1
|
Kusack JW, Tozer DC, Harvey KM, Schummer ML, Hobson KA. Assigning harvested waterfowl to geographic origin using feather δ2H isoscapes: What is the best analytical approach? PLoS One 2023; 18:e0288262. [PMID: 37428774 DOI: 10.1371/journal.pone.0288262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Establishing links between breeding, stopover, and wintering sites for migratory species is important for their effective conservation and management. Isotopic assignment methods used to create these connections rely on the use of predictable, established relationships between the isotopic composition of environmental hydrogen and that of the non-exchangeable hydrogen in animal tissues, often in the form of a calibration equation relating feather (δ2Hf) values derived from known-origin individuals and amount-weighted long-term precipitation (δ2Hp) data. The efficacy of assigning waterfowl to moult origin using stable isotopes depends on the accuracy of these relationships and their statistical uncertainty. Most current calibrations for terrestrial species in North America are done using amount-weighted mean growing-season δ2Hp values, but the calibration relationship is less clear for aquatic and semi-aquatic species. Our objective was to critically evaluate current methods used to calibrate δ2Hp isoscapes to predicted δ2Hf values for waterfowl. Specifically, we evaluated the strength of the relationships between δ2Hp values from three commonly used isoscapes and known-origin δ2Hf values three published datasets and one collected as part of this study, also grouping these data into foraging guilds (dabbling vs diving ducks). We then evaluated the performance of assignments using these calibrations by applying a cross-validation procedure. It remains unclear if any of the tested δ2Hp isoscapes better predict surface water inputs into food webs for foraging waterfowl. We found only marginal differences in the performance of the tested known-origin datasets, where the combined foraging-guild-specific datasets showed lower assignment precision and model fit compared to data for individual species. We recommend the use of the more conservative combined foraging-guild-specific datasets to assign geographic origin for all dabbling duck species. Refining these relationships is important for improved waterfowl management and contributes to a better understanding of the limitations of assignment methods when using the isotope approach.
Collapse
Affiliation(s)
- Jackson W Kusack
- Department of Biology, Biological and Geological Sciences Building, Western University, London, Ontario, Canada
- Long Point Waterfowl and Wetlands Research Program, Birds Canada, Port Rowan, Ontario, Canada
| | - Douglas C Tozer
- Long Point Waterfowl and Wetlands Research Program, Birds Canada, Port Rowan, Ontario, Canada
| | - Kayla M Harvey
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
| | - Michael L Schummer
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
| | - Keith A Hobson
- Department of Biology, Biological and Geological Sciences Building, Western University, London, Ontario, Canada
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
2
|
Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the Virginia rail, Rallus limicola. J Hered 2023; 114:428-435. [PMID: 37105531 PMCID: PMC10287147 DOI: 10.1093/jhered/esad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/29/2023] Open
Abstract
The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia 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 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
Collapse
Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| |
Collapse
|
3
|
Nicol S, Cros M, Peyrard N, Sabbadin R, Trépos R, Fuller RA, Woodworth BK. FlywayNet
: A hidden
semi‐Markov
model for inferring the structure of migratory bird networks from count data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sam Nicol
- CSIRO Land and Water Dutton Park Queensland Australia
| | | | | | | | | | - Richard A. Fuller
- School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| | - Bradley K. Woodworth
- School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| |
Collapse
|
4
|
Saracco JF, Cormier RL, Humple DL, Stock S, Taylor R, Siegel RB. Demographic responses to climate-driven variation in habitat quality across the annual cycle of a migratory bird species. Ecol Evol 2022; 12:e8934. [PMID: 35784033 PMCID: PMC9188024 DOI: 10.1002/ece3.8934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
The demography and dynamics of migratory bird populations depend on patterns of movement and habitat quality across the annual cycle. We leveraged archival GPS‐tagging data, climate data, remote‐sensed vegetation data, and bird‐banding data to better understand the dynamics of black‐headed grosbeak (Pheucticus melanocephalus) populations in two breeding regions, the coast and Central Valley of California (Coastal California) and the Sierra Nevada mountain range (Sierra Nevada), over 28 years (1992–2019). Drought conditions across the annual cycle and rainfall timing on the molting grounds influenced seasonal habitat characteristics, including vegetation greenness and phenology (maturity dates). We developed a novel integrated population model with population state informed by adult capture data, recruitment rates informed by age‐specific capture data and climate covariates, and survival rates informed by adult capture–mark–recapture data and climate covariates. Population size was relatively variable among years for Coastal California, where numbers of recruits and survivors were positively correlated, and years of population increase were largely driven by recruitment. In the Sierra Nevada, population size was more consistent and showed stronger evidence of population regulation (numbers of recruits and survivors negatively correlated). Neither region showed evidence of long‐term population trend. We found only weak support for most climate–demographic rate relationships. However, recruitment rates for the Coastal California region were higher when rainfall was relatively early on the molting grounds and when wintering grounds were relatively cool and wet. We suggest that our approach of integrating movement, climate, and demographic data within a novel modeling framework can provide a useful method for better understanding the dynamics of broadly distributed migratory species.
Collapse
Affiliation(s)
| | | | | | - Sarah Stock
- Division of Resources Management and Science Yosemite National Park El Portal California USA
| | - Ron Taylor
- The Institute for Bird Populations Petaluma California USA
| | | |
Collapse
|
5
|
Adde A, Casabona i Amat C, Mazerolle MJ, Darveau M, Cumming SG, O'Hara RB. Integrated modeling of waterfowl distribution in western Canada using aerial survey and citizen science (eBird) data. Ecosphere 2021. [DOI: 10.1002/ecs2.3790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Antoine Adde
- Département des sciences du bois et de la forêt Université Laval Québec Québec Canada
- Boreal Avian Modelling Project University of Alberta Edmonton Alberta Canada
| | - Clara Casabona i Amat
- Département des sciences du bois et de la forêt Université Laval Québec Québec Canada
| | - Marc J. Mazerolle
- Département des sciences du bois et de la forêt Université Laval Québec Québec Canada
| | - Marcel Darveau
- Département des sciences du bois et de la forêt Université Laval Québec Québec Canada
| | - Steven G. Cumming
- Département des sciences du bois et de la forêt Université Laval Québec Québec Canada
- Boreal Avian Modelling Project University of Alberta Edmonton Alberta Canada
| | - Robert B. O'Hara
- Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| |
Collapse
|
6
|
Zhu Q, Hobson KA, Zhao Q, Zhou Y, Damba I, Batbayar N, Natsagdorj T, Davaasuren B, Antonov A, Guan J, Wang X, Fang L, Cao L, David Fox A. Migratory connectivity of Swan Geese based on species' distribution models, feather stable isotope assignment and satellite tracking. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Qin Zhu
- School of Life Science University of Science and Technology of China Hefei China
| | - Keith A. Hobson
- Science and Technology Branch Environment and Climate Change Canada Saskatoon SK Canada
- Department of Biology University of Western Ontario London ON Canada
| | - Qingshan Zhao
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Yiqi Zhou
- Research Center for Eco‐Environment Sciences Chinese Academy of Sciences Beijing China
| | - Iderbat Damba
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Ornithology Laboratory Institute of Biology Mongolian Academy of Sciences Ulaanbaatar Mongolia
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center of Mongolia Ulaanbaatar Mongolia
| | | | | | | | - Jian Guan
- Department of Electronic Engineering and Information Science University of Science and Technology of China Hefei China
| | - Xin Wang
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Lei Fang
- School of Life Science University of Science and Technology of China Hefei China
| | - Lei Cao
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | | |
Collapse
|
7
|
Gómez C, Guerrero SL, FitzGerald AM, Bayly NJ, Hobson KA, Cadena CD. Range‐wide populations of a long‐distance migratory songbird converge during stopover in the tropics. ECOL MONOGR 2019. [DOI: 10.1002/ecm.1349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Camila Gómez
- Laboratorio de Biología Evolutiva de Vertebrados Departamento de Ciencias Biológicas Universidad de Los Andes Bogota 111711 Colombia
- SELVA: Investigación para la Conservación en el Neotrópico Bogota 111311 Colombia
| | - Sara L. Guerrero
- Laboratorio de Biología Evolutiva de Vertebrados Departamento de Ciencias Biológicas Universidad de Los Andes Bogota 111711 Colombia
| | - Alyssa M. FitzGerald
- Ecology and Evolutionary Biology State University of New York Albany New York 12222 USA
- University of California, Santa Cruz Santa Cruz California 95064 USA
- Fisheries Ecology Division, Southwest Fisheries Science Center National Marine Fisheries Institute, National Oceanic and Atmospheric Administration Santa Cruz California 95064 USA
| | - Nicholas J. Bayly
- SELVA: Investigación para la Conservación en el Neotrópico Bogota 111311 Colombia
| | | | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados Departamento de Ciencias Biológicas Universidad de Los Andes Bogota 111711 Colombia
| |
Collapse
|
8
|
Affiliation(s)
- Sam Yue
- School of Biological Sciences; University of Hong Kong; Pokfulam Hong Kong China
| | - Timothy C. Bonebrake
- School of Biological Sciences; University of Hong Kong; Pokfulam Hong Kong China
| | - Luke Gibson
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, and School of Biological Sciences; University of Hong Kong; Pokfulam Hong Kong China
| |
Collapse
|
9
|
Hart AG, Carpenter WS, Hlustik‐Smith E, Reed M, Goodenough AE. Testing the potential of Twitter mining methods for data acquisition: Evaluating novel opportunities for ecological research in multiple taxa. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Adam G. Hart
- School of Natural and Social SciencesUniversity of Gloucestershire Cheltenham UK
| | - William S. Carpenter
- School of Natural and Social SciencesUniversity of Gloucestershire Cheltenham UK
| | | | - Matt Reed
- School of Natural and Social SciencesUniversity of Gloucestershire Cheltenham UK
| | - Anne E. Goodenough
- School of Natural and Social SciencesUniversity of Gloucestershire Cheltenham UK
| |
Collapse
|
10
|
Gutiérrez-Tapia P, Azócar MI, Castro SA. A citizen-based platform reveals the distribution of functional groups inside a large city from the Southern Hemisphere: e-Bird and the urban birds of Santiago (Central Chile). Rev Chil de Hist Nat 2018. [DOI: 10.1186/s40693-018-0073-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
11
|
Coxen CL, Frey JK, Carleton SA, Collins DP. Species distribution models for a migratory bird based on citizen science and satellite tracking data. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.08.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
12
|
Ruegg KC, Anderson EC, Harrigan RJ, Paxton KL, Kelly JF, Moore F, Smith TB. Genetic assignment with isotopes and habitat suitability (
gaiah
), a migratory bird case study. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12800] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kristen C. Ruegg
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
- Department of Ecology and Evolutionary Biology University of California Santa Cruz CA 95064 USA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz CA 95060 USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
| | | | - Jeffrey F. Kelly
- Oklahoma Biological Survey University of Oklahoma Norman OK 73019 USA
- Department of Biology University of Oklahoma Norman OK 73019 USA
| | - Frank Moore
- Department of Biological Sciences University of Southern Mississippi Hattiesburg MS 39406 USA
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
- Department of Ecology and Evolutionary Biology University of California Los Angles CA 90095 USA
| |
Collapse
|
13
|
Fournier AMV, Sullivan AR, Bump JK, Perkins M, Shieldcastle MC, King SL. Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive
V
irginia rail. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12723] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Auriel M. V. Fournier
- School of Forest Resources and Environmental Sciences Michigan Technological University Houghton MI 49931 USA
| | - Alexis R. Sullivan
- Department of Ecology and Environmental Science Umeå Plant Science Centre Umeå University Umeå SE‐ 901 87 Sweden
| | - Joseph K. Bump
- School of Forest Resources and Environmental Sciences Michigan Technological University Houghton MI 49931 USA
| | - Marie Perkins
- Louisiana State University AgCenter Baton Rouge LA 79803 USA
| | | | - Sammy L. King
- U.S. Geological Survey Louisiana Cooperative Fish and Wildlife Research Unit School of Renewable Natural Resources Louisiana State University Baton Rouge LA 70816 USA
| |
Collapse
|