Physiology, Nutrition & Genetics

Contributed Oral

State-Dependent Decision-Making and Individual Variation in Large-Herbivore Space Use
Justine Becker, Ryan Long, Robert Pringle, Corina Tarnita

State-dependent behavioral theory predicts that animals alter their behavior in response to changes in individual energy dynamics in ways that maximize reproductive value. Considerable evidence now supports the idea that ungulates in temperate environments adjust their space-use behaviors in response to their nutritional condition, and this state-dependent decision making may contribute to observed individual differences in movement behavior within a population. To understand how widely applicable this theory is across large mammal fauna, there remains a need for further empirical tests that encompass a broader diversity of ecosystems and life-history strategies. Here, we test state-dependent behavioral theory and its importance for individual differences in movement and space use in two sympatric, congeneric tropical ungulate species that vary in body size. Using GPS telemetry and remote sensing data, we quantified the use of discrete, regularly distributed foraging hotspots (termite mounds) as a function of individual nutritional condition, measured both in terms of stored energy reserves and lactation status in the spiral-horned antelope bushbuck (Tragelaphus sylvaticus) and greater kudu (Tragelaphus streptisceros). Our results support the hypothesis that individuals adjust their space use behavior in response to their nutritional state, but that this relationship is mediated by body size. In both species, we found that individuals in poor condition used the high-quality resource hotspots on termite mounds more often than individuals in better condition; however, bushbuck were more responsive to differences in lactation status while the larger-bodied kudu were more responsive to differences in energy reserves.  Bushbuck, but not kudu, in good condition also exhibited more inter-individual variation in mound use than poor condition individuals. Collectively, our findings highlight the importance of two interacting constraints—nutritional condition and body size—for behavioral flexibility and emphasize the value of state-dependent behavioral theory for integrating research on behavioral variation with studies of animal movement.

Genetic Monitoring of the Northern Idaho Ground Squirrel: Implications for Species Recovery Efforts
Molly Garrett, Soraia Barbosa, Diane Evans Mack, Courtney Conway, Paul Hohenlohe, Lisette Waits

Northern Idaho ground squirrels (Urocitellus brunneus, hereafter NIDGS) are endemic to Idaho and federally listed as a threatened species. They persist within only a fraction of their former range due to habitat and population connectivity loss, mostly as a result of forest encroachment likely due to fire suppression. Since 2002, we have collected genetic samples from this species and evaluated genetic diversity and gene flow using mitochondrial DNA sequencing and nuclear DNA microsatellites.  More recently, we identified 3,575 single nucleotide polymorphism loci (SNP) and evaluated connectivity and adaptive diversity for 15 populations and 80 individuals.  We identified three evolutionary significant units, 7 management units, and 5 adaptive units.  However, our SNP analyses were limited to samples with large amounts of high-quality DNA, and thus represent an incomplete sampling of individuals and populations.  To address this limitation, we developed a set of 500 SNP loci for a Genotyping-in-Thousands by sequencing (GT-seq) panel that is currently being applied to 1,603 samples and 29 populations of archived and newly collected genetic samples. This dataset will be used to evaluate genetic diversity at neutral and adaptive loci, evaluate genetic structure and connectivity, estimate Ne, and identify conservation units based on neutral and adaptive loci. This information will provide insights into the extent to which NIDGS populations have had or continue to have genetic connectivity across the landscape, which populations are most important for species persistence, which populations show adaptive genetic differentiation, and which habitat features are appropriate targets for management action. Further, results will be used to evaluate NIDGS representation across their range in the context of the 3 R’s (Resiliency, Redundancy, Representation) to inform future recovery actions and provide the foundation for an upcoming recovery plan revision.

Dynamic Selection for Forage Quality and Quantity in Response to Phenology and Insects in Arctic Caribou
Heather Johnson, Trevor Golden, Layne Adams, David Gustine, Elizabeth Lenart, Perry Barboza

Spatiotemporal variation in forage is a primary driver of ungulate behavior, yet little is known about the nutritional components they select and how selection varies across the growing season. We addressed these uncertainties in barren-ground caribou (Rangifer tarandus), which experience their most important foraging opportunities during the short Arctic summer. Recent declines in Arctic populations have raised concerns about the influence of climate change on summer foraging opportunities, given shifts in vegetation conditions and insect harassment, and their potential effects on caribou body condition and demography. We examined the summer foraging behavior of Arctic caribou by pairing locations from females in the Central Arctic Herd of Alaska with spatiotemporal predictions of biomass, digestible nitrogen (DN), and digestible energy (DE) to 1) assess selection for these nutritional components across the summer at landscape and patch scales, and 2) determine whether foraging opportunities were constrained by insect harassment. During early summer, at the landscape scale, caribou selected intermediate biomass and high DN and DE, following expectations of the forage maturation hypothesis. At the patch scale, however, caribou selected high values of all forage components, particularly DN, suggesting that protein may be limiting. Later in the summer, after DN declined below the threshold for protein gain, caribou exhibited a switch at both spatial scales, selecting for higher biomass, and to a lesser extent DE, likely enabling fat deposition. Mosquito activity strongly altered caribou forage selection and increased their movement rates, while oestrid fly activity had little influence. Our results demonstrate that early and late summer periods afford Arctic caribou distinct foraging opportunities, as they prioritize quality earlier in the summer and quantity later. Climate change may further constrain caribou access to DN as earlier, warmer Arctic summers may be associated with reduced DN and increased mosquito harassment.

A Genetic Assessment of Isle Royale Wolves’ Founding Population: A Multi-Molecular Marker Perspective
Samuel Hervey, Bridgett vonHoldt, John Vucetich, Mark Romanski, Jerrold Belant, Kristin Brzeski

The gray wolf (Canis lupus) population of Isle Royale National Park suffered an extreme population decline where by 2017 only two wolves that were both half-siblings and a father-daughter pair remained with low probability of producing viable young. This precipitous decline was in part due to the negative fitness consequences associated with inbreeding. To restore the Isle Royale ecosystem 19 gray wolves were translocated in 2018 and 2019 coming from Grand Portage, MN (n = 4), western Upper Peninsula, MI (n = 4), Jostle Lake, ON (n = 3), and Michipicoten Island, ON (n = 8). Wolves were genotyped using both microsatellites and single nucleotide polymorphisms (SNPs) to estimate population structure and relatedness within translocation groups and used to inform projections of genetic diversity. Population structure assigned the Isle Royale founders to gray wolves with minor evidence of admixture from eastern wolves (Canis lycaon cf) depending on the molecular marker used. In addition, we confirmed wolves translocated from Michipicoten Island were a single family-group. Through simulation and empirical analysis of the new Isle Royale founders we projected a loss in genetic variation over the next 50 years and an increase in inbreeding. However, varying levels of immigration may allow the retention of some genetic variation. Our findings indicate Isle Royale founders are genetically diverse and representative of the Great Lakes region, but the numerical dominance of a single family group may have negative implications for retaining genetic diversity and success of establishment for specific wolves, reinforcing the importance of continued monitoring of genetic fitness.

Large-Scale Genetic Monitoring Reveals Density-Dependent Dispersal in a Large Omnivore
Evan Kopsala, Joseph M. Northrup, Eric Howe, Christopher Kyle

Dispersal strategies govern population interactions, subsequently influencing productivity and diversity maintenance. Thus, characterizing dispersal patterns and quantifying drivers of dispersal are fundamental to our understanding of animal ecology and ultimately for species conservation and management. We sought to assess patterns and drivers of dispersal in a continuous black bear (Ursus americanus) population across a large heterogeneous area by quantifying genetic structure and gene flow directionality. Further, we assessed sex-specific variations in structure and directionality. We used microsatellite data from 3922 individual bears, divided into 73 spatially distinct nodes across an area > 1 000 000km2, to characterize genetic structure. These data were then coupled to network theory to quantify patterns of gene flow directionality. We used spatial modelling to test hypotheses regarding drivers of putative dispersal patterns. Specifically, we tested the relative influence of broad productivity gradients, bear density, and harvest. Additionally, we assessed differences across and between sexes in these patterns as a means of assessing sex-biased dispersal. Our findings show strong evidence that male-biased dispersal was positively density dependent. Model results showed evidence of a relationship between dispersal and broad productivity gradients quantified by forest type. Specifically, male bears displayed preferential dispersal towards mixed deciduous forest where there is higher food productivity relative to the less productive coniferous forest. Given the dense sampling scheme across a continuous population occupying a large heterogeneous landscape, these results provide key insight into dispersal patterns in wide-ranging mammals, as well as their underlying drivers. We postulate that observed male-biased density dependent dispersal patterns are likely the result of differential human-caused mortality and thus suggest population sinks exist in highly productive, but heavily harvested areas. Although this population of black bears in Ontario is not at risk, these results reveal the potential for substantial impacts from intensive harvesting on large carnivore populations.

Genotyping-in -Thousands By Sequencing (GT-Seq) Panel Development and Application to Non-Invasive DNA Samples to Monitor the Endangered Columbia Basin Pygmy Rabbit
Stacey Nerkowski, Paul Hohenlohe, Kenneth Warheit, Lisette Waits

Loss and fragmentation of habitat has led to the near extirpation of the disjunct pygmy rabbit (Brachylagus idahoensis) population in the Columbia Basin (CB) of Washington State. In 2003, the CB pygmy rabbit (CBPYRA) was listed as an endangered distinct population segment under the US Endangered Species Act.  In 2001, sixteen CBPYRA were taken from the last remaining population in Washington to start a captive breeding program, and four Idaho rabbits were added to counteract the effects of inbreeding. Rabbits were moved to semi-wild breeding enclosures in 2011, and additional rabbits were translocated from other populations within the western United States.  Since then ~1947 mixed ancestry rabbits have been released into the wild.  To monitor the mixed-ancestry CBPYRA populations, we first used RADseq on 123 rabbit samples from the CBPYRA population as well as source populations across the species range to identify 12,084 SNP loci, including loci showing signatures of local adaptation among populations as well as loci that are diagnostic for source population ancestry. The, we used a multiplex amplicon sequencing approach (GT-Seq), to effectively genotype non-invasive fecal samples collected during summer and winter monitoring surveys.  Using the identified SNPs, we selected and optimized a 497-locus GT-Seq panel, consisting of 210 neutral, 156 adaptive, and 137 ancestry-informative SNPs.  We assessed genotyping error rsates and population diversity parameters between RADseq and GT-Seq, and discordance between tissue and fecal genotypes.  Our SNP panel allows us to assess individual identity, parentage, ancestry, and locally adaptive loci within the reintroduced populations of CBPYRA. 

Population Genomics to Inform Oral Rabies Vaccination Strategies for Wildlife
Matthew Hopken, Zaid Abdo, Richard Chipman, Amy Gilbert, Jesús Maldonado, Antoinette Piaggio, Mirian Tsuchiya

Wildlife vaccination to control pathogens that impact humans and domestic animals is a complicated process involving a multitude of target and non-target host ecological and social strategies. Variation in host pathogen susceptibility, movement patterns, and genetic diversity can impact disease processes and vaccination outcomes. The raccoon (Procyon lotor) rabies virus variant was accidentally translocated from south eastern states to naïve raccoon populations in mid- Atlantic states in the late 1970’s and became enzootic throughout the eastern U.S. The USDA Wildlife Services National Rabies Management Program developed and refined a large-scale oral vaccination strategy to control the spread and eventually eliminate raccoon rabies virus. Raccoon movement patterns can lead to immunologically naïve or infected animals crossing the vaccination zone by natural dispersal or human-assisted long-range movements. Delineation of host population structure and movement patterns can help refine vaccination strategies to increase management effectiveness.  We present preliminary population genomic analyses from raccoon samples collected during oral rabies vaccination activities in the eastern U.S. We used RADseq and a draft raccoon genome to identify single nucleotide polymorphisms (SNPs) from 380 tissue samples collected in states ranging from Maine to Alabama. We delineated population structure and quantified genetic diversity. We then used a subset of SNPs and microhaplotypes identified from the RADseq data to identify recent migrants and estimate geographic origin of individual raccoons. We developed a panel of 2,000 loci for rapid, cost effective genotyping that we will be used in studies of raccoon social structure and landscape genomics to assist rabies vaccination strategies.

Noninvasive Genetic Investigation of Canids on Galveston Island, Texas
Tanner Barnes, Kristin Brzeski, Lisette Waits, Jennifer Adams, Melissa Karlin

Introgression through hybridization can blur species distinctions, creating conservation and policy challenges. With recent advancements in sequencing technology, researchers are better able to detect introgression events and thus better develop policy and conservation action when necessary. This is especially true for two species of canids, the coyote (Canis latrans) and red wolf (Canis rufus), which historically hybridized along the American Gulf Coast as red wolf populations declined in the mid-1900s. Red wolves were declared extinct from the Gulf Coast by 1980, but in 2018 coyote tissue samples with substantial red wolf ancestry were rediscovered on Galveston Island, Texas. To date, little is known regarding the extent of red wolf ancestry in Galveston Island coyotes or how many potential introgressed coyotes persist on Galveston Island. We used noninvasive genetic techniques to investigate population size, pack composition, and the extent of introgression of red wolf ancestry in the population of canids on Galveston Island. We sampled in three field seasons in January 2020, July 2020, and January 2021 each lasting 3-4 weeks. During these sampling sessions we collected 259 scats and 36 tissues, from which we successfully extracted DNA from 96 scats and 32 tissue samples. We sequenced the mitochondrial DNA control sequence from these 128 samples and individual ID, relatedness, and red wolf ancestry proportions determinations are ongoing using multi-locus microsatellite genotypes. Our study has the potential to benefit the endangered red wolf through the rediscovery of lost genetic variation and advance a better understanding of how hybridization facilitates adaptation.

Population Genomic Analyses Suggest Florida Crested Caracara Is a Distinct Subspecies
Natalie Payne, Melanie Culver

Introduction: The crested caracara (Caracara plancus), previously known as Caracara cheriway in the northern portion of its range, is a resident, nonmigratory raptor occurring throughout South and Central America and reaching the northern edge of its range in the southern United States, including a relict population in central Florida. This threatened population is thought to have been isolated since the last ice age, and previous studies have found no evidence of interbreeding with caracaras outside Florida.

Objectives: Our objectives were to 1) use SNPs to determine the genetic diversity, effective population size, and extent of inbreeding to establish a baseline for the genetic well-being of the threatened Florida population, 2) investigate the extent of the Florida population’s isolation by analyzing population structure among caracaras from Florida, Arizona, and Texas, and 3) incorporate analyses of mitochondrial DNA haplotypes to further clarify taxonomy of the crested caracara at the northern edge of its range.

Methods: We utilized double digest restriction-site associated DNA sequencing (ddRADseq) and sequencing of a 717-bp region of the mitochondrial ND2 gene using blood samples from Florida, Arizona, and Texas.

Results: Analyses of population structure suggest two major clusters are best supported, one which contains only Florida individuals and another which contains Arizona and Texas individuals. The Florida population is strongly differentiated from Arizona and Texas, while Arizona and Texas are moderately differentiated from each other. The Florida population’s mitochondrial haplotypes are monophyletic, while Arizona and Texas share mitochondrial haplotypes.

Conclusions: Analyses of nuclear and mitochondrial DNA confirm the Florida population’s high degree of isolation from Arizona and Texas, whereas Arizona and Texas populations appear to be more recently connected but show moderate differentiation. The results of this study provide substantial genetic evidence that the Florida crested caracara may be a separate subspecies from Arizona and Texas caracaras.

Contributed Oral
Location: Virtual Date: November 4, 2021 Time: 1:00 pm - 2:00 pm