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Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the black rail, Laterallus jamaicensis. J Hered 2023; 114:436-443. [PMID: 37119047 PMCID: PMC10287143 DOI: 10.1093/jhered/esad025] [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: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/30/2023] Open
Abstract
The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.
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Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
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Proença-Ferreira A, Borda-de-Água L, Porto M, Mira A, Moreira F, Pita R. dispfit: An R package to estimate species dispersal kernels. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Beissinger SR, Peterson SM, Hall LA, Van Schmidt N, Tecklin J, Risk BB, Richmond OM, Kovach TJ, Kilpatrick AM. Stability of patch-turnover relationships under equilibrium and nonequilibrium metapopulation dynamics driven by biogeography. Ecol Lett 2022; 25:2372-2383. [PMID: 36209497 PMCID: PMC9828715 DOI: 10.1111/ele.14111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/27/2022] [Accepted: 07/31/2022] [Indexed: 01/12/2023]
Abstract
Two controversial tenets of metapopulation biology are whether patch quality and the surrounding matrix are more important to turnover (colonisation and extinction) than biogeography (patch area and isolation) and whether factors governing turnover during equilibrium also dominate nonequilibrium dynamics. We tested both tenets using 18 years of surveys for two secretive wetland birds, black and Virginia rails, during (1) a period of equilibrium with stable occupancy and (2) after drought and arrival of West Nile Virus (WNV), which resulted in WNV infections in rails, increased extinction and decreased colonisation probabilities modified by WNV, nonequilibrium dynamics for both species and occupancy decline for black rails. Area (primarily) and isolation (secondarily) drove turnover during both stable and unstable metapopulation dynamics, greatly exceeding the effects of patch quality and matrix conditions. Moreover, slopes between turnover and patch characteristics changed little between equilibrium and nonequilibrium, confirming the overriding influences of biogeographic factors on turnover.
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Affiliation(s)
- Steven R. Beissinger
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Sean M. Peterson
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,Department of Environmental BiologyState University of New York College of Environmental Science and ForestryNew YorkUSA
| | - Laurie A. Hall
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field StationCaliforniaUSA
| | - Nathan Van Schmidt
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,US Geological Survey, Fort Collins Science CenterFort CollinsColoradoUSA
| | - Jerry Tecklin
- Sierra Foothills Research and Extension CenterBrowns ValleyCaliforniaUSA,21170 Shields Camp RoadNevada CityCaliforniaUSA
| | - Benjamin B. Risk
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,Department of Biostatistics and BioinformaticsEmory UniversityAtlantaGeorgiaUSA
| | - Orien M. Richmond
- Department of Environmental Science, Policy & ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA,Rocky Mountain Arsenal National Wildlife RefugeCommerce CityColoradoUSA
| | - Tony J. Kovach
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA,California Department of Public Health/Vector Borne Disease SectionCaliforniaUSA
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
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Thorstensen MJ, Vandervelde CA, Bugg WS, Michaleski S, Vo L, Mackey TE, Lawrence MJ, Jeffries KM. Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish. Front Genet 2022; 13:795355. [PMID: 35547248 PMCID: PMC9081360 DOI: 10.3389/fgene.2022.795355] [Citation(s) in RCA: 4] [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: 10/14/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.
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Affiliation(s)
- Matt J. Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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Brewer CT, Rauch-Davis WA, Fraser EE. The Use of Intrinsic Markers for Studying the Migratory Movements of Bats. Animals (Basel) 2021; 11:3477. [PMID: 34944252 PMCID: PMC8698158 DOI: 10.3390/ani11123477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022] Open
Abstract
Mortality of migratory bat species at wind energy facilities is a well-documented phenomenon, and mitigation and management are partially constrained by the current limited knowledge of bat migratory movements. Analyses of biochemical signatures in bat tissues ("intrinsic markers") can provide information about the migratory origins of individual bats. Many tissue samples for intrinsic marker analysis may be collected from living and dead bats, including carcasses collected at wind energy facilities. In this paper, we review the full suite of available intrinsic marker analysis techniques that may be used to study bat migration, with the goal of summarizing the current literature and highlighting knowledge gaps and opportunities. We discuss applications of the stable isotopes of hydrogen, oxygen, nitrogen, carbon, sulfur; radiogenic strontium isotopes; trace elements and contaminants; and the combination of these markers with each other and with other extrinsic markers. We further discuss the tissue types that may be analyzed for each and provide a synthesis of the generalized workflow required to link bats to origins using intrinsic markers. While stable hydrogen isotope techniques have clearly been the leading approach to infer migratory bat movement patterns across the landscape, here we emphasize a variety of lesser used intrinsic markers (i.e., strontium, trace elements, contaminants) that may address new study areas or answer novel research questions.
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Affiliation(s)
| | | | - Erin E. Fraser
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland, 20 University Drive, Corner Brook, NL A2H 5G4, Canada; (C.T.B.); (W.A.R.-D.)
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Affiliation(s)
- Eamon J. Harrity
- Idaho Cooperative Fish and Wildlife Research Unit, Department of Fish & Wildlife SciencesUniversity of Idaho 875 Perimeter Drive, Mail Stop 1141 Moscow ID 83844 USA
| | - Courtney J. Conway
- U.S. Geological Survey, Idaho Cooperative Fish and Wildlife Research Unit, Department of Fish & Wildlife SciencesUniversity of Idaho 875 Perimeter Drive, Mail Stop 1141 Moscow ID 83844 USA
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Hall LA, Van Schmidt ND, Beissinger SR. Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments. J Anim Ecol 2018; 87:691-702. [DOI: 10.1111/1365-2656.12811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 01/19/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Laurie A. Hall
- Department of Environmental Science, Policy and Management Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Nathan D. Van Schmidt
- Department of Environmental Science, Policy and Management Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Steven R. Beissinger
- Department of Environmental Science, Policy and Management Museum of Vertebrate Zoology University of California Berkeley CA USA
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