Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?

Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500–3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70–200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today\u27s contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms

Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains

The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying \u3c10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g. post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages

Targeting alphas can make coyote control more effective and socially acceptable

Research at the UC Hopland Research and Extension Center (HREC) has improved our understanding of how to reduce sheep depredation while minimizing the impact on coyotes. Analysis of a 14-year data set of HREC coyote-control efforts found that sheep depredation losses were not correlated with the number of coyotes removed in any of three time scales analyzed (yearly, seasonally and monthly) during corresponding intervals for the next 2 years. Field research using radiotelemetry to track coyotes supported and explained this finding. For example, in 1995, dominant “alphas” from four territories were associated with 89% of 74 coyote-killed lambs; “betas” and transients were not associated with any of these kills. Relatively few coyotes were killing sheep, and these animals were difficult to capture by conventional methods at the time of year when depredation was highest. However, selective removal of only the problem alpha coyotes effectively reduced losses at HREC

Targeting alphas can make coyote control more effective and socially acceptable

Research at the UC Hopland Research and Extension Center (HREC) has improved our understanding of how to reduce sheep depredation while minimizing the impact on coyotes. Analysis of a 14-year data set of HREC coyote-control efforts found that sheep depredation losses were not correlated with the number of coyotes removed in any of three time scales analyzed (yearly, seasonally and monthly) during corresponding intervals for the next 2 years. Field research using radiotelemetry to track coyotes supported and explained this finding. For example, in 1995, dominant “alphas” from four territories were associated with 89% of 74 coyote-killed lambs; “betas” and transients were not associated with any of these kills. Relatively few coyotes were killing sheep, and these animals were difficult to capture by conventional methods at the time of year when depredation was highest. However, selective removal of only the problem alpha coyotes effectively reduced losses at HREC

Both Reintroduction and Recolonization Likely Contributed to the Re-establishment of a Fisher Population in East-central Alberta

Recently, Stewart et al. (2017) investigated the origins of contemporary fisher populations in the Cooking Lake Moraine (CLM) of east-central Alberta, Canada, where fishers (Pekania pennanti) from Ontario and Manitoba, Canada were reintroduced in the early 1990s. To address this objective, Stewart et al. (2017) compared microsatellite alleles from extant fisher populations in the CLM to those from Ontario, Manitoba, and other Alberta populations. They reported that the CLM population clustered with adjacent native Alberta populations, consistent with recolonization, but also that 2 of 109 microsatellite alleles in the CLM occurred only in the source populations from Ontario and Manitoba. Rather than allowing for the possibility that these alleles descended from reintroduced fishers, the authors speculated that they represented random mutations among fishers that recolonized the area naturally from nearby populations in Alberta, and concluded that the reintroduction had failed completely. We disagree with this conclusion for 2 reasons. We contend it is more likely that the 2 alleles represent a genetic signature from the individuals released during the reintroduction, rather than being the result of mutations. We further suggest that, irrespective of the genetic legacy of introduced fishers in the recovered population, the presence of reintroduced fishers in the CLM may have helped facilitate natural recolonization of the area by fishers from surrounding areas. In our view, Stewart et al.’s (2017) findings do not demonstrate conclusively that the reintroduction program failed; on the contrary, we argue that their findings indicate that reintroduced fishers likely contributed to the long-term persistence of fishers in the CLM. The uncertainty surrounding this case underscores the importance of genetic monitoring following reintroductions.https://digitalcommons.snc.edu/faculty_staff_works/1032/thumbnail.jp

Anticoagulant rodenticides on our public and community lands: spatial distribution of exposure and poisoning of a rare forest carnivore.

Anticoagulant rodenticide (AR) poisoning has emerged as a significant concern for conservation and management of non-target wildlife. The purpose for these toxicants is to suppress pest populations in agricultural or urban settings. The potential of direct and indirect exposures and illicit use of ARs on public and community forest lands have recently raised concern for fishers (Martes pennanti), a candidate for listing under the federal Endangered Species Act in the Pacific states. In an investigation of threats to fisher population persistence in the two isolated California populations, we investigate the magnitude of this previously undocumented threat to fishers, we tested 58 carcasses for the presence and quantification of ARs, conducted spatial analysis of exposed fishers in an effort to identify potential point sources of AR, and identified fishers that died directly due to AR poisoning. We found 46 of 58 (79%) fishers exposed to an AR with 96% of those individuals having been exposed to one or more second-generation AR compounds. No spatial clustering of AR exposure was detected and the spatial distribution of exposure suggests that AR contamination is widespread within the fisher's range in California, which encompasses mostly public forest and park lands Additionally, we diagnosed four fisher deaths, including a lactating female, that were directly attributed to AR toxicosis and documented the first neonatal or milk transfer of an AR to an altricial fisher kit. These ARs, which some are acutely toxic, pose both a direct mortality or fitness risk to fishers, and a significant indirect risk to these isolated populations. Future research should be directed towards investigating risks to prey populations fishers are dependent on, exposure in other rare forest carnivores, and potential AR point sources such as illegal marijuana cultivation in the range of fishers on California public lands

Patterns of Natural and Human-Caused Mortality Factors of a Rare Forest Carnivore, the Fisher (Pekania pennanti) in California.

Wildlife populations of conservation concern are limited in distribution, population size and persistence by various factors, including mortality. The fisher (Pekania pennanti), a North American mid-sized carnivore whose range in the western Pacific United States has retracted considerably in the past century, was proposed for threatened status protection in late 2014 under the United States Endangered Species Act by the United States Fish and Wildlife Service in its West Coast Distinct Population Segment. We investigated mortality in 167 fishers from two genetically and geographically distinct sub-populations in California within this West Coast Distinct Population Segment using a combination of gross necropsy, histology, toxicology and molecular methods. Overall, predation (70%), natural disease (16%), toxicant poisoning (10%) and, less commonly, vehicular strike (2%) and other anthropogenic causes (2%) were causes of mortality observed. We documented both an increase in mortality to (57% increase) and exposure (6%) from pesticides in fishers in just the past three years, highlighting further that toxicants from marijuana cultivation still pose a threat. Additionally, exposure to multiple rodenticides significantly increased the likelihood of mortality from rodenticide poisoning. Poisoning was significantly more common in male than female fishers and was 7 times more likely than disease to kill males. Based on necropsy findings, suspected causes of mortality based on field evidence alone tended to underestimate the frequency of disease-related mortalities. This study is the first comprehensive investigation of mortality causes of fishers and provides essential information to assist in the conservation of this species

High-fat diet exacerbates SIV pathogenesis and accelerates disease progression

Copyright: © 2019. American Society for Clinical Investigation.Consuming a high-fat diet (HFD) is a risk factor for obesity and diabetes; both of these diseases are also associated with systemic inflammation, similar to HIV infection. A HFD induces intestinal dysbiosis and impairs liver function and coagulation, with a potential negative impact on HIV/SIV pathogenesis. We administered a HFD rich in saturated fats and cholesterol to nonpathogenic (African green monkeys) and pathogenic (pigtailed macaques) SIV hosts. The HFD had a negative impact on SIV disease progression in both species. Thus, increased cell-associated SIV DNA and RNA occurred in the HFD-receiving nonhuman primates, indicating a potential reservoir expansion. The HFD induced prominent immune cell infiltration in the adipose tissue, an important SIV reservoir, and heightened systemic immune activation and inflammation, altering the intestinal immune environment and triggering gut damage and microbial translocation. Furthermore, HFD altered lipid metabolism and HDL oxidation and also induced liver steatosis and fibrosis. These metabolic disturbances triggered incipient atherosclerosis and heightened cardiovascular risk in the SIV-infected HFD-receiving nonhuman primates. Our study demonstrates that dietary intake has a discernable impact on the natural history of HIV/SIV infections and suggests that dietary changes can be used as adjuvant approaches for HIV-infected subjects, to reduce inflammation and the risk of non-AIDS comorbidities and possibly other infectious diseases.This study was funded through NIH/NHLBI/NIAID/NIDDK/ NCRR R01 grants HL117715 (to IP), HL123096 (to IP), AI119346 (to CA), DK113919 (to IP and CA), DK119936 (to CA), RR025781 (to CA and IP), and AI104373 (to RMR). RMR was funded by grant PTDC/ MAT-APL/31602/2017 from the Fundação para a Ciência e Tecnologia (Portugal). DNF and CCW were supported by the University of Colorado GI and Liver Innate Immunity Program. KDR and BBP were partly supported by the NIH Training Grant T32AI065380. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio