Contributed Paper
ROOM: CC, Room 22

8:10AM Applications of Whole Genome Sequencing in Mule Deer of California
Daphne A. Gille; Michael R. Buchalski
Whole genome sequencing is a promising molecular tool that has the potential to transform wildlife conservation and management. In California, mule deer (Odocoileus hemionus) are an important game species that is intensively managed by the Department of Fish and Wildlife. Despite significance to the state and widespread interest in the species, there are scant genomic resources that can be used to support and inform an effective genetic management strategy. To address this, we first performed a complete de novo genome assembly of the mule deer using novel high throughput sequencing techniques. Long range information was obtained from Illumina HiSeq 4000 paired-end reads and emulsion PCR to generate linked reads according to the 10X Genomics system. Chromosome-level scaffolding was achieved through the in vivo crosslinking technique developed by Phase Genomics known as Proximo™ Hi-C. We annotated this draft assembly with MAKER2, creating a much needed tool that can be broadly used by cervid researchers to answer a variety of genetic or genomic questions. We then used this draft assembly to evaluate adaptive differentiation among putative subspecies designations in California. Mule deer (O.h. californicus) are currently distinguished from black-tailed deer (O.h. columbianus) based on previous studies using microsatellite and mitochondrial data, as well as one study that used a candidate gene approach. The presence of four additional subspecies of mule deer (O.h. eremicus, O.h. fuliginatus, O.h. hemionus, and O.h. inyoensis), previously defined by morphology and climatic conditions, currently have little genetic support. By conducting low-coverage whole genome resequencing on the Illumina NovaSeq 6000 platform of up to 50 individuals per putative subspecies, in conjunction with the analysis of high resolution climate data and thorough sampling of putative hybrid zones, we identified functional diversity among these groups.
8:30AM The Influence of Crop Type and Phenology on Mule Deer Movement in an Agricultural Area
Laura S. Warner; Levi J. Heffelfinger; Dave G. Hewitt; Shawn S. Gray; Warren C. Conway; Timothy E. Fulbright; Randy W. DeYoung; Louis A. Harveson
Agricultural crops provide an important source of nutrition to mule deer (Odocoileus hemionus) in many areas. However, the influence of crops on deer movement is not well-understood. Anecdotal observations suggest that deer in the Texas Panhandle make large seasonal movements driven by crop phenology to access specific crop types. Understanding the idiosyncrasies of deer movement in an agricultural area is crucial to effective management of deer herds in the face of expanding and changing farming practices. We captured and marked 94 adult mule deer with GPS collars in two regions in the Texas Panhandle. Fixes were taken every two hours from October 2015 through October 2017. Crop growth was tracked within each study area to develop a local growth curve for each crop type. We used adaptive kernel home range analysis to calculate 95% home ranges for each deer. GPS points within home ranges that marked deer presence in a crop field were separated by week of the growing season and associated with a crop type and stage. Home range parameters were compared between deer that used crops (78% of collared individuals) and deer that did not use crops. We found that home range size and movement distances were not affected by crop use. Winter wheat (Triticum spp.) received the greatest use, especially during the tillering and stem-elongation growth stages, which mainly occur during winter. GPS points were more likely to be in rangeland near crops during summer. These results suggest that crop distribution throughout the study areas was such that deer did not have to travel long distances to gain access, but crops were still used seasonally. Knowledge of these mule deer movement trends in agricultural areas will ensure that deer herds are managed on the proper spatial and temporal scales.
8:50AM Windows of Nutrients for Migratory Caribou in Alaska
Perry S. Barboza; Lindsay Van Someren; Keith W. Oster; David D. Gustine; Heather E. Johnson
We tested the hypothesis that supplies of nutrients limit production of arctic caribou (Rangifer tarandus) by sampling forages (n = 1296) in the migratory ranges of the Central Arctic Herd (CAH) and the Western Arctic Herd (WAH). Digestible energy content fell below the minimum threshold value of 9 kJ/g only among graminoids, and only beyond 64-75 days from parturition (6 June), whereas all forages fell below the minimum threshold value for digestible N (1% of dry matter) before female caribou would have weaned their calves at 100 days from parturition. The window for digestible N was shortest for browse, which fell below 1% at 30-41 days from parturition, whereas digestible N contents of graminoids were adequate until 46-57 days from parturition. Spatial distribution of forage mineral content was associated with variation in soil pH, while temporal variation was related to plant maturity, and thus N and fiber content of forages. Concentrations of sodium were below minimum requirements in all forage species for most of the summer and adequate only on the Coastal Plain during the second half of summer. Phosphorus declined below requirements in all forages by mid-summer. Female caribou may favor the Coastal Plain because concentrations of N are not only greater than those on the Brooks Range, the window of usable N on the Coastal Plain extends the period of protein gain for females and their calves by 17 days. Migration to the coast may also allow parturient females to replenish sodium stores depleted by foraging inland through the long arctic winters, while also extending the availability of adequate phosphorus by 43 days. Phenological windows for N and mineral gain in female caribou are both spatially and temporally dynamic and likely to affect the distribution and growth of the arctic caribou populations.
9:10AM Comparing Foraging Strategies of Caribou with Different Nutritional Demands
Kristin A. Denryter; Rachel C. Cook; John G. Cook; Katherine L. Parker; Michael P. Gillingham
Nutrition influences performance of individuals and populations of large ungulates and thus links animals with their environments. How differences in nutritional demands of ungulates influence foraging behaviors, including choice of foraging strategy (e.g., time minimizing or energy maximizing), is largely unknown, but understanding these relationships may be important to interpreting larger-scale behavioral processes in highly mobile ungulates. Our primary goals were to determine if caribou (Rangifer tarandus) with different levels of nutritional requirements used time-minimizing or energy-maximizing foraging strategies and if differences in nutritional values of a variety of vegetation communities affected foraging responses at per-minute and daily time scales. We compared bite rates, intake rates, dietary quality (dietary digestible energy (DDE) and dietary digestible protein (DDP)), diet selection, foraging time, and travel rates of three classes of tame, female caribou, each with different levels of nutritional demands (i.e., lactating and non-lactating adults; subadults (1-2 years old)) during summer in the mountains and boreal forests of northeastern British Columbia. We found no evidence of consistent differences in bite rates, travel rates, DDE, DDP, or diet selection by caribou across nutritional classes. Foraging time and thus daily intakes of dry matter, DDE, and DDP were higher among caribou with higher nutritional demands than caribou with lower demands — an effect that was more pronounced when the nutritional value of plant communities was higher (indicated by higher per-minute intake). Regardless of the level of nutritional demands, or whether available forage was adequate to support daily nutritional demands, caribou allocated as much time as possible to foraging each day with limits imposed by digestion, passage rates, and rest. Thus, our caribou exhibited an energy-maximizing strategy in summer. Our results may provide a mechanistic link between fine-scale foraging decisions and higher-order behavioral processes like habitat selection, movements, and distributions of animals.
9:30AM Predicting Ungulate Parturition Using GPS Movement Data
Matthew Hayes; Ryan Long; Eric Wald; Emma Fuller; Kevin Monteith
Parturition is a key life-history characteristic of ungulates; the timing and location of parturition has implications for ecology and management of these populations. To determine when and where ungulates give birth, biologists typically use vaginal implant transmitters (VITs), which are expelled upon birth of a neonate. A key drawback of this method is the intensive and expensive monitoring that is required. During parturition, movement patterns of ungulates changes dramatically compared with their typical movement patterns. Although patterns may vary across species, atypical movement associated with the birthing event, in the form of a mother returning to a neonate repeatedly, offers an opportunity to identify timing and location of parturition solely by fine-scaled movement data. Exploiting these maternal movement patterns, we developed a machine learning technique which couples metrics calculated from GPS movement data to define the day of parturition in mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus) and Alaskan moose (shiras shirasi). We validated models with known parturition dates from GPS and VIT studies. Predicted accuracy on the training data was within 12 – 72 hours of actual parturition for mule deer, elk and Alaskan moose. This technique relies only on movement data, meaning that a single model is needed no matter how different the habitats or ranges the species lives in. Once a species-specific model is built, prediction is possible on data from that species in the absence of training data, facilitating use of GPS movement data from species without prior VIT studies. This novel approach to identify parturition provides the opportunity to improve our understanding of the key, but often poorly understood, life-history event of ungulate parturition.


Contributed Paper
Location: Cleveland CC Date: October 11, 2018 Time: 8:10 am - 9:50 am