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Dice’s cottontail, Sylvilagus dicei, only was recognized as a valid species in 1981 after having been subsumed in synonymy with S. brasiliensis and S. gabbi, which latter also at times had been syn...

Over the past 30 years, the California condor (Gymnogyps californianus) population has rebounded from 22 individuals to over 200 birds living in the wild. Historical impacts to the population have been largely anthropogenic. In this study, we explore mortality and cause of death data from condors that died during the years 2010-2014 and compare these to mortality data described by Rideout et al. in 2012, covering the years 1992-2009. In addition, morphologic and genetic analysis of the contents of the upper gastrointestinal (GI) tract was performed on the 2010-2014 condor mortalities to determine animal origins of the last meal eaten. The maximum population at risk within this time frame was 329 birds. During this time, 88 condors died and underwent post-mortem examination, and 41 birds were lost to tracking efforts and presumed dead (crude mortality rate of 39%; 129/329). A cause of death was determined for 66 of the 88 necropsied birds. Lead toxicosis remained a significant negative factor in condor population recovery, being related to the deaths of 37 adult and juvenile condors (proportional mortality rate 56%). Compared to condors succumbing to other causes of death, cattle were less often part of the last meal of lead-intoxicated condors. Based on these data, continued efforts to mitigate the impact of lead on California condors should be pursued.

The essential purpose of biodiversity conservation is to protect individual species and to preserve habitats and ecosystems which have declined in quantity and quality over time as a result of human activities. In some instances, laws have been passed to protect vulnerable resources from overexploitation and to support efforts that address biodiversity conservation. Enforcement of laws intended to protect natural resources can only be accomplished if it can be demonstrated that violations have occurred. With respect to biodiversity conservation, this means being able to protect both the species impacted and their habitat. The protection of individual species requires the ability to characterize species, as well as how those species are structured in animal communities. Forensic science is deeply rooted in international legal systems, dating back to the first use of fingerprints to identify deceased humans in China in the 700s. The field of wildlife forensic genetics is currently used to support wildlife law enforcement investigations. The evolution of wildlife forensic genetics closely follows the use of genetic technologies in the field of human forensic identification, with some significant differences in its application for wildlife law enforcement. In this chapter, we will provide an overview of how wildlife forensic genetics intersects with biodiversity conservation efforts and provide case studies which illustrate the diverse application of forensic genetics to the enforcement of wildlife conservation laws.

The majority of DNA casework processed by forensic laboratories focuses on human samples, but material from canids (dogs, wolves, coyotes) can also be encountered. Undomesticated canids can be the center of forensic investigations in the U.S. since some species are endangered. As many wolf species are similar morphologically, identification in the field by wildlife officers is not always straight-forward, making molecular based-approaches ideal. While some published methods using mitochondrial DNA targets can discriminate among Canis species, they are either not compatible with highly degraded samples or cannot differentiate closely related sub-species. Although some U.S. laboratories regularly perform veterinary/wildlife casework including canid identifications, their validated methods and reference genetic databases are not publicly available. We aimed to assess the utility of alternative regions in the mitochondrial genome for discriminating among canid species, including the complete genome. To achieve this, we utilized a commercial hybridization capture panel composed of biotinylated RNA “baits” designed for the domestic dog to enrich canid mitochondrial genomes for next-generation sequencing. We used this panel to successfully sequence complete mitochondrial genomes for 51 samples, representing four U.S. forensically relevant canids (coyote, wolf, Mexican wolf, dog). While the complete mitochondrial genome permitted discrimination, we also assessed previously published mitochondrial DNA targets (n, 5) for resolution and identified four alternate ∼200 bp fragments from ND1, ND5, COI and CYTB genes that could help resolve canids. The utility of these alternate regions should be assessed in future studies using forensic-type samples representing canids from diverse geographic areas, prior to casework implementation.

We document isolation and characterization of 13 tri- and tetranucleotide microsatellite DNA markers in brook trout (Salvelinus fontinalis). These markers displayed moderate to high levels of allelic diversity (averaging 20.5 alleles/locus) and heterozygosity (averaging 53.5%) in a range-wide survey of more than 13,000 fish. A comparison of two geographically proximal populations located on opposite sides of the eastern continental divide in Maryland, USA, found no deviations from Hardy–Weinberg equilibrium and minimal linkage disequilibrium. Microsatellite markers developed for S. fontinalis yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate phylogeographic structure; and (3) provide unique demographic perspectives of population sizes and historical demographics. This suite of markers also provided considerable cross-species amplification utility among related salmonids.

Efforts over several decades to restore lake trout Salvelinus namaycush in U.S. waters of the upper Great Lakes have emphasized the stocking of juveniles from each of six hatchery broodstocks. Retention of genetic diversity across all offspring life history stages throughout the hatchery system has been an important component of the restoration hatchery and stocking program. Different stages of the lake trout hatchery program were examined to determine how effective hatchery practices have been in minimizing the loss of genetic diversity in broodstock adults and in progeny stocked. Microsatellite loci were used to estimate allele frequencies, measures of genetic diversity, and relatedness for wild source populations, hatchery broodstocks, and juveniles. We also estimated the effective number of breeders for each broodstock. Hatchery records were used to track destinations of fertilized eggs from all spawning dates to determine whether adult contributions to stocking programs were proportional to ...

The biological diversity of lake trout Salvelinus namaycush in the upper Great Lakes was historically high, consisting of many recognizable morphological types and discrete spawning populations. During the 1950s and 1960s, lake trout populations were extirpated from much of the Great Lakes primarily as a result of overfishing and predation by the parasitic sea lamprey Petromyzon marinus. Investigations of how genetic diversity is partitioned among remnant wild lake trout populations and hatchery broodstocks have been advocated to guide lake trout management and conservation planning. Using microsatellite genetic markers, we estimated measures of genetic diversity and the apportionment of genetic variance among 6 hatchery broodstocks and 10 wild populations representing three morphotypes (lean, humper, and siscowet). Analyses revealed that different hatchery broodstocks and wild populations contributed disproportionally to the total levels of genetic diversity. The genetic affinities of hatchery l...

We demonstrate the effectiveness of a genetic algorithm for discovering multi-locus combinations that provide accurate individual assignment decisions and estimates of mixture composition based on likelihood classification. Using simulated data representing different levels of inter-population differentiation (Fst ∼ 0.01 and 0.10), genetic diversities (four or eight alleles per locus), and population sizes (20, 40, 100 individuals in baseline populations), we show that subsets of loci can be identified that provide comparable levels of accuracy in classification decisions relative to entire multi-locus data sets, where 5, 10, or 20 loci were considered. Microsatellite data sets from hatchery strains of lake trout, Salvelinus namaycush, representing a comparable range of inter-population levels of differentiation in allele frequencies confirmed simulation results. For both simulated and empirical data sets, assignment accuracy was achieved using fewer loci (e.g., three or four loci out of eight for empirical lake trout studies). Simulation results were used to investigate properties of the ‘leave-one-out’ (L1O) method for estimating assignment error rates. Accuracy of population assignments based on L1O methods should be viewed with caution under certain conditions, particularly when baseline population sample sizes are low (

Populations of wild lake trout Salvelinus namaycush have been extirpated from nearly all their historical habitats across the Great Lakes. Efforts to restore self-sustaining lake trout populations in U.S. waters have emphasized the stocking of coded-wire-tagged juveniles from six hatchery strains (Seneca Lake, Lewis Lake, Green Lake, Apostle Islands, Isle Royale, and Marquette) into vacant habitats. Strain-specific stocking success has historically been based on estimates of the survival and catch rates of coded-wire-tagged adults returning to spawning sites. However, traditional marking methods and estimates of relative strain abundance provide no means of assessing strain fitness (i.e., the realized contributions to natural recruitment) except by assuming that young-of-the-year production is proportional to adult spawner abundance. We used microsatellite genetic data collected from six hatchery strains with likelihood-based individual assignment tests (IA) and mixed-stock analysis (MSA) to iden...

Classification methods used in machine learning (e.g., artificial neural networks, decision trees, and k-nearest neighbor clustering) are rarely used with population genetic data. We compare different nonparametric machine learning techniques with parametric likelihood estimations commonly employed in population genetics for purposes of assigning individuals to their population of origin ("assignment tests"). Classifier accuracy was compared across simulated data sets representing different levels of population differentiation (low and high F(ST)), number of loci surveyed (5 and 10), and allelic diversity (average of three or eight alleles per locus). Empirical data for the lake trout (Salvelinus namaycush) exhibiting levels of population differentiation comparable to those used in simulations were examined to further evaluate and compare classification methods. Classification error rates associated with artificial neural networks and likelihood estimators were lower for simulated data sets compared to k-nearest neighbor and decision tree classifiers over the entire range of parameters considered. Artificial neural networks only marginally outperformed the likelihood method for simulated data (0-2.8% lower error rates). The relative performance of each machine learning classifier improved relative likelihood estimators for empirical data sets, suggesting an ability to "learn" and utilize properties of empirical genotypic arrays intrinsic to each population. Likelihood-based estimation methods provide a more accessible option for reliable assignment of individuals to the population of origin due to the intricacies in development and evaluation of artificial neural networks.

Humpers are one of at least three morphological variants of wild lake trout Salvelinus namaycush that maintain self-sustaining populations in Lake Superior. In an early study, bumpers from Isle Royale were shown to have a sharply truncated age distribution that was attributed to high mortality after age 11, but we suspected that these fish were underaged. In August of 1989 and 1992 we collected spawning humper lake trout from the same area and estimated their ages using both scales and sagittal otoliths. Humpers in our sample ranged from 5 to 13 years, based on scale annuli, but counts of sagitta annuli revealed ages of 8 to 28 years. Individual discrepancies between ages from scales and sagittae varied from –2 to 20 years, but differences between scale and otolith ages did not increase with individual age. We applied the von Bertalanffy growth model to the humper length-at-age data to indirectly assess the accuracy of aging estimates. The model significantly overestimated mean asymptotic length ...

Naturally-reproducing populations of lake trout (Salvelinus namaycush) have been reestablished in most of Lake Superior, but have not been restored to 1929-1943 average abundance. Progress toward lake trout restoration in Lake Superior is described, management actions are reviewed, and the effectiveness of those actions is evaluated; especially stocking lake trout as a tool for building spawning stocks, and subsequently, populations of wild recruits. Widespread destruction of lake trout stocks in the 1950s due to an intense fishery and sea lamprey (Petromyzon marinus) predation resulted in lower overall phenotypic diversity than was previously present. Stocking of yearling lake trout, begun in the 1950s, produced high densities of spawners that reproduced wherever inshore spawning habitat was widespread. Sea lampreys were greatly reduced, beginning in 1961, using selective chemical toxicants and barrier dams, but continue to exert substantial mortality. Fishery regulation was least effective in Wisconsin, where excessive gillnet effort caused high by-catch of lake trout until 1991, and in eastern Michigan, where lake trout restoration was deferred in favor of a tribal fishery for lake whitefish (Coregonus clupeaformis) in 1985. Restoration of stocks was quicker in offshore areas where remnant wild lake trout survived and fishing intensity was low, and was slower in inshore areas where stocked lake trout reproduced successfully and fishing intensity was high. Inshore stocks of wild lake trout are currently about 61 % of historic abundance in Michigan and 53% in Wisconsin. Direct comparison of modern and historic abundances of inshore lake trout stocks in Minnesota and Ontario is impossible due to lack of historic stock assessment data. Stocks in Minnesota are less abundant at present than in Michigan or Wisconsin, and stocks in Ontario are similar to those in Michigan. Further progress in stock recovery can only be achieved if sea lampreys are depressed and if fisheries are constrained further than at present.

The goal of lake trout rehabilitation efforts in the Great Lakes has been to reestablish inshore lake trout (Salvelinus namaycush) populations to self-sustaining levels. A combination of sea lamprey control, stocking of hatchery-reared lake trout, and catch restrictions were used to enhance remnant lake trout stocks in Lake Superior and reestablish lake trout in Lakes Michigan, Huron, Erie, and Ontario. Genetic diversity is important for the evolution and maintenance of successful adaptive strategies critical to population restoration. The loss of genetic diversity among wild lake trout stocks in the Great Lakes imposes a severe constraint on lake trout rehabilitation. The objective of this synthesis is to address whether the particular strain used for stocking combined with the choice of stocking location affects the success or failure of lake trout rehabilitation. Poor survival, low juvenile recruitment, and inefficient habitat use are three biological impediments to lake trout rehabilitation that can be influenced by genetic traits. Evidence supports the hypothesis that the choices of appropriate lake trout strain and stocking locations enhance the survival of lake trout stocked into the Great Lakes. Genetic strategies proposed for lake trout rehabilitation include conservation of genetic diversity in remnant stocks, matching of strains with target environments, stocking a greater variety of lake trout phenotypes, and rehabilitation of diversity at all trophic levels.

Humans have played a significant role in reducing levels of genetic diversity and differentiation of many teleost fishes, leading to homogenization across biological entities. We compare patterns of historical and contemporary genetic structure for three sympatric Great Lake’s lake trout (Salvelinus namaycush) morphs (lean, siscowet, and humper) that differ in patterns of habitat occupancy, susceptibility to overfishing and predation by invasive sea lamprey (Petromyzon marinus). Differential susceptibilities to overfishing and predation were expected to result in different impacts to levels of genetic diversity loss for each morphotype. Genetic data was collected for samples at three points in time: 1948 (pre-collapse), 1959 (collapse) and 1990s (current), corresponding to periods of intensive fishing, mortality due to lamprey and recovery, respectively. The lean morph preferentially targeted by the fishery and recognized as highly preyed upon by sea lamprey was more highly impacted genetically than other morphs, as evidenced by greater loss of genetic diversity first during the period of overfishing, then during the period of high sea lamprey abundance once the fishery collapsed. The siscowet morph also experienced genetic bottlenecks during the period of overfishing (pre-collapse period). Results indicate significant levels of genetic differentiation among morphs historically prior to declines in abundance and also among contemporary populations, suggesting that periods of population decline and resurgence in abundance and distribution did not result in loss of genetic distinctiveness among morphs.

Paroaria dominicana, Saltator similis, Sporophila frontalis and Cyanoloxia brissonii are bird species severely exploited by the illegal wildlife trade in Brazil. As part of an effort to characterize the genetic populations within each species to infer the most likely population of origin of seized animals, four microsatellite enriched genomic libraries were constructed and cross amplification of selected primers was tested for all four species. Eight polymorphic loci were selected for P. dominicana with mean observed and expected heterozigosities (mean Ho and He) of 0.750 and 0.768 respectively. Nine were selected for S. similis with mean Ho and He of 0.688 and 0.760. Seven for C. brissonii with mean Ho and He of 0.805 and 0.811. Three loci for S. frontalis with mean Ho and He of 0.851 and 0.903. These markers will be useful for population studies and for the development of paternity tests to be used by commercial breeders.

International audience; Methods for assigning individuals to population of origin are widely used in ecological genetics, resources management, and forensics. Characteristics of genetic data obtained from putative source populations that enhance accuracy of assignment are well established. How non-independence within and among unknown individuals to be classified [i.e., gene correlations within individual (inbreeding) and gene correlations among individuals within group (coancestry)] affect assignment accuracy is poorly understood. We used empirical data for six microsatellite loci and offspring from full-sib crosses of hatchery strains of lake trout (Salvelinus namaycush; Salmonidae) representing known levels of coancestry (mean θ = 0.006 and 0.06) within families to investigate how gene correlations can affect assignment. Additional simulations were conducted to further investigating the influence of allelic diversity (2, 6 or 10 alleles per locus) and inbreeding (F = 0.00, 0.05, and 0.15) on assignment accuracy for cases of low and high inter-population variance in allele frequency (mean F st = 0.01 and 0.1, respectively). Inbreeding had no effect on accuracy of assignments. In contrast, variance in assignment accuracy across replicated simulations, and for each empirical case study increased with increasing coancestry, reflecting non-independence of probabilities of correct assignment among members of kin groups. Empirical estimates of assignment error rates should be interpreted with caution if appreciable levels of coancestry are suspected. Additional emphasis should be placed on sampling designs (spatially and temporally) that define or minimize the potential for sampling related individuals.

Lake trout (Salvelinus namaycush) in the upper Laurentian Great Lakes of North America experienced striking reductions in abundance and distribution during the mid-twentieth century. Complete collapse of populations was documented for Lake Michigan, and a few remnant populations remained only in lakes Huron and Superior. Using DNA obtained from historical scale collections, we analysed patterns of genetic diversity at five microsatellite loci from archived historical samples representing 15 populations (range 1940-1959) and from three contemporary remnant populations across lakes Huron and Superior (total n = 893). Demographic declines in abundance and the extirpation of native lake trout populations during the past 40 years have resulted in the loss of genetic diversity between lakes owing to extirpation of Lake Michigan populations and a temporal trend for reduction in allelic richness in the populations of lakes Superior and Huron. Naturally reproducing populations in Lake Superior, which had been considered to be remnants of historical populations, and which were believed to be responsible for the resurgence of lake trout numbers and distribution, have probably been affected by hatchery supplementation.

Three phenotypes of Salvelinus namaycush in Lake Superior, the lean, siscowet, and humper, are traditionally identified primarily by fat content and body shape. Their taxonomic status is in question because of intermediates as well as the possibility that the diagnostic characters are ecophenotypic. Two osteological characters, the dorsal opercular notch (first recorded by Agassiz in his description of the siscowet) and radii on the anterodorsal part of the supraethmoid, differ between most leans and siscowets. The notch in the opercle near its articulation with the hyomandibular bone is present in humpers, usually present in siscowets, and usually absent in leans. Radii on the anterodorsal surface of the supraethmoid bone usually are found in siscowets and humpers but usually are absent in leans. The correlations among these characters and other features of the phenotype indicate a significant level of differentiation between the three phenotypes. Available evidence suggests that the differentiation is genetic. The frequency of mixed phenotypes is evidence of limited gene flow among the phenotypes. The siscowet and humper phenotypes apparently originated in Lake Superior in postglacial time.