ORCID Profile
0000-0002-6466-3618
Current Organisation
Colorado State University
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Publisher: Wiley
Date: 11-2019
DOI: 10.1111/MEC.15261
Abstract: Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic ersity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms (SNPs) were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic ersity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic ersity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.
Publisher: Wiley
Date: 28-09-2021
DOI: 10.1111/MEC.16181
Publisher: Cold Spring Harbor Laboratory
Date: 09-01-2021
DOI: 10.1101/2021.01.09.426055
Abstract: Identifying drivers of transmission prior to an epidemic—especially of an emerging pathogen—is a formidable challenge for proactive disease management efforts. We tested a novel approach in the Florida panther, hypothesizing that apathogenic feline immunodeficiency virus (FIV) transmission could predict transmission dynamics for pathogenic feline leukemia virus (FeLV). We derived a transmission network using FIV whole genome sequences, and used exponential random graph models to determine drivers structuring this network. We used these drivers to predict FeLV transmission pathways among panthers and compared predicted outbreak dynamics against empirical FeLV outbreak data. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. Prospective FIV-based modeling predicted FeLV dynamics at least as well as simpler, often retrospective approaches, with evidence that FIV-based predictions captured the spatial structuring of the observed FeLV outbreak. Our finding that an apathogenic agent can predict transmission of an analogously transmitted pathogen is an innovative approach that warrants testing in other host-pathogen systems to determine generalizability. Use of such apathogenic agents holds promise for improving predictions of pathogen transmission in novel host populations, and could thereby provide new strategies for proactive pathogen management in human and animal systems.
Publisher: Cold Spring Harbor Laboratory
Date: 30-09-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 05-11-2018
Abstract: Over 50 years ago, Dan Janzen proposed an integrative framework relating latitudinal differences in climate variability to elevational trends in species ersity. We show that tropical species in three independent insect clades have ( i ) narrower thermal breadths, ( ii ) decreased dispersal and higher population structure, and ( iii ) higher cryptic ersity and speciation rates. This research tests all of the key predictions of Janzen’s hypothesis in related taxa. Our work advances the understanding of how climate variability shapes global ersity patterns, moving beyond simple correlations, to mechanistic links between climate, local adaptation, dispersal, and montane species richness.
Publisher: Springer Science and Business Media LLC
Date: 16-01-2023
DOI: 10.1007/S10592-022-01492-0
Abstract: Genetic ersity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic ersity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global bio ersity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic ersity. It is possible and necessary that the GBF strives to maintain genetic ersity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
Publisher: Wiley
Date: 12-11-2019
DOI: 10.1111/MEC.15274
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 in idual 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.
Publisher: Oxford University Press (OUP)
Date: 12-01-2019
Abstract: The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of bio ersity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented “Big Data” tools in disease research however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural “Genomics of Disease in Wildlife” workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) “Improving communication,” 2) “Methodological and analytical advancements,” 3) “Translation into practice,” 4) “Integrating landscape ecology and genomics,” and 5) “Emerging new questions.” Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.
Publisher: Wiley
Date: 26-10-2022
Abstract: Understanding the causes of population variation in host response to disease, and the mechanisms of persistence, can serve as vital information for species conservation. One such mechanism of population persistence that has gained support is the demographic process of compensatory recruitment. Host populations may persist by increasing recruitment to compensate for reduced survival due to infection, thus limiting the negative effects of the disease on population trajectories. However, high‐elevation populations are inherently vulnerable to stochastic processes and may be limited in their ability to exhibit compensatory recruitment relative to lower elevation populations. We use long‐term mark–recapture data from five populations of boreal toads Anaxyrus boreas boreas , across an elevational gradient in Colorado, before and after pathogen arrival to assess whether populations can persist with Batrachochytrium dendrobatidis ( Bd ) via compensatory recruitment. Prior to pathogen arrival, we found a life‐history trade‐off between survival and recruitment across elevations, where high‐elevation toads have high survival but lower recruitment and vice versa at lower elevations. Pathogen arrival had a strong negative effect on apparent annual survival and recruitment leading to negative population growth rates and dramatically reduced host abundances. The data did not support the occurrence of compensatory recruitment. Synthesis and applications . Our unique dataset indicates that demographic responses to pathogens may be environmentally (i.e. elevationally) context dependent and highlights the value of long‐term monitoring. We recommend that practitioners verify that potential persistence mechanisms occur across multiple populations and relevant environmental gradients to counter any assumptions of the mechanism existing species‐wide. Quantifying variation in population responses to disease will aid in understanding the bounds of such persistence mechanisms and identify particularly vulnerable populations where mechanisms are nonexistent.
Publisher: Research Square Platform LLC
Date: 12-06-2021
DOI: 10.21203/RS.3.RS-590207/V1
Abstract: Hunting can fundamentally alter wildlife population dynamics, but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here we present a study that leverages a unique landscape-scale experiment coupled with pathogen transmission tracing, network simulation and phylodynamics to provide insights into how hunting shapes viral dynamics in puma ( Puma concolor ). We show that removing hunting pressure enhances the role of males in transmission, increases the viral population growth rate and the role of evolutionary forces on the pathogen compared to when hunting was reinstated. Changes in transmission could be linked to short term social changes while the male population increased. These findings are supported through comparison with a region with stable hunting management over the same time period. This study shows that routine wildlife management can have impacts on pathogen transmission and evolution not previously considered.
Publisher: Wiley
Date: 20-02-2020
DOI: 10.1111/EVA.12927
Publisher: Springer Science and Business Media LLC
Date: 27-01-2022
DOI: 10.1038/S41559-021-01635-5
Abstract: Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulation and phylodynamics to provide insights into how hunting shapes feline immunodeficiency virus (FIV) dynamics in puma (Puma concolor). We show that removing hunting pressure enhances the role of males in transmission, increases the viral population growth rate and increases the role of evolutionary forces on the pathogen compared to when hunting was reinstated. Changes in transmission observed with the removal of hunting could be linked to short-term social changes while the male puma population increased. These findings are supported through comparison with a region with stable hunting management over the same time period. This study shows that routine wildlife management can have impacts on pathogen transmission and evolution not previously considered.
Publisher: Cold Spring Harbor Laboratory
Date: 31-08-2020
DOI: 10.1101/2020.08.28.254672
Abstract: Genetic ersity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of bio ersity-genes, species and ecosystems-globally. However, assessment and monitoring of genetic ersity are often overlooked, and there are large knowledge and policy gaps regarding genetic ersity conservation. In this study, we present the first quantitative analysis of genetic ersity assessments conducted by Parties to the CBD. We conducted a detailed, systematic analysis of 114 CBD 5th (submitted 2014) and 6th (submitted 2018) National Reports to quantitatively assess actions, progress on targets, values and indicators related to genetic ersity. First, we found that the importance of genetic ersity is recognised by most Parties to the CBD, and that recognition increased over time. However, genetic targets mainly addressed genetic ersity within cultivated plants, farm animals, and crop wild relatives, with little focus on other wild species. Also, actions for conserving genetic ersity primarily concerned ex-situ facilities and policy, rather than monitoring and intervention for maintaining genetic ersity in situ . The most commonly used indicators of genetic ersity status were the number of genetic resources in conservation facilities, number of threatened breeds, and Red List Index, which are not well correlated to genetic erosion in most species -- highlighting that genetic change is poorly monitored by current indicators. Lastly, analyses of genetic data observations, indigenous use and knowledge of genetic ersity, and strategies being developed and implemented to conserve genetic ersity are highly under-reported. We make several recommendations for the post-2020 CBD Bio ersity Framework to improve awareness, assessment, and monitoring, and facilitate consistent and complete reporting of progress of genetic ersity in future National Reports. An analysis of genetic ersity in CBD National Reports neglects non-domesticated species and demonstrates need for sufficient indicators.
Publisher: Elsevier BV
Date: 08-2020
Publisher: Springer Science and Business Media LLC
Date: 04-01-2021
DOI: 10.1038/S42003-020-01548-2
Abstract: Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here, we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma ( Puma concolor ) from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development (UB). We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas roads might have facilitated viral spread in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.
Publisher: Wiley
Date: 20-08-2021
DOI: 10.1002/ECY.3503
Abstract: Frameworks exclusively considering functional ersity are gaining popularity, as they complement and extend the information provided by taxonomic ersity metrics, particularly in response to disturbance. Taxonomic ersity should be included in functional ersity frameworks to uncover the functional mechanisms causing species loss following disturbance events. We present and test a predictive framework that considers temporal functional and taxonomic ersity responses along disturbance gradients. Our proposed framework allows us to test different multidimensional metrics of taxonomic ersity that can be directly compared to calculated multidimensional functional ersity metrics. It builds on existing functional ersity–disturbance frameworks both by using a gradient approach and by jointly considering taxonomic and functional ersity. We used previously unpublished stream insect community data collected prior to, and for the two years following, an extreme flood event that occurred in 2013. Using 14 northern Colorado mountain streams, we tested our framework and determined that taxonomic ersity metrics calculated using multidimensional methods resulted in concordance between taxonomic and functional ersity responses. By considering functional and taxonomic ersity together and using a gradient approach, we were able to identify some of the mechanisms driving species losses following this extreme disturbance event.
Location: United States of America
No related grants have been discovered for W. Chris Funk.