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Effects of Anthropogenic Habitat Fragmentation on the Genetic Connectivity of the Threatened and Endemic Campylorhynchus yucatanicus (Aves, Trogloditydae) in the Yucatan Peninsula, Mexico. DIVERSITY 2022. [DOI: 10.3390/d14121108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying connectivity patterns among remnant bird populations and their relationships with land use practices and adjacent habitat fragments is key to implementing appropriate long-term management strategies for species conservation. The coastal scrub and dune vegetation complex of the northern Yucatan Peninsula is rich in endemisms and has been affected by human development, which threatens the survival of the Yucatan Wren (Campylorhynchus yucatanicus) population, an endemic bird species. To identify possible anthropogenic barriers to the connectivity of C. yucatanicus along 14 localities in the Yucatan (Mexico) coastal north, we explored the relationship between the species population’s genetic variability at each sampled site and landscape structure using regression models, in addition to the relationship between genetic distance and landscape resistance. Seven nuclear microsatellite loci were used as genetic markers. Four genetic populations were highlighted by the clustering method implemented in the Geneland program. Human settlement and availability of adequate habitat were significantly related to genetic distance (Fst), suggesting limited connectivity among sites due to ongoing land use changes. We suggest changing the IUCN threat category of C. yucatanicus to endangered as we found a significant loss of genetic variability in addition to restricted distribution, small population, habitat degradation, and loss of connectivity.
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Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01451-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSpecies are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
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Boukteb A, Sakaguchi S, Ichihashi Y, Kharrat M, Nagano AJ, Shirasu K, Bouhadida M. Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq. FRONTIERS IN PLANT SCIENCE 2021; 12:618245. [PMID: 33927733 PMCID: PMC8078179 DOI: 10.3389/fpls.2021.618245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 05/25/2023]
Abstract
Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.
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Affiliation(s)
- Amal Boukteb
- Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | | | - Mohamed Kharrat
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
| | | | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mariem Bouhadida
- Field Crop Laboratory, National Institute of Agricultural Research of Tunisia, Carthage University, Tunis, Tunisia
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4
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Barr K, Beichman AC, Kalhori P, Rajbhandary J, Bay RA, Ruegg K, Smith TB. Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird ( Agelaius tricolor). Evol Appl 2021; 14:674-684. [PMID: 33767743 PMCID: PMC7980274 DOI: 10.1111/eva.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Annabel C. Beichman
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Jasmine Rajbhandary
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
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5
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Riparian areas potentially provide crucial corridors through fragmented landscape for black-capped vireo (Vireo atricapilla) source-sink system. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01314-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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García J, Morán‐Ordóñez A, García JT, Calero‐Riestra M, Alda F, Sanz J, Suárez‐Seoane S. Current landscape attributes and landscape stability in breeding grounds explain genetic differentiation in a long‐distance migratory bird. Anim Conserv 2020. [DOI: 10.1111/acv.12616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. García
- Department of Biodiversity and Environmental Management University of León León Spain
| | | | - J. T. García
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - M. Calero‐Riestra
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - F. Alda
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga TN USA
| | - J. Sanz
- Laboratorio de Teledetección de la Universidad de Valladolid (LATUV) Valladolid Spain
| | - S. Suárez‐Seoane
- Department of Organisms and Systems Biology (BOS: Ecology Unit) Research Unit of Biodiversity (UMIBUO‐CSIC‐PA)University of Oviedo Oviedo Spain
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Rossi NA, Menchaca-Rodriguez A, Antelo R, Wilson B, McLaren K, Mazzotti F, Crespo R, Wasilewski J, Alda F, Doadrio I, Barros TR, Hekkala E, Alonso-Tabet M, Alonso-Giménez Y, Lopez M, Espinosa-Lopez G, Burgess J, Thorbjarnarson JB, Ginsberg JR, Vliet KA, Amato G. High levels of population genetic differentiation in the American crocodile (Crocodylus acutus). PLoS One 2020; 15:e0235288. [PMID: 32614920 PMCID: PMC7332040 DOI: 10.1371/journal.pone.0235288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus.
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Affiliation(s)
- Natalia A. Rossi
- Wildlife Conservation Society, Bronx, New York, United States of America
- Sackler Institute of Comparative Genomics, American Museum of Natural History, Manhattan, New York, United States of America
- Department of Ecology, Evolution and Environmental Biology, Columbia University, Columbia, New York, United States of America
| | | | - Rafael Antelo
- Fundación Palmarito Casanare, Bogotá, Colombia
- Estación Biológica El Frío, Apure, Venezuela
| | - Byron Wilson
- Department of Life Sciences, University of the West Indies, Mona, Jamaica
| | - Kurt McLaren
- Department of Life Sciences, University of the West Indies, Mona, Jamaica
| | - Frank Mazzotti
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Rafael Crespo
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Joe Wasilewski
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Tito R. Barros
- Museo de Biología de la Universidad del Zulia, Maracaibo, Venezuela
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, Bronx, New York, United States of America
| | | | | | - Manuel Lopez
- Refugio de Fauna Monte Cabaniguán-Ojo de Agua, Las Tunas, Cuba
| | | | - Joe Burgess
- US Forest Service, Idleyld Park, Oregon, United States of America
| | | | - Joshua R. Ginsberg
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Kent A. Vliet
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - George Amato
- Sackler Institute of Comparative Genomics, American Museum of Natural History, Manhattan, New York, United States of America
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Crates R, Olah G, Adamski M, Aitken N, Banks S, Ingwersen D, Ranjard L, Rayner L, Stojanovic D, Suchan T, von Takach Dukai B, Heinsohn R. Genomic impact of severe population decline in a nomadic songbird. PLoS One 2019; 14:e0223953. [PMID: 31647830 PMCID: PMC6812763 DOI: 10.1371/journal.pone.0223953] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/02/2019] [Indexed: 01/27/2023] Open
Abstract
Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.
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Affiliation(s)
- Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - George Olah
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Marcin Adamski
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Nicola Aitken
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Sam Banks
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | | | - Louis Ranjard
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Laura Rayner
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Tomasz Suchan
- W. Szafer institute of Botany, Polish Academy of Sciences, Krakow, Poland
| | - Brenton von Takach Dukai
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
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9
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Hauser SS, Walker L, Leberg PL. Asymmetrical gene flow of the recently delisted passerine black-capped vireo ( Vireo atricapilla) indicates source-sink dynamics in central Texas. Ecol Evol 2019; 9:463-470. [PMID: 30680128 PMCID: PMC6342116 DOI: 10.1002/ece3.4764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
- Present address:
Department of Biological SciencesUniversity of Wisconsin – MilwaukeeMilwaukeeWisconsin
| | - Lauren Walker
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
- Present address:
National Park ServiceYellowstone National ParkMammothWyoming
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
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10
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Morgan DT, Green MC, Morrison ML, Simpson TR. Tree Species Use and Seasonal Response to Food Availability of Black-Capped Vireo. SOUTHEAST NAT 2018. [DOI: 10.1656/058.017.0415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- David T. Morgan
- Wildlife Ecology Program, Department of Biology, Texas State University, San Marcos, TX 78666
| | - M. Clay Green
- Wildlife Ecology Program, Department of Biology, Texas State University, San Marcos, TX 78666
| | - Michael L. Morrison
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843
| | - Thomas R. Simpson
- Wildlife Ecology Program, Department of Biology, Texas State University, San Marcos, TX 78666
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11
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Tavares SB, Samarra FIP, Pascoal S, Graves JA, Miller PJO. Killer whales ( Orcinus orca) in Iceland show weak genetic structure among diverse isotopic signatures and observed movement patterns. Ecol Evol 2018; 8:11900-11913. [PMID: 30598785 PMCID: PMC6303705 DOI: 10.1002/ece3.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/07/2022] Open
Abstract
Local adaption through ecological niche specialization can lead to genetic structure between and within populations. In the Northeast Pacific, killer whales (Orcinus orca) of the same population have uniform specialized diets that are non-overlapping with other sympatric, genetically divergent, and socially isolated killer whale ecotypes. However, killer whales in Iceland show intrapopulation variation of isotopic niches and observed movement patterns: some individuals appear to specialize on herring and follow it year-round while others feed upon herring only seasonally or opportunistically. We investigated genetic differentiation among Icelandic killer whales with different isotopic signatures and observed movement patterns. This information is key for management and conservation purposes but also for better understanding how niche specialization drives genetic differentiation. Photo-identified individuals (N = 61) were genotyped for 22 microsatellites and a 611 bp portion of the mitochondrial DNA (mtDNA) control region. Photo-identification of individuals allowed linkage of genetic data to existing data on individual isotopic niche, observed movement patterns, and social associations. Population subdivision into three genetic units was supported by a discriminant analysis of principal components (DAPC). Genetic clustering corresponded to the distribution of isotopic signatures, mtDNA haplotypes, and observed movement patterns, but genetic units were not socially segregated. Genetic differentiation was weak (F ST < 0.1), suggesting ongoing gene flow or recent separation of the genetic units. Our results show that killer whales in Iceland are not as genetically differentiated, ecologically discrete, or socially isolated as the Northeast Pacific prey-specialized killer whales. If any process of ecological divergence and niche specialization is taking place among killer whales in Iceland, it is likely at a very early stage and has not led to the patterns observed in the Northeast Pacific.
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Affiliation(s)
- Sara B. Tavares
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Filipa I. P. Samarra
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
- Marine and Freshwater Research InstituteReykjavíkIceland
| | - Sonia Pascoal
- Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Jeff A. Graves
- Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
| | - Patrick J. O. Miller
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsSt Andrews, FifeUK
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12
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Yıldırım Y, Anderson MJ, Hansson B, Patel S, Millar CD, Rainey PB. Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand. PLoS One 2018; 13:e0202197. [PMID: 30114275 PMCID: PMC6095540 DOI: 10.1371/journal.pone.0202197] [Citation(s) in RCA: 6] [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: 12/25/2017] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.
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Affiliation(s)
- Yeşerin Yıldırım
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D. Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
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13
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Viengkone M, Derocher AE, Richardson ES, Obbard ME, Dyck MG, Lunn NJ, Sahanatien V, Robinson BG, Davis CS. Assessing spatial discreteness of Hudson Bay polar bear populations using telemetry and genetics. Ecosphere 2018. [DOI: 10.1002/ecs2.2364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Michelle Viengkone
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Andrew E. Derocher
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Evan S. Richardson
- Wildlife Research Division, Science and Technology Branch; Environment and Climate Change Canada; Biological Sciences Building; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Martyn E. Obbard
- Wildlife Research and Monitoring Section; Ontario Ministry of Natural Resources and Forestry; Trent University; Peterborough Ontario K9J 7B8 Canada
| | - Markus G. Dyck
- Department of Environment; Government of Nunavut; Igloolik Nunavut X0A 0L0 Canada
| | - Nicholas J. Lunn
- Wildlife Research Division, Science and Technology Branch; Environment and Climate Change Canada; Biological Sciences Building; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Vicki Sahanatien
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Barry G. Robinson
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - Corey S. Davis
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
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14
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Khimoun A, Arnoux E, Martel G, Pot A, Eraud C, Condé B, Loubon M, Théron F, Covas R, Faivre B, Garnier S. Contrasted patterns of genetic differentiation across eight bird species in the Lesser Antilles. Genetica 2016; 144:125-38. [PMID: 26797853 DOI: 10.1007/s10709-016-9883-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 11/26/2022]
Abstract
Archipelagoes are considered as "natural laboratories" for studying processes that shape the distribution of diversity. The Lesser Antilles provide a favorable geographical context for divergence to occur. However, although morphological subspecies have been described across this archipelago in numerous avian species, the potential for the Lesser Antilles in driving intra-specific genetic divergence in highly mobile organisms such as birds remains understudied. Here, we assessed level of intra-specific genetic diversity and differentiation between three islands of the Lesser Antilles (Guadeloupe, Dominica and Martinique) using a multi-species approach on eight bird species. For each species, we built a set of microsatellite markers from cross-species amplifications. Significant patterns of inter-island and/or within-island genetic differentiation were detected in all species. However, levels of intra-specific genetic differentiation among the eight bird species were not always consistent with the boundaries of subspecies previously described in the sampled islands. These results suggest different histories of colonization/expansion and/or different species-specific ecological traits affecting gene flow, advocating for multi-species studies of historical and contemporary factors shaping the distribution of diversity on islands.
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Affiliation(s)
- Aurélie Khimoun
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.
| | - Emilie Arnoux
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Guillaume Martel
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Alexandre Pot
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Cyril Eraud
- CNERA Avifaune migratrice, Office National de la Chasse et de la Faune Sauvage, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Béatriz Condé
- Cellule Technique des Antilles Françaises, Office National de la Chasse et de la Faune Sauvage, 5 rue de la Dorade, 79229, Les Trois-Ilets, Martinique, France
| | - Maxime Loubon
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Franck Théron
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Rita Covas
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Bruno Faivre
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Stéphane Garnier
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
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15
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Kvistad L, Ingwersen D, Pavlova A, Bull JK, Sunnucks P. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species. PLoS One 2015; 10:e0143746. [PMID: 26649426 PMCID: PMC4674126 DOI: 10.1371/journal.pone.0143746] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population.
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Affiliation(s)
- Lynna Kvistad
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - James K. Bull
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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16
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Vázquez-Miranda H, Barr KR, Farquhar CC, Zink RM. Fluctuating fire regimes and their historical effects on genetic variation in an endangered shrubland specialist. Ecol Evol 2015; 5:5487-98. [PMID: 27069600 PMCID: PMC4813106 DOI: 10.1002/ece3.1811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/15/2022] Open
Abstract
The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire‐dependent communities. We studied an endangered juniper–oak shrubland specialist, the black‐capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, predation, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long‐term history of the fire regime and ecological niche models representing the mid‐Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present.
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Affiliation(s)
- Hernán Vázquez-Miranda
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul Minnesota 55108 USA
| | - Kelly R Barr
- Hopkins Marine Station Stanford University Pacific Grove California 93950 USA
| | - C Craig Farquhar
- Wildlife Division Texas Parks and Wildlife Department Austin Texas 78744 USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul Minnesota 55108 USA
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17
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Athrey G, Lance RF, Leberg PL. Using Genealogical Mapping and Genetic Neighborhood Sizes to Quantify Dispersal Distances in the Neotropical Passerine, the Black-Capped Vireo. PLoS One 2015; 10:e0140115. [PMID: 26461257 PMCID: PMC4603878 DOI: 10.1371/journal.pone.0140115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 09/22/2015] [Indexed: 11/25/2022] Open
Abstract
Dispersal is a key demographic process, ultimately responsible for genetic connectivity among populations. Despite its importance, quantifying dispersal within and between populations has proven difficult for many taxa. Even in passerines, which are among the most intensely studied, individual movement and its relation to gene flow remains poorly understood. In this study we used two parallel genetic approaches to quantify natal dispersal distances in a Neotropical migratory passerine, the black-capped vireo. First, we employed a strategy of sampling evenly across the landscape coupled with parentage assignment to map the genealogical relationships of individuals across the landscape, and estimate dispersal distances; next, we calculated Wright’s neighborhood size to estimate gene dispersal distances. We found that a high percentage of captured individuals were assigned at short distances within the natal population, and males were assigned to the natal population more often than females, confirming sex-biased dispersal. Parentage-based dispersal estimates averaged 2400m, whereas gene dispersal estimates indicated dispersal distances ranging from 1600–4200 m. Our study was successful in quantifying natal dispersal distances, linking individual movement to gene dispersal distances, while also providing a detailed look into the dispersal biology of Neotropical passerines. The high-resolution information was obtained with much reduced effort (sampling only 20% of breeding population) compared to mark-resight approaches, demonstrating the potential applicability of parentage-based approaches for quantifying dispersal in other vagile passerine species.
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Affiliation(s)
- Giridhar Athrey
- Department of Poultry Science, Texas A&M University, 2472 TAMU, College Station, Texas, United States of America
- Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, Texas, United States of America
- Department of Biology, University of Louisiana at Lafayette, P.O. Box 42451, Lafayette, LA, United States of America
- * E-mail:
| | - Richard F. Lance
- Environmental Laboratory, USACE, Vicksburg, MS, United States of America
| | - Paul L. Leberg
- Department of Biology, University of Louisiana at Lafayette, P.O. Box 42451, Lafayette, LA, United States of America
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18
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Klinga P, Mikoláš M, Zhelev P, Höglund J, Paule L. Genetic differentiation of western capercaillie in the Carpathian Mountains: the importance of post glacial expansions and habitat connectivity. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Klinga
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
| | - Martin Mikoláš
- Faculty of Forestry and Wood Sciences; Czech University of Life Sciences; Kamýcka cesta 1176 CZ-165 21 Praha 6-Suchdol Czech Republic
- PRALES; Odtrnovie 563 SK-013 22 Rosina Slovakia
| | - Petar Zhelev
- Faculty of Forestry; University of Forestry; Kliment Ohridski Blvd. 10 BG-17456 Sofia Bulgaria
| | - Jacob Höglund
- Department of Ecology and Genetics; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Ladislav Paule
- Faculty of Forestry; Technical University; SK-96053 Zvolen Slovakia
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19
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Dennison S, McAlpin S, Chapple DG, Stow AJ. Genetic Divergence among Regions Containing the Vulnerable Great Desert Skink (Liopholis kintorei) in the Australian Arid Zone. PLoS One 2015; 10:e0128874. [PMID: 26061141 PMCID: PMC4464518 DOI: 10.1371/journal.pone.0128874] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/02/2015] [Indexed: 11/18/2022] Open
Abstract
Knowledge of genetic structure and patterns of connectivity is valuable for implementation of effective conservation management. The arid zone of Australia contains a rich biodiversity, however this has come under threat due to activities such as altered fire regimes, grazing and the introduction of feral herbivores and predators. Suitable habitats for many species can be separated by vast distances, and despite an apparent lack of current geographical barriers to dispersal, habitat specialisation, which is exhibited by many desert species, may limit connectivity throughout this expansive region. We characterised the genetic structure and differentiation of the great desert skink (Liopholis kintorei), which has a patchy, but widespread distribution in the western region of the Australian arid zone. As a species of cultural importance to local Aboriginal groups and nationally listed as Vulnerable, it is a conservation priority for numerous land managers in central Australia. Analysis of mitochondrial ND4 sequence data and ten nuclear microsatellite loci across six sampling localities through the distribution of L. kintorei revealed considerable differentiation among sites, with mitochondrial FST and microsatellite F'ST ranging from 0.047-0.938 and 0.257-0.440, respectively. The extent of differentiation suggests three main regions that should be managed separately, in particular the southeastern locality of Uluru. Current genetic delineation of these regions should be maintained if future intervention such as translocation or captive breeding is to be undertaken.
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Affiliation(s)
- Siobhan Dennison
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
- Australian Wildlife Conservancy, PO Box 8070, Subiaco East, WA, Australia
| | - Steve McAlpin
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Adam J. Stow
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
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20
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Barr KR, Kus BE, Preston KL, Howell S, Perkins E, Vandergast AG. Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus). Mol Ecol 2015; 24:2349-63. [DOI: 10.1111/mec.13176] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Kelly R. Barr
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Barbara E. Kus
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Kristine L. Preston
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Scarlett Howell
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Emily Perkins
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
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21
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Hillman SS, Drewes RC, Hedrick MS, Hancock TV. Physiological vagility and its relationship to dispersal and neutral genetic heterogeneity in vertebrates. ACTA ACUST UNITED AC 2014; 217:3356-64. [PMID: 25013113 DOI: 10.1242/jeb.105908] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vagility is the inherent power of movement by individuals. Vagility and the available duration of movement determine the dispersal distance individuals can move to interbreed, which affects the fine-scale genetic structure of vertebrate populations. Vagility and variation in population genetic structure are normally explained by geographic variation and not by the inherent power of movement by individuals. We present a new, quantitative definition for physiological vagility that incorporates aerobic capacity, body size, body temperature and the metabolic cost of transport, variables that are independent of the physical environment. Physiological vagility is the speed at which an animal can move sustainably based on these parameters. This meta-analysis tests whether this definition of physiological vagility correlates with empirical data for maximal dispersal distances and measured microsatellite genetic differentiation with distance {[F(ST)/[1-F(ST))]/ln distance} for amphibians, reptiles, birds and mammals utilizing three locomotor modes (running, flying, swimming). Maximal dispersal distance and physiological vagility increased with body mass for amphibians, reptiles and mammals utilizing terrestrial movement. The relative slopes of these relationships indicate that larger individuals require longer movement durations to achieve maximal dispersal distances. Both physiological vagility and maximal dispersal distance were independent of body mass for flying vertebrates. Genetic differentiation with distance was greatest for terrestrial locomotion, with amphibians showing the greatest mean and variance in differentiation. Flying birds, flying mammals and swimming marine mammals showed the least differentiation. Mean physiological vagility of different groups (class and locomotor mode) accounted for 98% of the mean variation in genetic differentiation with distance in each group. Genetic differentiation with distance was not related to body mass. The physiological capacity for movement (physiological vagility) quantitatively predicts genetic isolation by distance in the vertebrates examined.
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Affiliation(s)
- Stanley S Hillman
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Robert C Drewes
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Michael S Hedrick
- Department of Biological Science, California State University, East Bay, Hayward, CA 94542, USA
| | - Thomas V Hancock
- Department of Biology, Portland State University, Portland, OR 97201, USA
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22
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Porlier M, Garant D, Perret P, Charmantier A. Habitat-linked population genetic differentiation in the blue tit Cyanistes caeruleus. ACTA ACUST UNITED AC 2012; 103:781-91. [PMID: 23087385 DOI: 10.1093/jhered/ess064] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although the recent emergence of the field of landscape genetics has led to several studies investigating the effects of habitat composition between populations on genetic differentiation, much less is known on the impact of within-habitat ecological characteristics on levels of gene flow and genetic differentiation among populations. Using data on 840 individuals sampled in 8 sites in Corsica and 1 in southern France and analyzed at 10 microsatellite loci, we assessed the spatial and temporal population genetic structure of blue tits (Cyanistes caeruleus) in Corsica and identified the ecological factors, both between- and within-sampling sites, responsible for the observed genetic structure. We found temporally stable fine-scale genetic structure within Corsica, with genetic differentiation values among populations corresponding to ~25% of levels observed between Corsica and the mainland. This structure was not explained by the geographic distance among populations or by the presence of physical barriers but was instead related to local habitat types (deciduous or evergreen oaks). Our results are thus consistent with previously documented phenotypic differences among habitats in morphological and reproductive traits. These findings suggest that although individuals have high dispersal ability, local adaptation might reduce gene flow among populations located in different habitats.
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Affiliation(s)
- Melody Porlier
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Qc, J1K 2R1 Canada.
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23
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Athrey G, Barr KR, Lance RF, Leberg PL. Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla). Evol Appl 2012; 5:540-52. [PMID: 23028396 PMCID: PMC3461138 DOI: 10.1111/j.1752-4571.2011.00233.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022] Open
Abstract
Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.
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Affiliation(s)
- Giridhar Athrey
- Department of Biology, University of Louisiana at LafayetteLafayette, LA, USA
| | - Kelly R Barr
- Department of Biology, University of Louisiana at LafayetteLafayette, LA, USA
| | - Richard F Lance
- Environmental Laboratory, US Army Engineer Research and Development CenterVicksburg, MS, USA
| | - Paul L Leberg
- Department of Biology, University of Louisiana at LafayetteLafayette, LA, USA
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24
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ATHREY GIRI, LANCE RICHARDF, LEBERG PAULL. How far is too close? restricted, sex-biased dispersal in black-capped vireos. Mol Ecol 2012; 21:4359-70. [DOI: 10.1111/j.1365-294x.2012.05694.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Nagy JA, Johnson DL, Larter NC, Campbell MW, Derocher AE, Kelly A, Dumond M, Allaire D, Croft B. Subpopulation structure of caribou (Rangifer tarandus L.) in arctic and subarctic Canada. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2011; 21:2334-2348. [PMID: 21939065 DOI: 10.1890/10-1410.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Effective management and conservation of species, subspecies, or ecotypes require an understanding of how populations are structured in space. We used satellite-tracking locations and hierarchical and fuzzy clustering to quantify subpopulations within the behaviorally different barren-ground caribou (Rangifer tarandus groenlandicus), Dolphin and Union island caribou (R. t. groenlandicus x pearyi), and boreal (R. t. caribou) caribou ecotypes in the Northwest Territories and Nunavut, Canada. Using a novel approach, we verified that the previously recognized Cape Bathurst, Bluenose-West, Bluenose-East, Bathurst, Beverly, Qamanirjuaq, and Lorillard barren-ground subpopulations were robust and that the Queen Maude Gulf and Wager Bay barren-ground subpopulations were organized as individuals. Dolphin and Union island and boreal caribou formed one and two distinct subpopulation, respectively, and were organized as individuals. Robust subpopulations were structured by strong annual spatial affiliation among females; subpopulations organized as individuals were structured by migratory connectivity, barriers to movement, and/or habitat discontinuity. One barren-ground subpopulation used two calving grounds, and one calving ground was used by two barren-ground subpopulations, indicating that these caribou cannot be reliably assigned to subpopulations solely by calving-ground use. They should be classified by annual spatial affiliation among females. Annual-range size and path lengths varied significantly among ecotypes, including mountain woodland caribou (R. t. caribou), and reflected behavioral differences. An east-west cline in annual-range sizes and path lengths among migratory barren-ground subpopulations likely reflected differences in subpopulation size and habitat conditions and further supported the subpopulation structure identified.
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Affiliation(s)
- John A Nagy
- Department of Environment and Natural Resources, Government of the Northwest Territories, P.O. Box 1320, Yellowknife, Northwest Territories X1A 2L9, Canada.
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26
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KANNO YOICHIRO, VOKOUN JASONC, LETCHER BENJAMINH. Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks. Mol Ecol 2011; 20:3711-29. [DOI: 10.1111/j.1365-294x.2011.05210.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Abstract
Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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28
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Abstract
This article reviews recent developments in Bayesian algorithms that explicitly include geographical information in the inference of population structure. Current models substantially differ in their prior distributions and background assumptions, falling into two broad categories: models with or without admixture. To aid users of this new generation of spatially explicit programs, we clarify the assumptions underlying the models, and we test these models in situations where their assumptions are not met. We show that models without admixture are not robust to the inclusion of admixed individuals in the sample, thus providing an incorrect assessment of population genetic structure in many cases. In contrast, admixture models are robust to an absence of admixture in the sample. We also give statistical and conceptual reasons why data should be explored using spatially explicit models that include admixture.
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Affiliation(s)
- Olivier François
- Grenoble IT, Joseph Fourier University, CNRS UMR 5525, TIMC, Group of Computational and Mathematical Biology, 38706 La Tronche, France
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29
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TATARENKOV A, HEALEY CIM, AVISE JC. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration. Mol Ecol 2009; 19:257-68. [DOI: 10.1111/j.1365-294x.2009.04464.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Heller R, Siegismund HR. Relationship between three measures of genetic differentiation G(ST), D(EST) and G'(ST): how wrong have we been? Mol Ecol 2009; 18:2080-3; discussion 2088-91. [PMID: 19645078 DOI: 10.1111/j.1365-294x.2009.04185.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R Heller
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark.
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Porlier M, Bélisle M, Garant D. Non-random distribution of individual genetic diversity along an environmental gradient. Philos Trans R Soc Lond B Biol Sci 2009; 364:1543-54. [PMID: 19414469 DOI: 10.1098/rstb.2009.0010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies.
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Affiliation(s)
- Mélody Porlier
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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