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Data from: A test of somatic mosaicism in the androgen receptor gene of Canada lynx (Lynx canadensis)
Prentice, Melanie B.; Bowman, Jeff; Wilson, Paul J. — 2016-10-14 Background: The androgen receptor, an X-linked gene, has been widely studied in human populations because it contains highly polymorphic trinucleotide repeat motifs that have been associated with a number of adverse human health and behavioral effects. A previous study on the androgen receptor gene in carnivores reported somatic mosaicism in the tissues of a number of species including Eurasian lynx (Lynx lynx). We investigated this claim in a closely related species, Canada lynx (Lynx canadensis). The presence of somatic mosaicism in lynx tissues could have implications for the future study of exonic trinucleotide repeats in landscape genomic studies, in which the accurate reporting of genotypes would be highly problematic. Methods: To determine whether mosaicism occurs in Canada lynx, two lynx individuals were sampled for a variety of tissue types (lynx 1) and tissue locations (lynx 1 and 2), and 1,672 individuals of known sex were genotyped to further rule out mosaicism. Results: We found no evidence of mosaicism in tissues from the two necropsied individuals, or any of our genotyped samples. Conclusions: Our results indicate that mosaicism does not manifest in Canada lynx. Therefore, the use of hide samples for further work involving trinucleotide repeat polymorphisms in Canada lynx is warranted. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Signatures of selection in mammalian clock genes with coding trinucleotide repeats: implications for studying the genomics of high-pace adaptation
Prentice, Melanie B.; Bowman, Jeff; Lalor, Jillian L.; McKay, Michelle M.; Thomson, Lindsay A.; Watt, Cristen M.; McAdam, Andrew G.; Murray, Dennis L.; Wilson, Paul J. — 2017-08-23 Climate change is predicted to affect the reproductive ecology of wildlife; however, we have yet to understand if and how species can adapt to the rapid pace of change. Clock genes are functional genes likely critical for adaptation to shifting seasonal conditions through shifts in timing cues. Many of these genes contain coding trinucleotide repeats, which offer the potential for higher rates of change than single nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate to faster rates of adaptation in changing environments. We characterized repeats in 22 clock genes across all annotated mammal species and evaluated the potential for selection on repeat motifs in three clock genes (NR1D1, CLOCK, and PER1) in three congeneric species pairs with different latitudinal range limits: Canada lynx and bobcat (Lynx canadensis and L. rufus), northern and southern flying squirrels (Glaucomys sabrinus and G. volans), and white-footed and deer mouse (Peromyscus leucopus and P. maniculatus). Signatures of positive selection were found in both the interspecific comparison of Canada lynx and bobcat, and intraspecific analyses in Canada lynx. Northern and southern flying squirrels showed differing frequencies at common CLOCK alleles and a signature of balancing selection. Regional excess homozygosity was found in the deer mouse at PER1 suggesting disruptive selection, and further analyses suggested balancing selection in the white-footed mouse. These preliminary signatures of selection and the presence of trinucleotide repeats within many clock genes warrant further consideration of the importance of candidate gene motifs for adaptation to climate change.
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Mast productivity, red-backed vole productivity and rate of increase, northern saw-whet owl rate of increase, and fisher harvest age ratios for central Ontario, 1994-2016
Greenhorn, Janet; Bowman, Jeff; Denomme-Brown, Simon; Ethier, Danielle — 2021-08-09 <p>Harvest management quotas for fishers (<i>Pekania pennanti</i>) in some jurisdictions are estimated from the previous year’s harvest, and stem from the hypothesis that age ratios in the harvest are largely influenced by ‘top-down’ trapping pressure.  The influence of ‘bottom-up’ food supply on fisher harvest age ratios might be underappreciated, which could result in a misallocation of quotas in management planning. We assessed a variety of data sources to test the influence of bottom-up processes on fisher populations in Ontario, Canada. We found evidence that bottom-up trophic effects influence the harvested fisher age structure in some regions of Ontario. Evidence also suggests that harvest pressure had little top-down influence on age ratios over the course of our study, and that basing management strategies on this assumption may lead to unintentional overharvest in years of low productivity.  We suggest several trophic linkages with potential to facilitate fisher management, including connections among berry and seed crops, small mammals, and Northern saw-whet owls (<i>Aegolius acadicus</i>).</p>
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Data from: Historical surveys reveal a long-term decline in muskrat populations
Sadowski, Carrie; Bowman, Jeff — 2022-04-07 <p>The muskrat (<i>Ondatra zibethicus</i>) is an iconic species in Canada, valued for both its fur and its integral role in wetland ecosystems, and widely regarded for its perseverance. However, the resilience of this semi-aquatic mammal seems to be in question now as increasing evidence points to widespread population declines. Recent analyses of harvest data across North America suggest a reduction in their numbers, but this has not been widely corroborated by population surveys. In this study we replicated historic muskrat house count surveys at two large Great Lakes coastal wetlands and present confirmation that declines in muskrat harvest correspond to actual declines in muskrat abundance. At the Point Pelee National Park marsh and the Matchedash Bay-Gray Marsh wetland we found that mean muskrat house counts declined by 93% and 91% respectively between historic surveys 40-50 years ago and contemporary surveys over the past seven years. The factors responsible for these dramatic declines remain unclear but there may be a relationship with changes in the habitat quality of these wetlands that have occurred over the same time frame. Not only is the loss of muskrats an issue for the resulting loss of the wetland ecosystem services they provide, but it may be an indication of broader marsh ecosystem degradation. As such, a scarcity of muskrats should be considered a red flag for the state of biodiversity in our wetlands. Continued surveys and ongoing research are needed to shed more light on the current status of muskrat populations and their marsh habitats across their native range.</p>
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Vocalizations of the squirrel family
Newar, Sasha; Bowman, Jeff — 2020-07-06 <p>The dataset <b>Squirrel_Calls</b> is a collection of vocal records (defined as primary literature that numerically describes the vocalization of at least 1 squirrel species) where each row corresponds to a single call type of one species. The details of the row include a summary of the literature metadata, categorical descriptions of the call and the caller as well as numerical values of the call frequencies. The dataset <b>Squirrel_Ecological_Traits</b> is a corresponding set of ecological traits for all the species listed in the Squirrel_Calls dataset. The traits listed (mass, time partitioning, gliding capabilities, habitat, and sociality) reflect hypotheses and predictions explored in the associated article. At the end of this document, there is a complete list of the literature references used to assemble these datasets. <b>Squirrel_Script </b>is the R script used to produce the statistics and models used in the corresponding paper. <b>Squirrel_Tree </b>is a nexus file compiling the data of 1000 trees downloaded from VertLife.org which were subsetted from their published mammalian supertree. The nexus file was used in the R script.</p>
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Continent-wide effects of urbanization on bird and mammal genetic diversity
Schmidt, Chloé; Domaratzki, Michael; Kinnunen, Riikka; Bowman, Jeff; Garroway, Colin — 2020-01-20 <p>Urbanization and associated<b> </b>environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.</p>
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Data from: Spatial segregation and habitat partitioning of bobcat and Canada lynx
Dryad
Marrotte, Robby R.; Bowman, Jeff; Morin, Samantha — 2020-10-19 <p style="margin-bottom:11px;">Harvest records suggest that the abundance of bobcats (<i>Lynx rufus</i>) has increased and the leading edge of their distribution has spread northward, while the trailing edge of the Canada lynx (<i>Lynx canadensis</i>) range has contracted in Ontario, Canada. There has been a debate about whether these closely related felids might compete in areas of sympatry, but there is little research on sympatric populations of bobcat and lynx. Both species are found on the north shore of Lake Huron in Ontario, Canada, which provided an opportunity to investigate their spatial patterns and habitat use. We surveyed snowmobile routes for snow tracks over 3 winters and estimated probability of occupancy for the two felid species while accounting for detectability. Bobcat and lynx tracks were never found on the same survey route. Bobcat occupancy increased with habitat heterogeneity whereas lynx occupancy increased with homogeneity. Our results fit with the common assumption of the generalist and specialist natures of bobcat and lynx, respectively. Our findings suggest that bobcats invaded former lynx territory after these areas became vacant. The story of the bobcat and the lynx is one of the loss of a unique, boreal specialist due to anthropogenic change, and eventual replacement by an adaptable generalist.</p>
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Seasonal roost selection of wild turkeys at their northern range edge
Dryad
Adey, Elizabeth; Baici, Jennifer; Bowman, Jeff — 2023-10-12 <p>Wild turkeys (<em>Meleagris gallopavo</em>) are diurnally active birds that spend the dark hours roosting in trees. We tested the hypothesis that multiple benefits exist for roost tree selection by wild turkeys, including thermoregulation, resource acquisition, and protection from predators. We compared 48 roost trees used by eastern wild turkeys (M. g. <em>silvestris</em>) in Ontario, Canada to 48 non-roost trees sampled contemporaneously during 2017-2019 to determine roost site selection between seasons. Mean (± SE) roost tree height (21.4 ± 0.8 m) was taller than non-roost trees (18.2 ± 0.8 m), and roost trees were also larger in diameter at breast height (58.1 ± 5.5 cm versus 38.7 ± 3.1 cm). Using ibuttons to collect microclimate temperatures at the tree, we found that mean temperature (± SE) of a deciduous roost (14.5 ± 0.1°C) was higher than temperature at either a coniferous roost (13.9 ± 0.1°C) or ambient temperature (13.2 ± 0.1°C) during the summer months. In winter however, we did not find any relationship between temperature and tree type. Roosts were closer to buildings (150.8 ± 26.0 m) in the winter compared to summer and year-round roosts, and winter roosts were also farther away from crops (395.2 ± 63.7 m) compared to roost sites used year-round. Summer roosts were closer to roads (143 ± 36.3 m) than the roosts in the winter and roosts used year-round. Our data suggest that thermoregulation is not the driving force behind roost selection; instead, predator avoidance appears to play the most important role, with some weaker evidence in support of proximity to resources.</p>
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Vocal range and ultraviolet-induced photoluminescence in gliding mammals and their relatives
Dryad
Newar, Sasha; Schneiderová, Irena; Hughes, Bryan; Bowman, Jeff — 2024-02-27 <p>Gliding is only present in six extant groups of mammals – interestingly, despite divergent evolutionary histories, all mammalian gliders are strictly nocturnal. Gliding mammals also seem to have relatively high rates of ultrasound use and ultraviolet-induced photoluminescence (UVP) in contrast with their close relatives. Therefore, we hypothesized that, despite diverging lineages, gliding mammals use similar modes of cryptic communication compared to their non-gliding counterparts. We developed two datasets containing the vocal range (minimum-maximum of the dominant harmonic; kHz) and UVP of 73 and 82 species, respectively; we report five novel vocal repertoires and 57 novel observations of the presence or absence of UVP. We complemented these datasets with information about body size, diel activity patterns, habitat openness, and sociality to explore possible covariates related to vocal production and UVP. We found that the maximum of the dominant harmonic was significant higher in gliding mammals when vocalizing than their non-gliding relatives. Additionally, we found that nocturnality was the only significant predictor of UVP, consistent with the previous hypothesis that luminophores primarily drive UVP in mammal fur. In contrast, however, we did not find UVP ubiquitous in nocturnal mammals, suggesting that some unknown process may contribute to variation in this trait.</p>
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Data from: Multi-species genetic connectivity in a terrestrial habitat network
Dryad
Marrotte, Robby R.; Bowman, Jeff; Brown, Michael G. C.; Cordes, Chad; Morris, Kimberley Y.; Prentice, Melanie B.; Wilson, Paul J. — 2018-10-02 Background: Habitat fragmentation reduces genetic connectivity for multiple species, yet conservation efforts tend to rely heavily on single-species connectivity estimates to inform land-use planning. Such conservation activities may benefit from multi-species connectivity estimates, which provide a simple and practical means to mitigate the effects of habitat fragmentation for a larger number of species. To test the validity of a multi-species connectivity model, we used neutral microsatellite genetic datasets of Canada lynx (Lynx canadensis), American marten (Martes americana), fisher (Pekania pennanti), and southern flying squirrel (Glaucomys volans) to evaluate multi-species genetic connectivity across Ontario, Canada. Results: We used linear models to compare node-based estimates of genetic connectivity for each species to point-based estimates of landscape connectivity (current density) derived from circuit theory. To our knowledge, we are the first to evaluate current density as a measure of genetic connectivity. Our results depended on landscape context: habitat amount was more important than current density in explaining multi-species genetic connectivity in the northern part of our study area, where habitat was abundant and fragmentation was low. In the south however, where fragmentation was prevalent, genetic connectivity was correlated with current density. Contrary to our expectations however, locations with a high probability of movement as reflected by high current density were negatively associated with gene flow. Subsequent analyses of circuit theory outputs showed that high current density was also associated with high effective resistance, underscoring that the presence of pinch points is not necessarily indicative of gene flow. Conclusions: Overall, our study appears to provide support for the hypothesis that landscape pattern is important when habitat amount is low. We also conclude that while current density is proportional to the probability of movement per unit area, this does not imply increased gene flow, since high current density tends to be a result of neighbouring pixels with high cost of movement (e.g., low habitat amount). In other words, pinch points with high current density appear to constrict gene flow.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Climate connectivity of the bobcat in the Great Lakes region
Dryad
Marrotte, Robby R.; Bowman, Jeff; Wilson, Paul J. — 2021-10-19 <p>The Great Lakes and the St. Lawrence River are imposing barriers for wildlife and the additive effect of urban and agricultural development that dominates the lower Great Lakes region likely further reduces functional connectivity for many terrestrial species. As the climate warms species will need to track climate across these barriers. It is important, therefore, to investigate land cover and bioclimatic hypotheses that may explain the northward expansion of species through the Great Lakes. We investigated the functional connectivity of a vagile generalist, the bobcat, as a representative generalist forest species common to the region. We genotyped tissue samples collected across the region at 14 microsatellite loci and compared different landscape hypotheses that might explain the observed gene flow or functional connectivity. We found that the Great Lakes and the additive influence of forest stands with either low or high canopy cover and deep lake-effect snow have disrupted gene flow, whereas intermediate forest cover has facilitated gene flow. Functional connectivity in southern Ontario is relatively low and was limited in part by the low amount of forest cover. Pathways across the Great Lakes were through the Niagara region and through the Lower Peninsula of Michigan over the Straits of Mackinac and the St. Mary’s River. These pathways are important routes for bobcat range expansion north of the Great Lakes and are also likely pathways that many other mobile habitat generalists must navigate to track the changing climate. The extent to which species can navigate these routes will be important for determining the future biodiversity of areas north of the Great Lakes.</p>
Dryad Translation missing: fr.blacklight.search.logo
Data from: Node-based measures of connectivity in genetic networks
Koen, Erin L.; Bowman, Jeff; Wilson, Paul J. — 2015-04-30 At-site environmental conditions can have strong influences on genetic connectivity, and in particular on the immigration and settlement phases of dispersal. However, at-site processes are rarely explored in landscape genetic analyses. Networks can facilitate the study of at-site processes, where network nodes are used to model site-level effects. We used simulated genetic networks to compare and contrast the performance of 7 node-based (as opposed to edge-based) genetic connectivity metrics. We simulated increasing node connectivity by varying migration in two ways: we increased the number of migrants moving between a focal node and a set number of recipient nodes, and we increased the number of recipient nodes receiving a set number of migrants. We found that two metrics in particular, the average edge weight and the average inverse edge weight, varied linearly with simulated connectivity. Conversely, node degree was not a good measure of connectivity. We demonstrated the use of average inverse edge weight to describe the influence of at-site habitat characteristics on genetic connectivity of 653 American martens (Martes americana) in Ontario, Canada. We found that highly connected nodes had high habitat quality for marten (deep snow and high proportions of coniferous and mature forest) and were farther from the range edge. We recommend the use of node-based genetic connectivity metrics, in particular, average edge weight or average inverse edge weight, to model the influences of at-site habitat conditions on the immigration and settlement phases of dispersal.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis) on Newfoundland and Cape Breton Island
Dryad
Prentice, Melanie B.; Bowman, Jeff; Khidas, Kamal; Koen, Erin L.; Row, Jeffrey R.; Murray, Dennis L.; Wilson, Paul J. — 2018-04-14 Island populations have long been important for understanding the dynamics and mechanisms of evolution in natural systems. While genetic drift is often strong on islands due to founder events and population bottlenecks, the strength of selection can also be strong enough to counteract the effects of drift. Here, we used several analyses to identify the roles of genetic drift and selection on genetic differentiation and diversity of Canada lynx (Lynx canadensis) across eastern Canada, including the islands of Cape Breton and Newfoundland. Specifically, we assessed whether we could identify a genetic component to the observed morphological differentiation that has been reported across insular and mainland lynx. We used a dinucleotide repeat within the promoter region of a functional gene that has been linked to mammalian body size, insulin-like growth factor-1 (IGF-1). We found high genetic differentiation at neutral molecular markers but convergence of allele frequencies at the IGF-1 locus. Thus, we showed that while genetic drift has influenced the observed genetic structure of lynx at neutral molecular markers, natural selection has also played a role in the observed patterns of genetic diversity at the IGF-1 locus of insular lynx.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Sex-specific graphs: Relating group-specific topology to demographic and landscape data
Dryad
Bertrand, Philip; Bowman, Jeff; Dyer, Rodney; Manseau, Micheline; Wilson, Paul J.; Dyer, Rodney J. — 2017-05-05 Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life history traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have used genetic structure to investigate sex-specific functional connectivity. The recent use of graph theoretic approaches in landscape genetics has demonstrated network capacities to describe complex system behaviours where network topology represents genetic interaction among subunits. Here, we partition the overall genetic structure into sex-specific graphs, revealing different male and female dispersal dynamics of a fisher (Pekania [Martes] pennanti) metapopulation in southern Ontario. Our analyses based on network topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population level, could be partitioned among sex-specific strata. We found that female connectivity was negatively correlated with snow depth, whereas connectivity among males was not. Our findings underscore the potential of conducting sex-specific analysis by identifying landscape elements or configuration that differentially promotes or impedes functional connectivity between sexes, revealing processes that may otherwise remain cryptic. We propose that the sex-specific graph approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.
Dryad Translation missing: fr.blacklight.search.logo
Data from: Southern range dynamics of Canada lynx over seven decades
Dryad
Marrotte, Robby R.; Bowman, Jeff — 2022-02-22 <p style="margin-bottom:11px;">The range of the Canada lynx (<i>Lynx canadensis</i>) has contracted substantially from its historical range. Using harvest records, we found that the southern range of the lynx in Ontario in the late 1940s collapsed and then, in a short period of time, increased to its largest extent in the mid-1960s when the lynx range spread south of the boreal forest for a decade. After this expansion the southern range contracted northwards beginning in the 1970s. Most recently, there has been a slight expansion between 2010-2017. We have attributed these dynamics on the southern range periphery to the fluctuation of the boreal lynx population in the core of the species’ range. In addition, connectivity to boreal lynx populations and snow depth seemed to condition whether the lynx expanded into an area. However, we did not find any evidence to suggest that these changes were due to anthropogenic disturbances or competition. The boreal lynx population does not reach the peak abundance it once did, without which we would not expect to see large expansions of the southern lynx range as in the mid-1960s. Our results suggest that southern lynx range in Ontario have been driven by the magnitude of the boreal lynx population cycle, connectivity to the boreal forest, and snow conditions. Therefore, it is quite unlikely that southern lynx population in the Great Lakes will recover, since the warming climate and habitat changes are causing a northward contraction of the boreal forest and likely with it the core lynx populations.</p>
Dryad Translation missing: fr.blacklight.search.logo
Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
Dryad
Prentice, Melanie; Bowman, Jeff; Murray, Dennis; Khidas, Kamal; Wilson, Paul — 2020-11-20 Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
Dryad Translation missing: fr.blacklight.search.logo
Functional genetic diversity of domestic and wild American mink (Neovison vison )
Dryad
Morris, Kimberley Y.; Bowman, Jeff; Schulte-Hostedde, Albrecht; Wilson, Paul J. — 2020-08-07 <p>The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (<i>Neovison vison</i>) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 microsatellites located in functional genes and in a promoter region that is non-coding but thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only 4 of 17 genes were variable, and the number of alleles per locus were generally lower in captive mink than in wild mink. To determine if allele frequencies of wild populations were affected by domestic release events, we performed redundancy analysis and spatial analysis of principal components on four polymorphic loci (AR, ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1, and IGF1.</p>

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