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Escobar LE. Ecological Niche Modeling: An Introduction for Veterinarians and Epidemiologists. Front Vet Sci 2020; 7:519059. [PMID: 33195507 PMCID: PMC7641643 DOI: 10.3389/fvets.2020.519059] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/25/2020] [Indexed: 01/08/2023] Open
Abstract
Most infectious diseases in animals are not distributed randomly. Instead, diseases in livestock and wildlife are predictable in terms of the geography, time, and species affected. Ecological niche modeling approaches have been crucial to the advancement of our understanding of diversity and diseases distributions. This contribution is an introductory overview to the field of distributional ecology, with emphasis on its application for spatial epidemiology. A new, revised modeling framework is proposed for more detailed and replicable models that account for both the biology of the disease to be modeled and the uncertainty of the data available. Considering that most disease systems need at least two organisms interacting (i.e., host and pathogen), biotic interactions lie at the core of the pathogen's ecological niche. As a result, neglecting interacting organisms in pathogen dynamics (e.g., maintenance, reproduction, and transmission) may limit efforts to forecast disease distributions in veterinary epidemiology. Although limitations of ecological niche modeling are noted, it is clear that the application and value of ecological niche modeling to epidemiology will increase in the future. Potential research lines include the examination of the effects of biotic variables on model performance, assessments of protocols for model calibration in disease systems, and new tools and metrics for robust model evaluation. Epidemiologists aiming to employ ecological niche modeling theory and methods to reconstruct and forecast epidemics should familiarize themselves with ecological literature and must consider multidisciplinary collaborations including veterinarians to develop biologically sound, statistically robust analyses. This review attempts to increase the use of tools from ecology in disease mapping.
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Affiliation(s)
- Luis E Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Banerjee AK, Hou Z, Lin Y, Lan W, Tan F, Xing F, Li G, Guo W, Huang Y. Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia. ANNALS OF BOTANY 2020; 125:1113-1126. [PMID: 32173740 PMCID: PMC7262463 DOI: 10.1093/aob/mcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. METHODS We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. KEY RESULTS We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. CONCLUSIONS These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuangwei Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wentao Lan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fen Xing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanghe Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- For correspondence. E-mail
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Escobar LE, Pritzkow S, Winter SN, Grear DA, Kirchgessner MS, Dominguez-Villegas E, Machado G, Peterson AT, Soto C. The ecology of chronic wasting disease in wildlife. Biol Rev Camb Philos Soc 2020; 95:393-408. [PMID: 31750623 PMCID: PMC7085120 DOI: 10.1111/brv.12568] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
Abstract
Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.
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Affiliation(s)
- Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, 24061, U.S.A
| | - Sandra Pritzkow
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, University of Texas Medical School at Houston, Houston, TX, 77030, U.S.A
| | - Steven N. Winter
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, 24061, U.S.A
| | - Daniel A. Grear
- US Geological Survey National Wildlife Health Center, Madison, WI, 59711, U.S.A
| | | | | | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, U.S.A
| | - A. Townsend Peterson
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, 66045, U.S.A
| | - Claudio Soto
- Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, Department of Neurology, University of Texas Medical School at Houston, Houston, TX, 77030, U.S.A
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Rocha F, Dias RA. The common vampire bat Desmodus rotundus (Chiroptera: Phyllostomidae) and the transmission of the rabies virus to livestock: A contact network approach and recommendations for surveillance and control. Prev Vet Med 2019; 174:104809. [PMID: 31756671 DOI: 10.1016/j.prevetmed.2019.104809] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022]
Abstract
The importance of the common vampire bat Desmodus rotundus for the transmission of the rabies virus does not lie solely in its ability to transmit this disease to other mammals, but also in its capacity to adapt to environmental and climatic changes, granting them a wide geographical distribution. Control of this disease is currently based on culling of the vampire bat and vaccination of the livestock. A transmission model incorporating geographic and behavioral determinants of the vampire bat was proposed to direct and optimize the epidemiological surveillance and control of livestock rabies. This model was built using a bimodal network connecting 260 vampire bat roosts among themselves (roost-roost-network) and with 1557 farms (roost-farm network) in eastern Sao Paulo State, Brazil. These roosts were grouped in 9 communities, some very interconnected, and some not and the farms were grouped in 14 communities. From 2013 to 2017, 44 livestock rabies outbreaks occurred in the area, circulating among the farm communities during the entire period, with possible introductions from neighboring areas. Based on the network and environment parameters, it was possible to reasonably predict both the roosts' occupation type (harem, bachelor, overnight and empty) and livestock rabies outbreak occurrence. The network approach brings light to the importance of phylogenetic studies of bats and rabies virus. Finally, the understanding of the interactions between bats and their feeding sources, influenced by the environment, allows to establish more precise surveillance and control measures and, ultimately, with a lower cost-benefit ratio of these actions.
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Affiliation(s)
- Felipe Rocha
- Laboratory of Epidemiology and Biostatistics, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques Paiva, 87, 05508-270, São Paulo, SP, Brazil; Pan American Center for Foot-and-Mouth Disease and Veterinary Public Health (PANAFTOSA), Pan American Health Association/World Health Organization, Av. Gov. Leonel de Moura Brizola, 7778, 25045-002, Duque de Caxias, RJ, Brazil
| | - Ricardo Augusto Dias
- Laboratory of Epidemiology and Biostatistics, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques Paiva, 87, 05508-270, São Paulo, SP, Brazil.
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Stepien CA, Snyder MR, Elz AE. Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS One 2019; 14:e0203012. [PMID: 30917127 PMCID: PMC6436794 DOI: 10.1371/journal.pone.0203012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives.
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Affiliation(s)
- Carol A. Stepien
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Matthew R. Snyder
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Anna E. Elz
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
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Hayes MA, Piaggio AJ. Assessing the potential impacts of a changing climate on the distribution of a rabies virus vector. PLoS One 2018; 13:e0192887. [PMID: 29466401 PMCID: PMC5821341 DOI: 10.1371/journal.pone.0192887] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/24/2018] [Indexed: 11/23/2022] Open
Abstract
Common vampire bats (Desmodus rotundus) occur throughout much of South America to northern México. Vampire bats have not been documented in recent history in the United States, but have been documented within about 50 km of the U.S. state of Texas. Vampire bats feed regularly on the blood of mammals and can transmit rabies virus to native species and livestock, causing impacts on the health of prey. Thus cattle producers, wildlife management agencies, and other stakeholders have expressed concerns about whether vampire bats might spread into the southern United States. On the other hand, concerns about vampire-borne rabies can also result in wanton destruction at bat roosts in areas occupied by vampire bats, but also in areas not known to be occupied by this species. This can in turn negatively affect some bat roosts, populations, and species that are of conservation concern, including vampire bats. To better understand the current and possible future distribution of vampire bats in North America and help mitigate future cattle management problems, we used 7,094 vampire bat occurrence records from North America and species distribution modeling (SDM) to map the potential distribution of vampire bats in North America under current and future climate change scenarios. We analysed and mapped the potential distribution of this species using 5 approaches to species distribution modeling: logistic regression, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy. We then projected these models into 17 "worst-case" future climate scenarios for year 2070 to generate hypotheses about how the vampire bat distribution in North America might change in the future. Of the variables used in this analysis, minimum temperature of the coldest month had the highest variable importance using all 5 SDM approaches. These results suggest two potential near-future routes of vampire bat dispersal into the U.S., one via southern Texas, and a second into southern Florida. Some of our SDM models support the hypothesis that suitable habitat for vampire bats may currently exist in parts of the México-U.S. borderlands, including extreme southern portions of Texas, as well as in southern Florida. However, this analysis also suggests that extensive expansion into the south-eastern and south-western U.S. over the coming ~60 years appears unlikely.
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Affiliation(s)
- Mark A. Hayes
- Normandeau Associates Inc., Gainesville, Florida, United States of America
| | - Antoinette J. Piaggio
- National Wildlife Research Center, U.S. Department of Agriculture, Fort Collins, Colorado, United States of America
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Hayes MA, Piaggio AJ. Assessing the potential impacts of a changing climate on the distribution of a rabies virus vector. PLoS One 2018. [PMID: 29466401 DOI: 10.1371/journal.-pone.0192887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Common vampire bats (Desmodus rotundus) occur throughout much of South America to northern México. Vampire bats have not been documented in recent history in the United States, but have been documented within about 50 km of the U.S. state of Texas. Vampire bats feed regularly on the blood of mammals and can transmit rabies virus to native species and livestock, causing impacts on the health of prey. Thus cattle producers, wildlife management agencies, and other stakeholders have expressed concerns about whether vampire bats might spread into the southern United States. On the other hand, concerns about vampire-borne rabies can also result in wanton destruction at bat roosts in areas occupied by vampire bats, but also in areas not known to be occupied by this species. This can in turn negatively affect some bat roosts, populations, and species that are of conservation concern, including vampire bats. To better understand the current and possible future distribution of vampire bats in North America and help mitigate future cattle management problems, we used 7,094 vampire bat occurrence records from North America and species distribution modeling (SDM) to map the potential distribution of vampire bats in North America under current and future climate change scenarios. We analysed and mapped the potential distribution of this species using 5 approaches to species distribution modeling: logistic regression, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy. We then projected these models into 17 "worst-case" future climate scenarios for year 2070 to generate hypotheses about how the vampire bat distribution in North America might change in the future. Of the variables used in this analysis, minimum temperature of the coldest month had the highest variable importance using all 5 SDM approaches. These results suggest two potential near-future routes of vampire bat dispersal into the U.S., one via southern Texas, and a second into southern Florida. Some of our SDM models support the hypothesis that suitable habitat for vampire bats may currently exist in parts of the México-U.S. borderlands, including extreme southern portions of Texas, as well as in southern Florida. However, this analysis also suggests that extensive expansion into the south-eastern and south-western U.S. over the coming ~60 years appears unlikely.
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Affiliation(s)
- Mark A Hayes
- Normandeau Associates Inc., Gainesville, Florida, United States of America
| | - Antoinette J Piaggio
- National Wildlife Research Center, U.S. Department of Agriculture, Fort Collins, Colorado, United States of America
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Piaggio AJ, Russell AL, Osorio IA, Jiménez Ramírez A, Fischer JW, Neuwald JL, Tibbels AE, Lecuona L, McCracken GF. Genetic demography at the leading edge of the distribution of a rabies virus vector. Ecol Evol 2017; 7:5343-5351. [PMID: 28770072 PMCID: PMC5528231 DOI: 10.1002/ece3.3087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 05/02/2017] [Indexed: 11/21/2022] Open
Abstract
The common vampire bat, Desmodus rotundus, ranges from South America into northern Mexico in North America. This sanguivorous species of bat feeds primarily on medium to large-sized mammals and is known to rely on livestock as primary prey. Each year, there are hotspot areas of D. rotundus-specific rabies virus outbreaks that lead to the deaths of livestock and economic losses. Based on incidental captures in our study area, which is an area of high cattle mortality from D. rotundus transmitted rabies, it appears that D. rotundus are being caught regularly in areas and elevations where they previously were thought to be uncommon. Our goal was to investigate demographic processes and genetic diversity at the north eastern edge of the range of D. rotundus in Mexico. We generated control region sequences (441 bp) and 12-locus microsatellite genotypes for 602 individuals of D. rotundus. These data were analyzed using network analyses, Bayesian clustering approaches, and standard population genetic statistical analyses. Our results demonstrate panmixia across our sampling area with low genetic diversity, low population differentiation, loss of intermediate frequency alleles at microsatellite loci, and very low mtDNA haplotype diversity with all haplotypes being very closely related. Our study also revealed strong signals of population expansion. These results follow predictions from the leading-edge model of expanding populations and supports conclusions from another study that climate change may allow this species to find suitable habitat within the U.S. border.
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Affiliation(s)
| | - Amy L. Russell
- Department of BiologyGrand Valley State UniversityAllendaleMIUSA
| | - Ignacio A. Osorio
- Committee of Promotion and Animal Health ProtectionRabies Campaign, San Luis Potosi CitySan Luis PotosiMéxico
| | - Alejandro Jiménez Ramírez
- Former State Chief of the National Campaign of Bovine Paralytic Rabies SENASICA/SAGARPAMéxico CityMéxico
- Present address:
MVZ.Marcelino Champagnat 505 Colonia Guadalupe Tepatitlán de MorelosJaliscoMexico
| | | | | | | | - Luis Lecuona
- USDA/APHIS/International ServicesDistrito FederalMéxico
| | - Gary F. McCracken
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
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