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Bonnin N, Piel AK, Brown RP, Li Y, Connell JA, Avitto AN, Boubli JP, Chitayat A, Giles J, Gundlapally MS, Lipende I, Lonsdorf EV, Mjungu D, Mwacha D, Pintea L, Pusey AE, Raphael J, Wich SA, Wilson ML, Wroblewski EE, Hahn BH, Stewart FA. Barriers to chimpanzee gene flow at the south-east edge of their distribution. Mol Ecol 2023; 32:3842-3858. [PMID: 37277946 PMCID: PMC10421595 DOI: 10.1111/mec.16986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023]
Abstract
Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.
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Affiliation(s)
- Noémie Bonnin
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Alex K. Piel
- Department of Anthropology, University College London, London, UK
| | - Richard P. Brown
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse A. Connell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexa N. Avitto
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Adrienne Chitayat
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Jasmin Giles
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Madhurima S. Gundlapally
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Elizabeth V. Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604, USA
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Lilian Pintea
- Conservation Science Department, the Jane Goodall Institute, Washington, DC, 20036, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Serge A. Wich
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fiona A. Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Department of Anthropology, University College London, London, UK
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2
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Huang RM, van Aarde RJ, Pimm SL, Chase MJ, Leggett K. Mapping potential connections between Southern Africa's elephant populations. PLoS One 2022; 17:e0275791. [PMID: 36219597 PMCID: PMC9553058 DOI: 10.1371/journal.pone.0275791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Southern Africa spans nearly 7 million km2 and contains approximately 80% of the world’s savannah elephants (Loxodonta africana) mostly living in isolated protected areas. Here we ask what are the prospects for improving the connections between these populations? We combine 1.2 million telemetry observations from 254 elephants with spatial data on environmental factors and human land use across eight southern African countries. Telemetry data show what natural features limit elephant movement and what human factors, including fencing, further prevent or restrict dispersal. The resulting intersection of geospatial data and elephant presences provides a map of suitable landscapes that are environmentally appropriate for elephants and where humans allow elephants to occupy. We explore the environmental and anthropogenic constraints in detail using five case studies. Lastly, we review all the major potential connections that may remain to connect a fragmented elephant metapopulation and document connections that are no longer feasible.
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Affiliation(s)
- Ryan M. Huang
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
- * E-mail: (RMH); (RJA)
| | - Rudi J. van Aarde
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
- * E-mail: (RMH); (RJA)
| | - Stuart L. Pimm
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Keith Leggett
- Fowlers Gap Arid Zone Research Station, UNSW Sydney, Sydney, Fowlers Gap, Australia
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González-Maya JF, Rojano C, Ávila R, Gómez-Junco GP, Moreno-Díaz C, Hurtado-Moreno AP, Paredes-Casas CA, Lemus-Mejía L, Zárrate-Charry DA. Puma concolor potential distribution and connectivity in the Colombian Llanos. MAMMALIA 2022. [DOI: 10.1515/mammalia-2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Understanding species distribution to target biodiversity conservation actions in countries with high biodiversity, scarce data availability and low study sites accessibility is very challenging. These issues limit management and conservation actions even on charismatic and potentially conflictive species like large carnivores. We developed a geographic assessment of the potential distribution, core patches and connectivity areas for Puma concolor in the Colombian Llanos (Orinoco region). To create this geographic representation, we used methodological approaches that work with scarce information and still provide a spatially-explicit distribution that could be used by stakeholders. Our results show the importance that the Llanos region has for the conservation of the species and the potential role that can have to ensure a resident long-term population. Based on our approach, more than 50,000 km2 (near to 30% of the study area) can be still considered as core habitats for the species, and most of them are still connected, with spatial gaps lower than the estimated dispersal distance of the species and several remaining steppingstones. Further research is required to validate our analysis and we expect our results can target research and conservation priorities within the region.
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Affiliation(s)
- José F. González-Maya
- Departamento de Ciencias Ambientales , CBS, Universidad, Autónoma Metropolitana Unidad Lerma , Av. de las Garzas No. 10, Col. El Panteón. C.P, 52005 , Lerma de Villada , Estado de México , Mexico
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Cesar Rojano
- Fundación Cunaguaro and Cunaguaro Consultores SA , Calle 20 #28-06 , Yopal , Casanare , Colombia
| | - Renzo Ávila
- Fundación Cunaguaro and Cunaguaro Consultores SA , Calle 20 #28-06 , Yopal , Casanare , Colombia
| | - Ginna P. Gómez-Junco
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Catalina Moreno-Díaz
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Angela P. Hurtado-Moreno
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Camilo A. Paredes-Casas
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Leonardo Lemus-Mejía
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
| | - Diego A. Zárrate-Charry
- Proyecto de Conservación de Aguas y Tierras – ProCAT Colombia , Carrera 11 # 96-43, Of. 303 , Bogotá D.C. , Colombia
- World Wild Fund for Nature (WWF) Colombia , Carrera 10 A # 69 A – 44 , Bogotá D.C. , Colombia
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5
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Epps CW, Weldy MJ, Crowhurst RS, Spaan RS. Estimating the distribution and habitat suitability for aardvarks (
Orycteropus afer
) in Kruger National Park, South Africa. Afr J Ecol 2021. [DOI: 10.1111/aje.12916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton W. Epps
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Matthew J. Weldy
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Rachel S. Crowhurst
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Robert S. Spaan
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
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6
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Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evol Appl 2021; 14:1673-1689. [PMID: 34178112 PMCID: PMC8210790 DOI: 10.1111/eva.13233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/10/2021] [Indexed: 01/16/2023] Open
Abstract
Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pretranslocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1143 deer sampled statewide in Arkansas. We then employed Simpson's diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of re-colonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a statewide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas is also applicable for other biodiversity elements with similarly complex demographic histories.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - Zachery D. Zbinden
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Bradley T. Martin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | | | - M. Cory Gray
- Research DivisionArkansas Game and Fish CommissionLittle RockARUSA
| | | | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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7
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Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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8
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Lohay GG, Weathers TC, Estes AB, McGrath BC, Cavener DR. Genetic connectivity and population structure of African savanna elephants ( Loxodonta africana) in Tanzania. Ecol Evol 2020; 10:11069-11089. [PMID: 33144949 PMCID: PMC7593188 DOI: 10.1002/ece3.6728] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 11/07/2022] Open
Abstract
Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals sampled in 2015 and 2017. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. In northern Tanzania, elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean F ST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean A R = 9.96), heterozygosity (mean µH E = 0.73), and effective population sizes (mean N e = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.
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Affiliation(s)
- George G. Lohay
- Biology DepartmentThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Thomas Casey Weathers
- Ecosystem Science and ManagementThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Anna B. Estes
- Environmental Studies DepartmentCarleton CollegeNorthfieldMNUSA
- The Nelson Mandela African Institution of Science and TechnologyArushaTanzania
| | | | - Douglas R. Cavener
- Biology DepartmentThe Pennsylvania State UniversityUniversity ParkPAUSA
- The Nelson Mandela African Institution of Science and TechnologyArushaTanzania
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9
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Kelson SJ, Miller MR, Thompson TQ, O'Rourke SM, Carlson SM. Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability. Mol Ecol 2020; 29:870-885. [PMID: 32012393 PMCID: PMC7078995 DOI: 10.1111/mec.15367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.
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Affiliation(s)
- Suzanne J Kelson
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Michael R Miller
- Department of Animal Science, University of California, Davis, CA, USA
| | - Tasha Q Thompson
- Department of Animal Science, University of California, Davis, CA, USA
| | - Sean M O'Rourke
- Department of Animal Science, University of California, Davis, CA, USA
| | - Stephanie M Carlson
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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10
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Alexander NB, Statham MJ, Sacks BN, Bean WT. Generalist dispersal and gene flow of an endangered keystone specialist (Dipodomys ingens). J Mammal 2019. [DOI: 10.1093/jmammal/gyz118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Movement ecology and dispersal capabilities inherently drive genetic structure across landscapes. Through understanding dispersal and gene flow of giant kangaroo rats (Dipodomys ingens), conservation efforts can be focused, and we can further understand how genetic structure persists in this highly endemic small mammal. Here, we genetically identify parent–offspring and sibship relationships among 239 giant kangaroo rats using 15 microsatellites in the northern part of the species range and describe the individual genetic-spatial variation using a Moran eigenvector map (MEM). We further employ two landscape genetic analyses (isolation by resistance [IBR] and least cost paths [LCPs]) and two individual-based genetic metrics (Dps and a codominant marker distance from GenAlEx) to determine landscape factors (precipitation, slope, vegetation community, and roads) that influence gene flow. We found 19 pairs of related individuals, of which 18 were less than 250 m apart, but one sibling pair was 5.52 km apart, suggesting greater dispersal capabilities than previously noted. We found hierarchal spatial genetic structure using a MEM, with 3–4 genetically similar regions and two genetically similar subregions. Finally, we found low correlative strength between landscape features and gene flow. IBR consistently outperformed LCPs, and there was evidence that regions with 250–350 mm of precipitation and slope ≤ 5° promoted connectivity. We recommend that managers focus on habitat protection rather than corridor maintenance, with the caveat that anthropogenic factors were minimally considered in this study.
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Affiliation(s)
- Nathan B Alexander
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, USA
- Department of Wildlife, Humboldt State University, Arcata, CA, USA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - William T Bean
- Department of Wildlife, Humboldt State University, Arcata, CA, USA
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11
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Green SE, Davidson Z, Kaaria T, Doncaster CP. Do wildlife corridors link or extend habitat? Insights from elephant use of a Kenyan wildlife corridor. Afr J Ecol 2018. [DOI: 10.1111/aje.12541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Siân E. Green
- Biological Sciences; University of Southampton; Southampton UK
- Marwell Wildlife; Colden Common; Winchester UK
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12
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Koenig SJ, Bender DJ. Increasing the function in distance-based functional connectivity assessments: a modified spatial interaction model (SIM) approach. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Osipova L, Okello MM, Njumbi SJ, Ngene S, Western D, Hayward MW, Balkenhol N. Fencing solves human‐wildlife conflict locally but shifts problems elsewhere: A case study using functional connectivity modelling of the African elephant. J Appl Ecol 2018. [DOI: 10.1111/1365-2664.13246] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liudmila Osipova
- Wildlife SciencesUniversity of Goettingen Goettingen Germany
- Bangor University Bangor UK
| | - Moses M. Okello
- Department of Tourism ManagementMoi University Nairobi Kenya
| | | | | | | | | | - Niko Balkenhol
- Wildlife SciencesUniversity of Goettingen Goettingen Germany
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14
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Riggio J, Mbwilo F, Van de Perre F, Caro T. The forgotten link between northern and southern Tanzania. Afr J Ecol 2018. [DOI: 10.1111/aje.12533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jason Riggio
- Department of Wildlife, Fish and Conservation Biology; University of California; Davis California
| | | | | | - Tim Caro
- Department of Wildlife, Fish and Conservation Biology; University of California; Davis California
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15
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Lobora AL, Nahonyo CL, Munishi LK, Caro T, Foley C, Prunier JG, Beale CM, Eggert LS. Incipient signs of genetic differentiation among African elephant populations in fragmenting miombo ecosystems in south-western Tanzania. Afr J Ecol 2018. [DOI: 10.1111/aje.12534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex L. Lobora
- Tanzania Wildlife Research Institute (TAWIRI); Arusha Tanzania
| | | | - Linus K. Munishi
- Nelson Mandela African Institution of Science and Technology (NM-AIST); Arusha Tanzania
| | - Tim Caro
- Department of Wildlife, Fish and Conservation Biology; University of California; Davis California
| | - Charles Foley
- Wildlife Conservation Society Tanzania Program; Arusha Tanzania
| | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Colin M. Beale
- Department of Biology; University of York; Heslington York UK
| | - Lori S. Eggert
- Division of Biological Sciences; University of Missouri; Columbia Missouri
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16
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Schlossberg S, Chase MJ, Griffin CR. Poaching and human encroachment reverse recovery of African savannah elephants in south-east Angola despite 14 years of peace. PLoS One 2018. [PMID: 29538387 PMCID: PMC5851583 DOI: 10.1371/journal.pone.0193469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
With populations of African savannah elephants (Loxodonta africana) declining across the continent, assessing the status of individual elephant populations is important for conservation. Angola’s elephant population represents a key linkage between the larger populations of Namibia and Botswana. Elephants in Angola were decimated during the 1975–2002 Angolan civil war, but a 2005 survey showed that populations were recolonizing former habitats. Between 2005 and 2015, no research was permitted on elephants in Angola, but elsewhere in Africa many elephant populations experienced a poaching crisis. In 2015, we were able to resume elephant research in Angola. We used aerial surveys and satellite monitoring of collared elephants to determine the current status of elephant populations in Angola and to learn how human populations may be affecting elephant habitat usage. The aerial survey revealed a population of 3,395 ± SE of 797 elephants, but populations had declined 21% from the 2005 estimate. The high number of carcasses observed on the survey suggests that populations may have increased after the 2005 survey but were declining rapidly as of 2015. Satellite-collared elephants avoided areas <6 km from human indicators but preferred areas nearer humans at scales of 6–40 km, suggesting that humans may be displacing elephants from preferred habitats near rivers. Taken together, these results suggest that Angola’s elephant population is experiencing intense poaching and may be losing habitat to human settlements. Without action to conserve their populations, Angola’s elephants face an uncertain future.
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Affiliation(s)
| | | | - Curtice R. Griffin
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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17
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Proft KM, Jones ME, Johnson CN, Burridge CP. Making the connection: expanding the role of restoration genetics in restoring and evaluating connectivity. Restor Ecol 2018. [DOI: 10.1111/rec.12692] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kirstin M. Proft
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Menna E. Jones
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Christopher N. Johnson
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
| | - Christopher P. Burridge
- School of Natural Sciences University of Tasmania, Private Bag 55 Hobart Tasmania 7001 Australia
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18
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Riggio J, Caro T. Structural connectivity at a national scale: Wildlife corridors in Tanzania. PLoS One 2017; 12:e0187407. [PMID: 29095901 PMCID: PMC5667852 DOI: 10.1371/journal.pone.0187407] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/19/2017] [Indexed: 11/25/2022] Open
Abstract
Wildlife corridors can help maintain landscape connectivity but novel methods must be developed to assess regional structural connectivity quickly and cheaply so as to determine where expensive and time-consuming surveys of functional connectivity should occur. We use least-cost methods, the most accurate and up-to-date land conversion dataset for East Africa, and interview data on wildlife corridors, to develop a single, consistent methodology to systematically assess wildlife corridors at a national scale using Tanzania as a case study. Our research aimed to answer the following questions; (i) which corridors may still remain open (i.e. structurally connected) at a national scale, (ii) which have been potentially severed by anthropogenic land conversion (e.g., agriculture and settlements), (iii) where are other remaining potential wildlife corridors located, and (iv) which protected areas with lower forms of protection (e.g., Forest Reserves and Wildlife Management Areas) may act as stepping-stones linking more than one National Park and/or Game Reserve. We identify a total of 52 structural connections between protected areas that are potentially open to wildlife movement, and in so doing add 23 to those initially identified by other methods in Tanzanian Government reports. We find that the vast majority of corridors noted in earlier reports as “likely to be severed” have actually not been cut structurally (21 of 24). Nonetheless, nearly a sixth of all the wildlife corridors identified in Tanzania in 2009 have potentially been separated by land conversion, and a third now pass across lands likely to be converted to human use in the near future. Our study uncovers two reserves with lower forms of protection (Uvinza Forest Reserve in the west and Wami-Mbiki Wildlife Management Area in the east) that act as apparently crucial stepping-stones between National Parks and/or Game Reserves and therefore require far more serious conservation support. Methods used in this study are readily applicable to other nations lacking detailed data on wildlife movements and plagued by inaccurate land cover datasets. Our results are the first step in identifying wildlife corridors at a regional scale and provide a springboard for ground-based follow-up conservation.
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Affiliation(s)
- Jason Riggio
- Department of Wildlife, Fish and Conservation Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Tim Caro
- Department of Wildlife, Fish and Conservation Biology, University of California Davis, Davis, California, United States of America
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19
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Tucker JM, Allendorf FW, Truex RL, Schwartz MK. Sex‐biased dispersal and spatial heterogeneity affect landscape resistance to gene flow in fisher. Ecosphere 2017. [DOI: 10.1002/ecs2.1839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jody M. Tucker
- Sequoia National Forest U.S. Forest Service, Pacific Southwest Region 1839 S. Newcomb Street Porterville California 93257 USA
| | - Fred W. Allendorf
- Division of Biological Sciences University of Montana 32 Campus Drive Missoula Montana 59812 USA
| | - Richard L. Truex
- U.S. Forest Service, Rocky Mountain Region 1617 Cole Boulevard Lakewood Colorado 80401 USA
| | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula Montana 59801 USA
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20
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Deines JM. Changes in Forest Composition in Ohio Between Euro-American Settlement and the Present. AMERICAN MIDLAND NATURALIST 2016. [DOI: 10.1674/0003-0031-176.2.247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Jillian M. Deines
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
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21
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Roffler GH, Schwartz MK, Pilgrim KL, Talbot SL, Sage GK, Adams LG, Luikart G. Identification of landscape features influencing gene flow: How useful are habitat selection models? Evol Appl 2016; 9:805-17. [PMID: 27330556 PMCID: PMC4908466 DOI: 10.1111/eva.12389] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 04/26/2016] [Indexed: 01/05/2023] Open
Abstract
Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.
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Affiliation(s)
- Gretchen H. Roffler
- US Geological SurveyAlaska Science CenterAnchorageAKUSA
- Wildlife Biology ProgramDepartment of Ecosystem Sciences and ConservationCollege of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
- Present address: Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAKUSA
| | - Michael K. Schwartz
- Wildlife Biology ProgramDepartment of Ecosystem Sciences and ConservationCollege of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
- US Forest Service Rocky Mountain Research StationMissoulaMTUSA
| | | | | | | | | | - Gordon Luikart
- Flathead Lake Biological StationUniversity of MontanaPolsonMTUSA
- Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaMissoulaMTUSA
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22
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Zhang YH, Wang IJ, Comes HP, Peng H, Qiu YX. Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae). Sci Rep 2016; 6:24041. [PMID: 27137438 PMCID: PMC4853719 DOI: 10.1038/srep24041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.
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Affiliation(s)
- Yong-Hua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Hans Peter Comes
- Department of Ecology &Evolution, Salzburg University, A-5020 Salzburg, Austria
| | - Hua Peng
- Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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23
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Epps CW, Keyghobadi N. Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol Ecol 2015; 24:6021-40. [DOI: 10.1111/mec.13454] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Clinton W. Epps
- Oregon State University; Nash Hall Room 104 Corvallis OR 97331 USA
| | - Nusha Keyghobadi
- Department of Biology; Western University; London ON N6A 5B7 Canada
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24
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Converse PE, Kuchta SR, Roosenburg WM, Henry PFP, Haramis GM, King TL. Spatiotemporal analysis of gene flow in Chesapeake Bay Diamondback Terrapins (Malaclemys terrapin). Mol Ecol 2015; 24:5864-76. [DOI: 10.1111/mec.13440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Paul E. Converse
- Department of Biological Sciences; Ohio University; Athens OH 45701 USA
| | - Shawn R. Kuchta
- Department of Biological Sciences; Ohio University; Athens OH 45701 USA
- Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH 45701 USA
| | - Willem M. Roosenburg
- Department of Biological Sciences; Ohio University; Athens OH 45701 USA
- Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH 45701 USA
| | - Paula F. P. Henry
- U.S. Geological Survey; Patuxent Wildlife Research Center; BARC-East Building 308 10300 Baltimore Avenue Beltsville MD 20705 USA
| | - G. Michael Haramis
- U.S. Geological Survey; Patuxent Wildlife Research Center; BARC-East Building 308 10300 Baltimore Avenue Beltsville MD 20705 USA
| | - Tim L. King
- U.S. Geological Survey; Leetown Science Center; Aquatic Ecology Laboratory; 11649 Leetown Road Kearneysville WV 25430 USA
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25
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Wasser SK, Brown L, Mailand C, Mondol S, Clark W, Laurie C, Weir BS. CONSERVATION. Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots. Science 2015; 349:84-7. [PMID: 26089357 PMCID: PMC5535781 DOI: 10.1126/science.aaa2457] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/22/2015] [Indexed: 11/02/2022]
Abstract
Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime.
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Affiliation(s)
- S K Wasser
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA.
| | - L Brown
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
| | - C Mailand
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - S Mondol
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - W Clark
- INTERPOL, Environmental Security Sub-Directorate (ENS), Lyon, France
| | - C Laurie
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
| | - B S Weir
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
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26
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Robin VV, Gupta P, Thatte P, Ramakrishnan U. Islands within islands: two montane palaeo-endemic birds impacted by recent anthropogenic fragmentation. Mol Ecol 2015; 24:3572-84. [DOI: 10.1111/mec.13266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/29/2022]
Affiliation(s)
- V. V. Robin
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Pooja Gupta
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Prachi Thatte
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bellary Road Bangalore 560065 India
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27
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Anderson SJ, Kierepka EM, Swihart RK, Latch EK, Rhodes OE. Assessing the permeability of landscape features to animal movement: using genetic structure to infer functional connectivity. PLoS One 2015; 10:e0117500. [PMID: 25719366 PMCID: PMC4342345 DOI: 10.1371/journal.pone.0117500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/26/2014] [Indexed: 11/19/2022] Open
Abstract
Human-altered environments often challenge native species with a complex spatial distribution of resources. Hostile landscape features can inhibit animal movement (i.e., genetic exchange), while other landscape attributes facilitate gene flow. The genetic attributes of organisms inhabiting such complex environments can reveal the legacy of their movements through the landscape. Thus, by evaluating landscape attributes within the context of genetic connectivity of organisms within the landscape, we can elucidate how a species has coped with the enhanced complexity of human altered environments. In this research, we utilized genetic data from eastern chipmunks (Tamias striatus) in conjunction with spatially explicit habitat attribute data to evaluate the realized permeability of various landscape elements in a fragmented agricultural ecosystem. To accomplish this we 1) used logistic regression to evaluate whether land cover attributes were most often associated with the matrix between or habitat within genetically identified populations across the landscape, and 2) utilized spatially explicit habitat attribute data to predict genetically-derived Bayesian probabilities of population membership of individual chipmunks in an agricultural ecosystem. Consistency between the results of the two approaches with regard to facilitators and inhibitors of gene flow in the landscape indicate that this is a promising new way to utilize both landscape and genetic data to gain a deeper understanding of human-altered ecosystems.
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Affiliation(s)
- Sara J. Anderson
- Biosciences Department, Minnesota State University Moorhead, 1104 7 Ave, Moorhead, MN, 56563, United States of America
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Elizabeth M. Kierepka
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Robert K. Swihart
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Emily K. Latch
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Olin E. Rhodes
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
- Savannah River Ecology Laboratory, PO Drawer E, Aiken, SC, 29802, United States of America
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28
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Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ. Elephant Natural History: A Genomic Perspective. Annu Rev Anim Biosci 2015; 3:139-67. [DOI: 10.1146/annurev-animal-022114-110838] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfred L. Roca
- Department of Animal Sciences,
- Institute for Genomic Biology, and
| | | | | | - Neal R. Benjamin
- Department of Animal Sciences,
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; , , , , ,
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29
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Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
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30
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de Flamingh A, Sole CL, van Aarde RJ. Genetic evidence for spatial structuring in a continuous African elephant (Loxodonta africana) population. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0686-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Flavenot T, Fellous S, Abdelkrim J, Baguette M, Coulon A. Impact of quarrying on genetic diversity: an approach across landscapes and over time. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0650-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol 2014; 23:5649-62. [DOI: 10.1111/mec.12938] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/07/2014] [Accepted: 09/21/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ian J. Wang
- Department of Environmental Science, Policy, and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Gideon S. Bradburd
- Center for Population Biology; Department of Evolution and Ecology; University of California; 2320 Storer Hall 1 Shields Ave Davis CA 95616 USA
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33
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Davis DJ, Wieman AC, Berendzen PB. The influence of historical and contemporary landscape variables on the spatial genetic structure of the rainbow darter (Etheostoma caeruleum) in tributaries of the upper Mississippi River. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0649-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Marrotte RR, Gonzalez A, Millien V. Landscape resistance and habitat combine to provide an optimal model of genetic structure and connectivity at the range margin of a small mammal. Mol Ecol 2014; 23:3983-98. [DOI: 10.1111/mec.12847] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 05/22/2014] [Accepted: 05/30/2014] [Indexed: 02/05/2023]
Affiliation(s)
- R. R. Marrotte
- Redpath Museum; McGill University; 859 Sherbrooke Street W. Montréal Québec Canada H3A 0C4
- Department of Biology; McGill University; 1205 Ave Docteur Penfield Montréal Québec Canada H3A 1B1
| | - A. Gonzalez
- Department of Biology; McGill University; 1205 Ave Docteur Penfield Montréal Québec Canada H3A 1B1
| | - V. Millien
- Redpath Museum; McGill University; 859 Sherbrooke Street W. Montréal Québec Canada H3A 0C4
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35
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Locating elephant corridors between Saadani National Park and the Wami-Mbiki Wildlife Management Area, Tanzania. Afr J Ecol 2014. [DOI: 10.1111/aje.12139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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