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Walter WD, Fameli A, Russo‐Petrick K, Edson JE, Rosenberry CS, Schuler KL, Tonkovich MJ. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease. Ecol Evol 2024; 14:e11347. [PMID: 38774134 PMCID: PMC11106048 DOI: 10.1002/ece3.11347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.
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Affiliation(s)
- W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alberto Fameli
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kelly Russo‐Petrick
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jessie E. Edson
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Krysten L. Schuler
- Cornell Wildlife Health Lab, New York State Wildlife Health ProgramIthacaNew YorkUSA
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2
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Rayne A, Blair S, Dale M, Flack B, Hollows J, Moraga R, Parata RN, Rupene M, Tamati‐Elliffe P, Wehi PM, Wylie MJ, Steeves TE. Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future. Evol Appl 2022; 15:751-772. [PMID: 35603033 PMCID: PMC9108313 DOI: 10.1111/eva.13367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping‐by‐sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables—including temperature, precipitation, and water flow regimes—in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place‐based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.
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Affiliation(s)
- Aisling Rayne
- University of Canterbury School of Biological Sciences Christchurch New Zealand
| | | | - Matthew Dale
- Waterscape Connections Ltd Dunedin New Zealand
- Te Rūnanga o Ngāi Tahu Dunedin New Zealand
| | - Brendan Flack
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
| | | | - Roger Moraga
- Tea Break Bioinformatics Ltd Palmerston North New Zealand
| | | | - Makarini Rupene
- University of Canterbury Ngāi Tahu Research Centre Christchurch New Zealand
- Environment Canterbury Christchurch New Zealand
| | | | - Priscilla M Wehi
- University of Otago, Centre for Sustainability Dunedin New Zealand
| | - Matthew J Wylie
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
- The New Zealand Institute for Plant and Food Research Limited Nelson New Zealand
| | - Tammy E Steeves
- University of Canterbury School of Biological Sciences Christchurch New Zealand
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3
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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.
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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
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4
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Martín-Rodríguez I, Escudero A, García-Fernández A. Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist. PeerJ 2021; 9:e10533. [PMID: 33505788 PMCID: PMC7789860 DOI: 10.7717/peerj.10533] [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: 06/25/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Background Gypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte. Methods We tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier. Results Results showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants. Discussion Natural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
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Affiliation(s)
- Irene Martín-Rodríguez
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Alfredo García-Fernández
- Área de Biodiversidad y Conservación. Departamento de Biología y Geología, Física y Química Orgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
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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.
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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
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6
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Rutten A, Cox K, Scheppers T, Broecke BV, Leirs H, Casaer J. Analysing the recolonisation of a highly fragmented landscape by wild boar using a landscape genetic approach. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | - Karen Cox
- K. Cox, Res. Inst. for Nature and Forest (INBO), Geraardsbergen, Belgium
| | | | - Bram Vanden Broecke
- B. Vanden Broecke and H. Leirs, Dept of Biology, Univ. of Antwerp, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Herwig Leirs
- B. Vanden Broecke and H. Leirs, Dept of Biology, Univ. of Antwerp, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Jim Casaer
- J. Casaer, Res. Inst. for Nature and Forest (INBO), Brussels, Belgium
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Guerrero J, Byrne AW, Lavery J, Presho E, Kelly G, Courcier EA, O'Keeffe J, Fogarty U, O'Meara DB, Ensing D, McCormick C, Biek R, Skuce RA, Allen AR. The population and landscape genetics of the European badger ( Meles meles) in Ireland. Ecol Evol 2018; 8:10233-10246. [PMID: 30397461 PMCID: PMC6206220 DOI: 10.1002/ece3.4498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/20/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023] Open
Abstract
The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date-comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.
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Affiliation(s)
- Jimena Guerrero
- Centre D'Ecologie Fonctionelle et EvolutiveCEFE‐CNRSMontpellierFrance
| | - Andrew W. Byrne
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - John Lavery
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Eleanor Presho
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Gavin Kelly
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Emily A. Courcier
- Department of Agriculture, Environment and Rural Affairs Northern Ireland (DAERA‐NI)Veterinary Epidemiology UnitBelfastUK
| | - James O'Keeffe
- Department of Agriculture Food and the Marine (DAFM)DublinIreland
| | | | - Denise B. O'Meara
- Department of Chemical and Life SciencesWaterford Institute of TechnologyWaterfordIreland
| | - Dennis Ensing
- Agriculture, Sustainable Agri‐Food Sciences DivisionAgri‐Food and Biosciences InstituteBelfastUK
| | - Carl McCormick
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Roman Biek
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Robin A. Skuce
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Adrian R. Allen
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
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8
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Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species. Heredity (Edinb) 2018; 122:441-457. [PMID: 30171190 DOI: 10.1038/s41437-018-0135-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/27/2018] [Accepted: 06/27/2018] [Indexed: 11/08/2022] Open
Abstract
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an approximate Bayesian computation (ABC) framework to test which scenario best fit the observed genetic data. Simulations indicated that phylogeographic and multilocus population-level sampling both could differentiate among refugial scenarios, although inferences made using mitochondrial data were less accurate when a longer coalescence time was assumed. Furthermore, all empirical genetic datasets were most consistent with expansion from a single refugium based on ABC. Our results indicate a stronger role for post-glacial range expansion, rather than isolation in allopatric refugia followed by range expansion, in structuring diversity in this species. To distinguish among complex historical scenarios, we recommend explicitly modeling the effects of range expansion and evaluating alternate refugial scenarios for wide-ranging taxa.
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Kanine JM, Kierepka EM, Castleberry SB, Mengak MT, Nibbelink NP, Glenn TC. Influence of landscape heterogeneity on the functional connectivity of Allegheny woodrats (Neotoma magister) in Virginia. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1093-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Fine-scale landscape genomics helps explain the slow spatial spread of Wolbachia through the Aedes aegypti population in Cairns, Australia. Heredity (Edinb) 2018; 120:386-395. [PMID: 29358725 DOI: 10.1038/s41437-017-0039-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 11/08/2022] Open
Abstract
The endosymbiotic bacterium Wolbachia suppresses the capacity for arbovirus transmission in the mosquito Aedes aegypti, and can spread spatially through wild mosquito populations following local introductions. Recent introductions in Cairns, Australia have demonstrated slower than expected spatial spread. Potential reasons for this include: (i) barriers to Ae. aegypti dispersal; (ii) higher incidence of long-range dispersal; and (iii) intergenerational loss of Wolbachia. We investigated these three potential factors using genome-wide single-nucleotide polymorphisms (SNPs) and an assay for the Wolbachia infection wMel in 161 Ae. aegypti collected from Cairns in 2015. We detected a small but significant barrier effect of Cairns highways on Ae. aegypti dispersal using distance-based redundancy analysis and patch-based simulation analysis. We detected a pair of putative full-siblings in ovitraps 1312 m apart, indicating long-distance female movement likely mediated by human transport. We also found a pair of full-siblings of different infection status, indicating intergenerational loss of Wolbachia in the field. These three factors are all expected to contribute to the slow spread of Wolbachia through Ae. aegypti populations, though from our results it is unclear whether Wolbachia loss and long-distance movement are sufficiently common to reduce the speed of spatial spread appreciably. Our findings inform the strategic deployment of Wolbachia-infected mosquitoes during releases, and show how parameter estimates from laboratory studies may differ from those estimated using field data. Our landscape genomics approach can be extended to other host/symbiont systems that are being considered for biocontrol.
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11
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Dohms KM, Graham BA, Burg TM. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine ( Perisoreus canadensis). Ecol Evol 2017; 7:9869-9889. [PMID: 29238522 PMCID: PMC5723591 DOI: 10.1002/ece3.3478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/08/2017] [Accepted: 08/19/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada.,Present address: Canadian Wildlife Service, Environment and Climate Change Canada Delta BC Canada
| | - Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada
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12
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Schmidt TL, Rašić G, Zhang D, Zheng X, Xi Z, Hoffmann AA. Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus. PLoS Negl Trop Dis 2017; 11:e0006009. [PMID: 29045401 PMCID: PMC5662242 DOI: 10.1371/journal.pntd.0006009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/30/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022] Open
Abstract
Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Aedes albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations. Aedes albopictus, the Asian Tiger Mosquito, is a highly invasive disease vector with a growing global distribution. Designing strategies to prevent invasion and to control Ae. albopictus populations in invaded regions requires knowledge of how Ae. albopictus disperses. Studies comparing Ae. albopictus populations have found little evidence of genetic structure even between distant populations, suggesting that dispersal along human transportation networks is common. However, a more specific understanding of dispersal processes has been unavailable due to an absence of studies using high-resolution genetic markers. Here we present a study using high-resolution markers, which investigates genetic structure among 152 Ae. albopictus from Guangzhou, China. We found that human transportation networks, particularly shipping terminals, had an influence on genetic structure. We also found genetic distance was correlated with geographical distance, the first such observation in this species. This study demonstrates how high-resolution markers can be used to investigate ecological processes that may otherwise escape detection. We conclude that strategies for controlling Ae. albopictus will have to consider both passive reinvasion along human transportation networks and active reinvasion from neighbouring regions.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Gordana Rašić
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Dongjing Zhang
- Department of Parasitology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Guangzhou, Guangdong, China
| | - Xiaoying Zheng
- Department of Parasitology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Guangzhou, Guangdong, China
| | - Zhiyong Xi
- Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Guangzhou, Guangdong, China.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Ary A Hoffmann
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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13
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Campbell LP, Alexander AM. Landscape Genetics of Aedes mcintoshi (Diptera: Culicidae), an Important Vector of Rift Valley Fever Virus in Northeastern Kenya. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:1258-1265. [PMID: 28431166 DOI: 10.1093/jme/tjx072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 06/07/2023]
Abstract
Rift Valley fever virus (RVFV) is a vector-borne, zoonotic disease that affects humans, wild ungulates, and domesticated livestock in Africa and the Arabian Peninsula. Rift Valley fever virus exhibits interepizootic and epizootic phases, the latter defined by widespread virus occurrence in domesticated livestock. Kenya appears to be particularly vulnerable to epizootics, with 11 outbreaks occurring between 1951 and 2007. The mosquito species Aedes mcintoshi (subgenus Neomelaniconion) is an important primary vector for RVFV in Kenya. Here, we investigate associations between genetic diversity and differentiation of one regional subclade of Ae. mcintoshi in Northeastern Kenya with environmental variables, using a multivariate statistical approach. Using CO1 (cytochrome oxidase subunit 1) sequence data deposited in GenBank, we found no evidence of isolation by distance contributing to genetic differentiation across the study area. However, we did find significant CO1 subpopulation structure and associations with recent mean precipitation values. In addition, variation in genetic diversity across our seven sample sites was associated with both precipitation and percentage clay in the soil. The large number of haplotypes found in this data set indicates that a great deal of diversity remains unsampled in this region. Additional sampling across a larger geographic area, combined with next-generation sequencing approaches that better characterize the genome, would provide a more robust assessment of genetic diversity and differentiation. Further understanding of the genetic structure of Ae. mcintoshi could provide useful information regarding the potential for RVFV to spread across East African landscapes.
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Affiliation(s)
- Lindsay P Campbell
- Biodiversity Institute, University of Kansas, Lawrence, KS
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS
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Kierepka EM, Kilgo JC, Rhodes OE. Effect of compensatory immigration on the genetic structure of coyotes. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21320] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - John C. Kilgo
- USDA Forest ServiceSouthern Research StationP.O. Box 700New EllentonSC29809USA
| | - Olin E. Rhodes
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
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15
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Slate D, Kirby JD, Morgan DP, Algeo TP, Trimarchi CV, Nelson KM, Rudd RJ, Randall AR, Carrara MS, Chipman RB. Cost and Relative Value of Road Kill Surveys for Enhanced Rabies Surveillance in Raccoon Rabies Management. Trop Med Infect Dis 2017; 2:tropicalmed2020013. [PMID: 30270872 PMCID: PMC6082077 DOI: 10.3390/tropicalmed2020013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 11/23/2022] Open
Abstract
Oral rabies vaccination (ORV) requires knowledge of the spatial-temporal distribution of rabies virus variants targeted for control. Rabies-exposure based public health surveillance alone may not provide a sound basis for ORV decisions. The value and cost of road kill surveys was evaluated for the late spring–early fall 2005–2007 as a part of enhanced rabies surveillance in northern New York, where raccoon rabies is enzootic and ORV has occurred since the late 1990s. Structured surveys were conducted to collect raccoons and other meso-carnivores for rabies testing at the New York State Rabies Laboratory. Of the 209 meso-carnivore heads collected and submitted for testing, 175 were testable by direct fluorescent antibody; none was rabid. Rabies was also not reported through public health surveillance in survey zones during 2005–2007. Overall, survey costs were $37,118 (2016 USD). Salaries and benefits accounted for 61% of costs, followed by fuel (22%), vehicle depreciation (14%), and sample shipping (3%). Mean daily distance driven was 303 ± 37 km and 381 ± 28 km for total road kills and raccoons, respectively. Costs/road kill collected and submitted was $176/all species and $224/raccoon. This study provides costs for planning road kill surveys and underscores the need to continually improve enhanced rabies surveillance approaches to support ORV decision making.
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Affiliation(s)
- Dennis Slate
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 59 Chenell Drive, Suite 2, Concord, NH 03301, USA.
| | - Jordona D Kirby
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 59 Chenell Drive, Suite 2, Concord, NH 03301, USA.
| | - Daniel P Morgan
- New York Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 230 Timerman Hall, SUNY Potsdam, Potsdam, NY 13676, USA.
| | - Timothy P Algeo
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 59 Chenell Drive, Suite 2, Concord, NH 03301, USA.
| | - Charles V Trimarchi
- Laboratory of Zoonotic Disease and Clinical Virology, Griffin Laboratory, Wadsworth Center, New York State Department of Health, 61 Mordella Road, Albany, NY 12205, USA.
| | - Kathleen M Nelson
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 59 Chenell Drive, Suite 2, Concord, NH 03301, USA.
| | - Robert J Rudd
- Rabies Laboratory, Griffin Laboratory, Wadsworth Center, New York State Department of Health, 5668 State Farm Rd., Slingerlands, NY 12159, USA.
| | - Adam R Randall
- New Jersey Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Pittstown, NJ 08867, USA.
| | - Mark S Carrara
- Forest Service, United States Department of Agriculture, Cedar City, UT 84721, USA.
| | - Richard B Chipman
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 59 Chenell Drive, Suite 2, Concord, NH 03301, USA.
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16
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Burkhart JJ, Peterman WE, Brocato ER, Romine KM, Willis MMS, Ousterhout BH, Anderson TL, Drake DL, Rowland FE, Semlitsch RD, Eggert LS. The influence of breeding phenology on the genetic structure of four pond-breeding salamanders. Ecol Evol 2017; 7:4670-4681. [PMID: 28690797 PMCID: PMC5496555 DOI: 10.1002/ece3.3060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/08/2017] [Accepted: 04/16/2017] [Indexed: 11/10/2022] Open
Abstract
Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co-occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum, A. maculatum, and A. opacum) and the Central Newt (Notophthalmus viridescens louisianensis) on the same landscape in Missouri, USA. While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species-level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis, species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis. Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species-level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade-off between larval period length and size at metamorphosis which in turn may influence the long-term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.
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Affiliation(s)
- Jacob J Burkhart
- Division of Biological Sciences University of Missouri Columbia MO USA
| | - William E Peterman
- School of Environment and Natural Resources The Ohio State University Columbus OH USA
| | - Emily R Brocato
- Division of Biological Sciences University of Missouri Columbia MO USA
| | - Kimberly M Romine
- Division of Biological Sciences University of Missouri Columbia MO USA
| | | | | | | | - Dana L Drake
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
| | - Freya E Rowland
- Division of Biological Sciences University of Missouri Columbia MO USA
| | | | - Lori S Eggert
- Division of Biological Sciences University of Missouri Columbia MO USA
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17
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Kierepka EM, Latch EK. High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure. Mol Ecol 2016; 25:6055-6076. [PMID: 27862522 DOI: 10.1111/mec.13915] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/13/2016] [Accepted: 11/01/2016] [Indexed: 01/05/2023]
Abstract
Habitat associations are a function of habitat preferences and dispersal capabilities, both of which can influence how species responded to Quaternary climatic changes and contemporary habitat heterogeneity. Predicting resultant genetic structure is not always straightforward, especially in species where high dispersal potential and habitat preferences yield opposing predictions. The American badger has high dispersal capabilities that predict widespread panmixia, but avoids closed-canopy forests and clay soils, which could restrict gene flow and create ecologically based population genetic structure. We used mitochondrial sequence and microsatellite data sets to characterize how these opposing forces contribute to genetic structure in badgers at a continent-wide scale. Our data revealed an overall lack of ecologically based population genetic structure, suggesting that high dispersal capabilities were sufficiently realized to overcome most habitat-based genetic structure. At a broadscale, badger gene flow is limited only by geographic distance (isolation by distance) and large water barriers (Lake Michigan and the Mississippi River). The absence of genetic structure in a species with strong avoidance of unsuitable habitats advances our understanding of when and how genetic structure emerges in widespread, highly mobile species.
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Affiliation(s)
- E M Kierepka
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - E K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
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18
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Inter-annual maintenance of the fine-scale genetic structure in a biennial plant. Sci Rep 2016; 6:37712. [PMID: 27883087 PMCID: PMC5121606 DOI: 10.1038/srep37712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
Within plant populations, space-restricted gene movement, together with environmental heterogeneity, can result in a spatial variation in gene frequencies. In biennial plants, inter-annual flowering migrants can homogenize gene frequencies between consecutive cohorts. However, the actual impact of these migrants on spatial genetic variation remains unexplored. Here, we used 10 nuclear microsatellite and one plastid genetic marker to characterize the spatial genetic structure within two consecutive cohorts in a population of the biennial plant Erysimum mediohispanicum (Brassicaceae). We explored the maintenance of this structure between consecutive flowering cohorts at different levels of complexity, and investigated landscape effects on gene flow. We found that cohorts were not genetically differentiated and showed a spatial genetic structure defined by a negative genetic-spatial correlation at fine scale that varied in intensity with compass directions. This spatial genetic structure was maintained when comparing plants from different cohorts. Additionally, genotypes were consistently associated with environmental factors such as light availability and soil composition, but to a lesser extent compared with the spatial autocorrelation. We conclude that inter-annual migrants, in combination with limited seed dispersal and environmental heterogeneity, play a major role in shaping and maintaining the spatial genetic structure among cohorts in this biennial plant.
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