1
|
Cerri J, Musto C, Stefanini FM, di Nicola U, Riganelli N, Fontana MC, Rossi A, Garbarino C, Merialdi G, Ciuti F, Berzi D, Delogu M, Apollonio M. A human-neutral large carnivore? No patterns in the body mass of gray wolves across a gradient of anthropization. PLoS One 2023; 18:e0282232. [PMID: 37262076 DOI: 10.1371/journal.pone.0282232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/11/2023] [Indexed: 06/03/2023] Open
Abstract
The gray wolf (Canis lupus) expanded its distribution in Europe over the last few decades. To better understand the extent to which wolves could re-occupy their historical range, it is important to test if anthropization can affect their fitness-related traits. After having accounted for ecologically relevant confounders, we assessed how anthropization influenced i) the growth of wolves during their first year of age (n = 53), ii) sexual dimorphism between male and female adult wolves (n = 121), in a sample of individuals that had been found dead in Italy between 1999 and 2021. Wolves in anthropized areas have a smaller overall variation in their body mass, during their first year of age. Because they already have slightly higher body weight at 3-5 months, possibly due to the availability of human-derived food sources. The difference in the body weight of adult females and males slightly increases with anthropization. However, this happens because of an increase in the body mass of males only, possibly due to sex-specific differences in dispersal and/or to "dispersal phenotypes". Anthropization in Italy does not seem to have any clear, nor large, effect on the body mass of wolves. As body mass is in turn linked to important processes, like survival and reproduction, our findings indicates that wolves could potentially re-occupy most of their historical range in Europe, as anthropized landscapes do not seem to constrain such of an important life-history trait. Wolf management could therefore be needed across vast spatial scales and in anthropized areas prone to social conflicts.
Collapse
Affiliation(s)
- Jacopo Cerri
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Carmela Musto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Federico M Stefanini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano "La Statale", Milano, Italy
| | | | | | - Maria C Fontana
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna Bruno Ubertino, Brescia, Italy
| | - Arianna Rossi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna Bruno Ubertino, Brescia, Italy
| | - Chiara Garbarino
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna Bruno Ubertino, Brescia, Italy
| | - Giuseppe Merialdi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna Bruno Ubertino, Brescia, Italy
| | | | | | - Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| |
Collapse
|
2
|
Kozakiewicz CP, Burridge CP, Lee JS, Kraberger SJ, Fountain-Jones NM, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, Craft ME, Funk WC, Crooks KR, VandeWoude S, Carver S. Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore. Virus Evol 2022; 9:veac122. [PMID: 36694819 PMCID: PMC9865512 DOI: 10.1093/ve/veac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/22/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
Collapse
Affiliation(s)
| | | | - Justin S Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA
| | | | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | | |
Collapse
|
3
|
Lin M, Escalona M, Sahasrabudhe R, Nguyen O, Beraut E, Buchalski MR, Wayne RK. A Reference Genome Assembly of the Bobcat, Lynx rufus. J Hered 2022; 113:615-623. [PMID: 35696092 PMCID: PMC9709964 DOI: 10.1093/jhered/esac031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
The bobcat (Lynx rufus) is a medium-sized carnivore well adapted to various environments and an indicator species for landscape connectivity. It is one of the 4 species within the extant Lynx genus in the family Felidae. Because of its broad geographic distribution and central role in food webs, the bobcat is important for conservation. Here we present a high-quality de novo genome assembly of a male bobcat located in Mendocino County, CA, as part of the California Conservation Genomics Project (CCGP). The assembly was generated using the standard CCGP pipeline from a combination of Omni-C and HiFi technologies. The primary assembly comprises 76 scaffolds spanning 2.4 Gb, represented by a scaffold N50 of 142 Mb, a contig N50 of 66.2 Mb, and a BUSCO completeness score of 95.90%. The bobcat genome will be an important resource for the effective management and conservation of this species and comparative genomics exploration.
Collapse
Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael R Buchalski
- Wildlife Genetics Research Unit, Wildlife Health Laboratory, California Department of Fish and Wildlife, Sacramento, CA 95834, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
4
|
Zimmerman SJ, Aldridge CL, Hooten MB, Oyler-McCance SJ. Scale-dependent influence of the sagebrush community on genetic connectivity of the sagebrush obligate Gunnison sage-grouse. Mol Ecol 2022; 31:3267-3285. [PMID: 35501946 PMCID: PMC9325045 DOI: 10.1111/mec.16470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision‐making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage‐grouse (Centrocercus minimus). We were interested in two spatial scales: among distinct populations rangewide and among leks (i.e., breeding grounds) within the largest population, Gunnison Basin. Populations and leks are nested within a landscape fragmented by rough terrain and anthropogenic features, although requisite sagebrush habitat is more contiguous within populations. Our best fit models for each scale confirm the importance of sagebrush habitat in connectivity, although the important sagebrush characteristics differ. For Gunnison Basin, taller shrubs and higher quality nesting habitat were the primary drivers of connectivity, while more sagebrush cover and less conifer cover facilitated connectivity rangewide. Our findings support previous assumptions that Gunnison sage‐grouse range contraction is largely the result of habitat loss and degradation. Importantly, we report direct estimates of resistance for landscape components that can be used to create resistance surfaces for prioritization of specific locations for conservation or management (i.e., habitat preservation, restoration, or development) or as we demonstrated, can be combined with simulation techniques to predict impacts to connectivity from potential management actions.
Collapse
Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Mevin B Hooten
- Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, Texas, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| |
Collapse
|
5
|
Saranholi BH, Sanches A, Moreira-Ramírez JF, Carvalho CDS, Galetti M, Galetti Jr PM. Long-term persistence of the large mammal lowland tapir is at risk in the largest Atlantic forest corridor. Perspect Ecol Conserv 2022. [DOI: 10.1016/j.pecon.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
6
|
Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
Collapse
Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| |
Collapse
|
7
|
Gagne RB, Crooks KR, Craft ME, Chiu ES, Fountain-Jones NM, Malmberg JL, Carver S, Funk WC, VandeWoude S. Parasites as conservation tools. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13719. [PMID: 33586245 DOI: 10.1111/cobi.13719] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Parasite success typically depends on a close relationship with one or more hosts; therefore, attributes of parasitic infection have the potential to provide indirect details of host natural history and are biologically relevant to animal conservation. Characterization of parasite infections has been useful in delineating host populations and has served as a proxy for assessment of environmental quality. In other cases, the utility of parasites is just being explored, for example, as indicators of host connectivity. Innovative studies of parasite biology can provide information to manage major conservation threats by using parasite assemblage, prevalence, or genetic data to provide insights into the host. Overexploitation, habitat loss and fragmentation, invasive species, and climate change are major threats to animal conservation, and all of these can be informed by parasites.
Collapse
Affiliation(s)
- Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota, USA
| | - Elliott S Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Jennifer L Malmberg
- Department of Veterinary Sciences, Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, Wyoming, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - W Chris Funk
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
8
|
Gagne RB, Kraberger S, McMinn R, Trumbo DR, Anderson CR, Logan KA, Alldredge MW, Griffin K, Vandewoude S. Viral Sequences Recovered From Puma Tooth DNA Reconstruct Statewide Viral Phylogenies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.734462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Monitoring pathogens in wildlife populations is imperative for effective management, and for identifying locations for pathogen spillover among wildlife, domestic species and humans. Wildlife pathogen surveillance is challenging, however, as sampling often requires the capture of a significant proportion of the population to understand host pathogen dynamics. To address this challenge, we assessed the ability to use hunter-collected teeth from puma across Colorado to recover genetic data of two feline retroviruses, feline foamy virus (FFV) and feline immunodeficiency virus (FIVpco) and show they can be utilized for this purpose. Comparative phylogenetic analyses of FIVpco and FFV from tooth and blood samples to previous analyses conducted with blood samples collected over a nine-year period from two distinct areas was undertaken highlighting the value of tooth derived samples. We found less FIVpco phylogeographic structuring than observed from sampling only two regions and that FFV data confirmed previous findings of endemic infection, minimal geographic structuring, and supported frequent cross-species transmission from domestic cats to pumas. Viral analysis conducted using intentionally collected blood samples required extensive financial, capture and sampling efforts. This analysis illustrates that viral genomic data can be cost effectively obtained using tooth samples incidentally-collected from hunter harvested pumas, taking advantage of samples collected for morphological age identification. This technique should be considered as an opportunistic method to provide broad geographic sampling to define viral dynamics more accurately in wildlife.
Collapse
|
9
|
Cancellare IA, Kierepka EM, Janecka J, Weckworth B, Kazmaier RT, Ward R. Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats. PeerJ 2021; 9:e11498. [PMID: 34141475 PMCID: PMC8180196 DOI: 10.7717/peerj.11498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/01/2021] [Indexed: 12/03/2022] Open
Abstract
Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.
Collapse
Affiliation(s)
- Imogene A Cancellare
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA.,Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Elizabeth M Kierepka
- Department of Forestry and Environmental Resources, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Jan Janecka
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | | | - Richard T Kazmaier
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Rocky Ward
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| |
Collapse
|
10
|
García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
Collapse
|
11
|
Neal KM, Fisher RN, Mitrovich MJ, Shaffer HB. Conservation Genomics of the Threatened Western Spadefoot, Spea hammondii, in Urbanized Southern California. J Hered 2021; 111:613-627. [PMID: 33245338 DOI: 10.1093/jhered/esaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/17/2020] [Accepted: 11/19/2020] [Indexed: 11/14/2022] Open
Abstract
Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least 2, and possibly 3 major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically, but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.
Collapse
Affiliation(s)
- Kevin M Neal
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, University of California Los Angeles, Los Angeles, CA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA
| | | | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, University of California Los Angeles, Los Angeles, CA
| |
Collapse
|
12
|
Schell CJ, Stanton LA, Young JK, Angeloni LM, Lambert JE, Breck SW, Murray MH. The evolutionary consequences of human-wildlife conflict in cities. Evol Appl 2021; 14:178-197. [PMID: 33519964 PMCID: PMC7819564 DOI: 10.1111/eva.13131] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.
Collapse
Affiliation(s)
- Christopher J. Schell
- School of Interdisciplinary Arts and SciencesUniversity of Washington TacomaTacomaWAUSA
| | - Lauren A. Stanton
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Julie K. Young
- USDA‐WS‐National Wildlife Research Center‐Predator Research FacilityMillvilleUTUSA
| | | | - Joanna E. Lambert
- Program in Environmental Studies and Department of Ecology and Evolutionary BiologyUniversity of Colorado‐BoulderBoulderCOUSA
| | - Stewart W. Breck
- USDA‐WS‐National Wildlife Research CenterFort CollinsCOUSA
- Department of Fish, Wildlife, and Conservation BiologyFort CollinsCOUSA
| | - Maureen H. Murray
- Urban Wildlife Institute and Davee Center for Epidemiology and EndocrinologyChicagoILUSA
| |
Collapse
|
13
|
Peterman WE, Pope NS. The use and misuse of regression models in landscape genetic analyses. Mol Ecol 2020; 30:37-47. [PMID: 33128830 DOI: 10.1111/mec.15716] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/21/2020] [Accepted: 10/22/2020] [Indexed: 12/27/2022]
Abstract
The field of landscape genetics has been rapidly evolving, adopting and adapting analytical frameworks to address research questions. Current studies are increasingly using regression-based frameworks to infer the individual contributions of landscape and habitat variables on genetic differentiation. This paper outlines appropriate and inappropriate uses of multiple regression for these purposes, and demonstrates through simulation the limitations of different analytical frameworks for making correct inference. Of particular concern are recent studies seeking to explain genetic differences by fitting regression models with effective distance variables calculated independently on separate landscape resistance surfaces. When moving across the landscape, organisms cannot respond independently and uniquely to habitat and landscape features. Analyses seeking to understand how landscape features affect gene flow should model a single conductance or resistance surface as a parameterized function of relevant spatial covariates, and estimate the values of these parameters by linking a single set of resistance distances to observed genetic dissimilarity via a loss function. While this loss function may involve a regression-like step, the associated nuisance parameters are not interpretable in terms of organismal movement and should not be conflated with what is actually of interest: the mapping between spatial covariates and conductance/resistance. The growth and evolution of landscape genetics as a field has been rapid and exciting. It is the goal of this paper to highlight past missteps and demonstrate limitations of current approaches to ensure that future use of regression models will appropriately consider the process being modeled, which will provide clarity to model interpretation.
Collapse
Affiliation(s)
- William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
14
|
Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
Collapse
Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| |
Collapse
|
15
|
Prentice MB, Bowman J, Murray DL, Khidas K, Wilson PJ. Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis). Mol Ecol 2020; 29:4637-4652. [PMID: 32989809 DOI: 10.1111/mec.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022]
Abstract
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
Collapse
Affiliation(s)
- Melanie B Prentice
- Department of Environmental & Life Sciences, Trent University, Peterborough, ON, Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Dennis L Murray
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Kamal Khidas
- Vertebrate Zoology and Beaty Centre for Species Discovery, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON, Canada
| |
Collapse
|
16
|
Kozakiewicz CP, Burridge CP, Funk WC, Craft ME, Crooks KR, Fisher RN, Fountain‐Jones NM, Jennings MK, Kraberger SJ, Lee JS, Lyren LM, Riley SPD, Serieys LEK, VandeWoude S, Carver S. Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development. Evol Appl 2020; 13:1806-1817. [PMID: 32908587 PMCID: PMC7463333 DOI: 10.1111/eva.12927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 12/18/2022] Open
Abstract
Urban development has major impacts on connectivity among wildlife populations and is thus likely an important factor shaping pathogen transmission in wildlife. However, most investigations of wildlife diseases in urban areas focus on prevalence and infection risk rather than potential effects of urbanization on transmission itself. Feline immunodeficiency virus (FIV) is a directly transmitted retrovirus that infects many felid species and can be used as a model for studying pathogen transmission at landscape scales. We investigated phylogenetic relationships among FIV isolates sampled from five bobcat (Lynx rufus) populations in coastal southern California that appear isolated due to major highways and dense urban development. Divergence dates among FIV phylogenetic lineages in several cases reflected historical urban growth and construction of major highways. We found strong FIV phylogeographic structure among three host populations north-west of Los Angeles, largely coincident with host genetic structure. In contrast, relatively little FIV phylogeographic structure existed among two genetically distinct host populations south-east of Los Angeles. Rates of FIV transfer among host populations did not vary significantly, with the lack of phylogenetic structure south-east of Los Angeles unlikely to reflect frequent contemporary transmission among populations. Our results indicate that major barriers to host gene flow can also act as barriers to pathogen spread, suggesting potentially reduced susceptibility of fragmented populations to novel directly transmitted pathogens. Infrequent exchange of FIV among host populations suggests that populations would best be managed as distinct units in the event of a severe disease outbreak. Phylogeographic inference of pathogen transmission is useful for estimating the ability of geographic barriers to constrain disease spread and can provide insights into contemporary and historical drivers of host population connectivity.
Collapse
Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyColorado State UniversityFort CollinsCOUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsCOUSA
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt PaulMNUSA
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsCOUSA
| | - Robert N. Fisher
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCAUSA
| | | | | | - Simona J. Kraberger
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Justin S. Lee
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Lisa M. Lyren
- Western Ecological Research CenterU.S. Geological SurveyThousand OaksCAUSA
| | - Seth P. D. Riley
- National Park ServiceSanta Monica Mountains National Recreation AreaThousand OaksCAUSA
| | - Laurel E. K. Serieys
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCAUSA
- Institute for Communities and Wildlife in AfricaBiological SciencesUniversity of Cape TownCape TownSouth Africa
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTASAustralia
| |
Collapse
|
17
|
Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Jones ME, Hohenlohe PA, Storfer A. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour. Mol Ecol 2020; 29:3217-3233. [PMID: 32682353 PMCID: PMC9805799 DOI: 10.1111/mec.15558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission.
Collapse
Affiliation(s)
| | - Lauren Ricci
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Amanda R. Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Sarah A. Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,corresponding author: Andrew Storfer, School of Biological Sciences, Washington State University, Pullman, WA, USA.
| |
Collapse
|
18
|
Cheng J, Kao H, Dong S. Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC PLANT BIOLOGY 2020; 20:391. [PMID: 32842966 PMCID: PMC7448513 DOI: 10.1186/s12870-020-02594-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. RESULTS In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. CONCLUSIONS This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.
Collapse
Affiliation(s)
- Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huixia Kao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shubin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
| |
Collapse
|
19
|
Schell CJ, Dyson K, Fuentes TL, Des Roches S, Harris NC, Miller DS, Woelfle-Erskine CA, Lambert MR. The ecological and evolutionary consequences of systemic racism in urban environments. Science 2020; 369:science.aay4497. [DOI: 10.1126/science.aay4497] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Urban areas are dynamic ecological systems defined by interdependent biological, physical, and social components. The emergent structure and heterogeneity of urban landscapes drives biotic outcomes in these areas, and such spatial patterns are often attributed to the unequal stratification of wealth and power in human societies. Despite these patterns, few studies have effectively considered structural inequalities as drivers of ecological and evolutionary outcomes and have instead focused on indicator variables such as neighborhood wealth. In this analysis, we explicitly integrate ecology, evolution, and social processes to emphasize the relationships that bind social inequities—specifically racism—and biological change in urbanized landscapes. We draw on existing research to link racist practices, including residential segregation, to the heterogeneous patterns of flora and fauna observed by urban ecologists. In the future, urban ecology and evolution researchers must consider how systems of racial oppression affect the environmental factors that drive biological change in cities. Conceptual integration of the social and ecological sciences has amassed considerable scholarship in urban ecology over the past few decades, providing a solid foundation for incorporating environmental justice scholarship into urban ecological and evolutionary research. Such an undertaking is necessary to deconstruct urbanization’s biophysical patterns and processes, inform equitable and anti-racist initiatives promoting justice in urban conservation, and strengthen community resilience to global environmental change.
Collapse
Affiliation(s)
- Christopher J. Schell
- School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA
| | - Karen Dyson
- College of Built Environments, University of Washington, Seattle, WA 98195, USA
- Dendrolytics, Seattle, WA 98195, USA
| | - Tracy L. Fuentes
- College of Built Environments, University of Washington, Seattle, WA 98195, USA
| | - Simone Des Roches
- College of Built Environments, University of Washington, Seattle, WA 98195, USA
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA 98195, USA
| | - Nyeema C. Harris
- Applied Wildlife Ecology Lab, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Danica Sterud Miller
- School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA
| | - Cleo A. Woelfle-Erskine
- School of Marine and Environmental Affairs, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Max R. Lambert
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
20
|
Marrotte RR, Bowman J, Wilson PJ. Climate connectivity of the bobcat in the Great Lakes region. Ecol Evol 2020; 10:2131-2144. [PMID: 32128144 PMCID: PMC7042766 DOI: 10.1002/ece3.6049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 11/05/2022] Open
Abstract
The Great Lakes and the St. Lawrence River are imposing barriers for wildlife, and the additive effect of urban and agricultural development that dominates the lower Great Lakes region likely further reduces functional connectivity for many terrestrial species. As the climate warms, species will need to track climate across these barriers. It is important therefore to investigate land cover and bioclimatic hypotheses that may explain the northward expansion of species through the Great Lakes. We investigated the functional connectivity of a vagile generalist, the bobcat, as a representative generalist forest species common to the region. We genotyped tissue samples collected across the region at 14 microsatellite loci and compared different landscape hypotheses that might explain the observed gene flow or functional connectivity. We found that the Great Lakes and the additive influence of forest stands with either low or high canopy cover and deep lake-effect snow have disrupted gene flow, whereas intermediate forest cover has facilitated gene flow. Functional connectivity in southern Ontario is relatively low and was limited in part by the low amount of forest cover. Pathways across the Great Lakes were through the Niagara region and through the Lower Peninsula of Michigan over the Straits of Mackinac and the St. Marys River. These pathways are important routes for bobcat range expansion north of the Great Lakes and are also likely pathways that many other mobile habitat generalists must navigate to track the changing climate. The extent to which species can navigate these routes will be important for determining the future biodiversity of areas north of the Great Lakes.
Collapse
Affiliation(s)
- Robby R. Marrotte
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Jeff Bowman
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Wildlife Research & Monitoring SectionOntario Ministry of Natural Resources & ForestryPeterboroughONCanada
| | | |
Collapse
|
21
|
Kozakiewicz CP, Burridge CP, Funk WC, Salerno PE, Trumbo DR, Gagne RB, Boydston EE, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, VandeWoude S, Crooks KR, Carver S. Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales. Mol Ecol 2019; 28:5068-5085. [PMID: 31613411 DOI: 10.1111/mec.15274] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/02/2023]
Abstract
Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.
Collapse
Affiliation(s)
| | | | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | | | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Roderick B Gagne
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Erin E Boydston
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA, USA
| | - Laurel E K Serieys
- Department of Environmental Studies, University of California Santa Cruz, Santa Cruz, CA, USA.,Institute for Communities and Wildlife in Africa, Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| |
Collapse
|