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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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Wann GT, Van Schmidt ND, Shyvers JE, Tarbox BC, McLachlan MM, O’Donnell MS, Titolo AJ, Coates PS, Edmunds DR, Heinrichs JA, Monroe AP, Aldridge CL. A regionally varying habitat model to inform management for greater sage-grouse persistence across their range. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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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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Yackulic CB, Dodrill M, Dzul M, Sanderlin JS, Reid JA. A need for speed in Bayesian population models: a practical guide to marginalizing and recovering discrete latent states. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02112. [PMID: 32112492 DOI: 10.1002/eap.2112] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Bayesian population models can be exceedingly slow due, in part, to the choice to simulate discrete latent states. Here, we discuss an alternative approach to discrete latent states, marginalization, that forms the basis of maximum likelihood population models and is much faster. Our manuscript has two goals: (1) to introduce readers unfamiliar with marginalization to the concept and provide worked examples and (2) to address topics associated with marginalization that have not been previously synthesized and are relevant to both Bayesian and maximum likelihood models. We begin by explaining marginalization using a Cormack-Jolly-Seber model. Next, we apply marginalization to multistate capture-recapture, community occupancy, and integrated population models and briefly discuss random effects, priors, and pseudo-R2 . Then, we focus on recovery of discrete latent states, defining different types of conditional probabilities and showing how quantities such as population abundance or species richness can be estimated in marginalized code. Last, we show that occupancy and site-abundance models with auto-covariates can be fit with marginalized code with minimal impact on parameter estimates. Marginalized code was anywhere from five to >1,000 times faster than discrete code and differences in inferences were minimal. Discrete latent states and fully conditional approaches provide the best estimates of conditional probabilities for a given site or individual. However, estimates for parameters and derived quantities such as species richness and abundance are minimally affected by marginalization. In the case of abundance, marginalized code is both quicker and has lower bias than an N-augmentation approach. Understanding how marginalization works shrinks the divide between Bayesian and maximum likelihood approaches to population models. Some models that have only been presented in a Bayesian framework can easily be fit in maximum likelihood. On the other hand, factors such as informative priors, random effects, or pseudo-R2 values may motivate a Bayesian approach in some applications. An understanding of marginalization allows users to minimize the speed that is sacrificed when switching from a maximum likelihood approach. Widespread application of marginalization in Bayesian population models will facilitate more thorough simulation studies, comparisons of alternative model structures, and faster learning.
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Affiliation(s)
- Charles B Yackulic
- Southwest Biological Science Center, U.S. Geological Survey, 2255 North Gemini Drive, Flagstaff, Arizona, 86001, USA
| | - Michael Dodrill
- Southwest Biological Science Center, U.S. Geological Survey, 2255 North Gemini Drive, Flagstaff, Arizona, 86001, USA
| | - Maria Dzul
- Southwest Biological Science Center, U.S. Geological Survey, 2255 North Gemini Drive, Flagstaff, Arizona, 86001, USA
| | - Jamie S Sanderlin
- USDA Forest Service, Rocky Mountain Research Station, Flagstaff, Arizona, 86001, USA
| | - Janice A Reid
- USDA Forest Service, Pacific Northwest Research Station, Roseburg Field Station, Roseburg, Oregon, 97331, USA
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Van Schmidt ND, Beissinger SR. The rescue effect and inference from isolation-extinction relationships. Ecol Lett 2020; 23:598-606. [PMID: 31981448 DOI: 10.1111/ele.13460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/23/2019] [Indexed: 11/28/2022]
Abstract
The rescue effect in metapopulations hypothesises that less isolated patches are unlikely to go extinct because recolonisation may occur between breeding seasons ('recolonisation rescue'), or immigrants may sufficiently bolster population size to prevent extinction altogether ('demographic rescue'). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonisation rescue for metapopulations of black rails (Laterallus jamaicensis) and Virginia rails (Rallus limicola) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonisation rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in non-equilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.
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Affiliation(s)
- Nathan D Van Schmidt
- Department of Environmental Science, Policy, and Management, University of California - Berkeley, Berkeley, CA, USA
| | - Steven R Beissinger
- Department of Environmental Science, Policy, and Management, University of California - Berkeley, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California - Berkeley, Berkeley, CA, USA
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Van Schmidt ND, Kovach T, Kilpatrick AM, Oviedo JL, Huntsinger L, Hruska T, Miller NL, Beissinger SR. Integrating social and ecological data to model metapopulation dynamics in coupled human and natural systems. Ecology 2019; 100:e02711. [DOI: 10.1002/ecy.2711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/08/2018] [Accepted: 01/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Nathan D. Van Schmidt
- Department of Environmental Science, Policy, and Management University of California–Berkeley 130 Mulford Hall No. 3114 Berkeley California 94720 USA
| | - Tony Kovach
- Department of Ecology and Evolutionary Biology University of California–Santa Cruz 130 McAllister Way Santa Cruz California 95060 USA
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary Biology University of California–Santa Cruz 130 McAllister Way Santa Cruz California 95060 USA
| | - Jose L. Oviedo
- Instituto de Políticas y Bienes Públicos Consejo Superior de Investigaciones Científicas Calle de Albasanz 26‐28 28037 Madrid Spain
| | - Lynn Huntsinger
- Department of Environmental Science, Policy, and Management University of California–Berkeley 130 Mulford Hall No. 3114 Berkeley California 94720 USA
| | - Tracy Hruska
- Department of Environmental Science, Policy, and Management University of California–Berkeley 130 Mulford Hall No. 3114 Berkeley California 94720 USA
| | - Norman L. Miller
- Department of Geography University of California–Berkeley 505 McCone Hall No. 4740 Berkeley California 94720 USA
| | - Steven R. Beissinger
- Department of Environmental Science, Policy, and Management University of California–Berkeley 130 Mulford Hall No. 3114 Berkeley California 94720 USA
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