here be deer: using noninvasive tools to estimate mule deer abundance

Widely spread across the western United States, mule deer are the most hunted large mammal in California and serve as the primary prey source of mountain lions – making them an economically and ecologically important harvested species. Populations of harvested species face pressures from both natural predators and competitors as well direct pressures from human hunters, and mule deer are no exception. Wildlife managers must accordingly keep close tabs on deer population numbers to ensure that harvest intensity is sustainable and deer abundance remains relatively stable. However, over the last 30 years, the California mule deer population has exhibited a steady trend of decline. Due to these sustained reductions in California mule deer populations, interest in improving and implementing routine population abundance assessments has arisen for state wildlife managers and citizen-lead mule deer organizations. Therefore, the California Department of Fish and Wildlife (CDFW) has partnered with scientists to develop and execute state-of-the-science deer abundance estimation techniques across the state and assess their effectiveness in various habitat types and landscapes.

​Here in San Diego County, the unique climate and topography provides the foundation for a diverse assemblage of species and ecosystem types. The intersection of these various habitats across the county presents logistical challenges when attempting to locate and count deer. Estimation techniques that are effective in open grasslands, such as helicopter wildlife surveys, may not be practical in the dense and concealing chaparral or oak forests that lie adjacent. Kylie Curtis, a Masters student in the Lewison Lab, is one such scientist that is working with CDFW to help overcome these complications and determine the most accurate abundance and density estimation techniques for mule deer inhabiting various habitat types. She will be focusing her efforts on an area in central San Diego County called San Felipe Valley. San Felipe Valley is made up of a mosaic of state and federally owned lands, and is an ecosystem defined by a unique blend of habitat types including chaparral, desert riparian woodland, grasslands, sage scrub, and oak woodlands. This diversity makes San Felipe Valley an excellent study area to determine the viability of estimation methods in a variety of habitats. Ms. Curtis will be focusing her efforts on assessing a method called capture recapture for its effectiveness estimating abundance of deer in the valley.

Capture recapture, also known as mark recapture, is a commonly used abundance estimation method when it is not feasible to count all of the individuals in a population. Traditionally, a portion of a population is captured, marked so that they can be identified in the future, and then released. Then, at a later time, another portion of the population is captured and researchers determine how many of the newly captured animals have marks. The basic assumption behind this method is that the number of marked animals in the second group should be proportional to the number of marked animals in the total population and using this assumption researchers can estimate the total population size by dividing the number of marked individuals by this proportion.

Usually, capture recapture involves physically marking animals with a visible tag. However, with genetic advances over the last 20 years, it is now feasible and affordable to mark animals by obtaining tissues, hairs, or fecal samples. This noninvasive marking process requires that DNA be extracted from the sample, and then the DNA is genotyped and given an individual identity. Once a unique genotype is obtained, this counts as a mark. When future samples are collected and genotyped it is possible that a genotype from one sample will match a genotype from a previous sample and this counts as a recapture of the same individual.

​For deer, one of the most readily available and easily collected sources of DNA is scat. Ms. Curtis spent six weeks this summer in San Felipe Valley collecting deer scat to use to estimate deer population size in the area. Along with field work partners Richard Cousins, a CDFW employee that has served over 40 years with the agency, and Tessa Cardinal, a generous volunteer fresh out of Point Loma Nazarene University with a biology degree and passion for large mammals, Ms. Curtis established 24 transects spaced relatively uniformly across the valley that followed deer trails. In the unforgiving summer heat and rough terrain, these workers walked many kilometers collecting scat and recording information on where each sample was collected. Ms. Curtis then took these samples back to the lab to extract DNA and identify individuals. Over the course of the summer, the team collected over 500 scat samples that will have to be processed and genotyped. This work is ongoing, but genotyping is expected to be completed by spring of next year. Once each sample is given an identity, Ms. Curtis can determine if there are recaptures and use this information for her analysis. This will ultimately produce the estimates and tools CDFW needs to continue monitoring deer populations in Southern California and ensuring the continued success of these populations.