering scientific evidence supporting suggested research and pedagogic strategies that can help increase the epistemic status of forensic science.

Author Keywords: case-specific research, epistemology, forensic science, hypothetico-deductive reasoning, logic, research models