Eric C. York

Bio: Eric C. York is an academic researcher from National Park Service. The author has contributed to research in topics: Litter (animal) & Carnivore. The author has an hindex of 7, co-authored 7 publications receiving 1805 citations.

A southern California freeway is a physical and social barrier to gene flow in carnivores.

Abstract: Roads present formidable barriers to dispersal. We examine movements of two highly mobile carnivores across the Ventura Freeway near Los Angeles, one of the busiest highways in the United States. The two species, bobcats and coyotes, can disappear from habitats isolated and fragmented by roads, and their ability to disperse across the Ventura Freeway tests the limits of vertebrates to overcome anthropogenic obstacles. We combine radiotelemetry data and genetically based assignments to identify individuals that have crossed the freeway. Although the freeway is a significant barrier to dispersal, we find that carnivores can cross the freeway and that 5–32% of sampled carnivores crossed over a 7-year period. However, despite moderate levels of migration, populations on either side of the freeway are genetically differentiated, and coalescent modelling shows their genetic isolation is consistent with a migration fraction less than 0.5% per generation. These results imply that individuals that cross the freeway rarely reproduce. Highways and development impose artificial home range boundaries on territorial and reproductive individuals and hence decrease genetically effective migration. Further, territory pile-up at freeway boundaries may decrease reproductive opportunities for dispersing individuals that do manage to cross. Consequently, freeways are filters favouring dispersing individuals that add to the migration rate but little to gene flow. Our results demonstrate that freeways can restrict gene flow even in wide-ranging species and suggest that for territorial animals, migration levels across anthropogenic barriers need to be an order of magnitude larger than commonly assumed to counteract genetic differentiation.

Estimating population size by genotyping faeces

Abstract: Population size is a fundamental biological parameter that is difficult to estimate. By genotyping coyote (Canis latrans) faeces systematically collected in the Santa Monica Mountains near Los Angeles, California, we exemplify a general, non-invasive method to census large mammals. Four steps are involved in the estimation. First, presumed coyote faeces are collected along paths or roadways where coyotes, like most carnivores, often defaecate and mark territorial boundaries. Second, DNA is extracted from the faeces and species identity and sex is determined by mitochondrial DNA and Y-chromosome typing. Third, hypervariable microsatellite loci are typed from the faeces. Lastly, rarefaction analysis is used to estimate population size from faecal genotypes. This method readily provides a point count estimate of population size and sex ratio. Additionally, we show that home range use paternity and kinship can be inferred from the distribution and relatedness patterns of faecal genotypes.

Effects of Urbanization and Habitat Fragmentation on Bobcats and Coyotes in Southern California

Abstract: Urbanization and habitat fragmentation are major threats to wildlife populations, especially mammalian carnivores. We studied the ecology and behavior of bobcats ( Lynx rufus ) and coyotes ( Canis latrans ) relative to development in a fragmented landscape in southern California from 1996 to 2000. We captured and radiocollared 50 bobcats and 86 coyotes, determined home ranges for 35 bobcats and 40 coyotes, and measured their exposure to development ( “urban association” ) as the percentage of each home range composed of developed or modified areas. Both species occupied predominantly natural home ranges. Adult female bobcats had low levels of urban association, significantly lower than coyotes, adult male bobcats, and young female bobcats. Home-range size was positively correlated with urban association for coyotes and adult male and young female bobcats, suggesting that human-dominated areas were less suitable than natural areas in some important way. Animals more associated with non-natural areas had higher levels of night activity, and both bobcats and coyotes were more likely to be in developed areas at night than during the day. Survival rates were relatively high and were not related to urban association, at least for animals>6–9 months of age. Mortality rates from human-related causes such as vehicle collisions and incidental poisoning were also independent of urban association. In this region, even the few animals that had almost no human development within their home range were vulnerable to human-related mortality. Carnivore conservation in urban landscapes must account for these mortality sources that influence the entire landscape, including reserves. For bobcats, preserving open space of sufficient quantity and quality for adult females is necessary for population viability. Educating local residents about carnivores is also critical for conserving populations in urban areas.

Competition and intraguild predation among three sympatric carnivores

Abstract: We examined the relative roles of dominance in agonistic interactions and energetic constraints related to body size in determining local abundances of coyotes (Canis latrans, 8–20 kg), gray foxes (Urocyon cinereoargenteus, 3–5 kg) and bobcats (Felis rufus, 5–15 kg) at three study sites (hereafter referred to as NP, CP, and SP) in the Santa Monica Mountains of California. We hypothesized that the largest and behaviorally dominant species, the coyote, would exploit a wider range of resources (i.e., a higher number of habitat and/or food types) and, consequently, would occur in higher density than the other two carnivores. We evaluated our hypotheses by quantifying their diets, food overlap, habitat-specific abundances, as well as their overall relative abundance at the three study sites. We identified behavioral dominance of coyotes over foxes and bobcats in Santa Monica because 7 of 12 recorded gray fox deaths and 2 of 5 recorded bobcat deaths were due to coyote predation, and no coyotes died as a result of their interactions with bobcats or foxes. Coyotes and bobcats were present in a variety of habitats types (8 out of 9), including both open and brushy habitats, whereas gray foxes were chiefly restricted to brushy habitats. There was a negative relationship between the abundances of coyotes and gray foxes (P=0.020) across habitats, suggesting that foxes avoided habitats of high coyote predation risk. Coyote abundance was low in NP, high in CP, and intermediate in SP. Bobcat abundance changed little across study sites, and gray foxes were very abundant in NP, absent in CP, and scarce in SP; this suggests a negative relationship between coyote and fox abundances across study sites, as well. Bobcats were solely carnivorous, relying on small mammals (lagomorphs and rodents) throughout the year and at all three sites. Coyotes and gray foxes also relied on small mammals year-round at all sites, though they also ate significant amounts of fruit. Though there were strong overall interspecific differences in food habits of carnivores (P<0.0001), average seasonal food overlaps were high due to the importance of small mammals in all carnivore diets [bobcat-gray fox: 0.79±0.09 (SD), n=4; bobcat-coyote: 0.69±0.16, n=6; coyote-gray fox: 0.52±0.05, n=4]. As hypothesized, coyotes used more food types and more habitat types than did bobcats and gray foxes and, overall, coyotes were the most abundant of the three species and ranged more widely than did gray foxes. We propose that coyotes limit the number and distribution of gray foxes in Santa Monica Mountains, and that those two carnivores exemplified a case in which the relationship between their body size and local abundance is governed by competitive dominance of the largest species rather than by energetic equivalences. However, in the case of the intermediate-sized bobcat no such a pattern emerged, likely due to rarity or inconsistency of agonistic interactions and/or behavioral avoidance of encounters by subordinate species.

An evaluation of territory mapping to estimate fisher density

Abstract: We evaluated winter-territory mapping as a method for estimating fisher (Martes pennanti) density in a 210-km2 survey area in north-central Massachusetts in 1994 and 1995 by comparing estimates wit...

Estimating the probability of identity among genotypes in natural populations: cautions and guidelines

Abstract: Individual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy-nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01-0.0001).

Predator interactions, mesopredator release and biodiversity conservation

Abstract: There is growing recognition of the important roles played by predators in regulating ecosystems and sustaining biodiversity. Much attention has focused on the consequences of predator-regulation of herbivore populations, and associated trophic cascades. However apex predators may also control smaller 'mesopredators' through intraguild interactions. Removal of apex predators can result in changes to intraguild interactions and outbreaks of mesopredators ('mesopredator release'), leading in turn to increased predation on smaller prey. Here we provide a review and synthesis of studies of predator interactions, mesopredator release and their impacts on biodiversity. Mesopredator suppression by apex predators is widespread geographically and taxonomically. Apex predators suppress mesopredators both by killing them, or instilling fear, which motivates changes in behaviour and habitat use that limit mesopredator distribution and abundance. Changes in the abundance of apex predators may have disproportionate (up to fourfold) effects on mesopredator abundance. Outcomes of interactions between predators may however vary with resource availability, habitat complexity and the complexity of predator communities. There is potential for the restoration of apex predators to have benefits for biodiversity conservation through moderation of the impacts of mesopredators on their prey, but this requires a whole-ecosystem view to avoid unforeseen negative effects. 'Nothing has changed since I began. My eye has permitted no change. I am going to keep things like this.' From 'Hawk Roosting', by Ted Hughes.

Noninvasive genetic sampling: look before you leap

Abstract: Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology, conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.

Putting the "landscape" in landscape genetics.

Abstract: Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term ‘landscape genetics’, provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.

gimlet: a computer program for analysing genetic individual identification data

Abstract: Growing interest in microsatellite genotyping, combined with noninvasive genetic sampling has led to the increased production of data. New tools to analyse these data are required. gimlet is a user-friendly software package designed to perform several simple tasks: (i) construction of consensus genotypes from repeated genotyping; (ii) estimation of genotyping error rates; (iii) identification of identical genotypes; (iv) comparison of new genotypes to a set of reference genotypes; (v) determination of the kinship; and (vi) estimation of several population parameters such as allele frequencies, heterozygosity, probability of identity, and population size.