1
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Tsai WLE, Escalona M, Garrett KL, Terrill RS, Sahasrabudhe R, Nguyen O, Beraut E, Seligmann W, Fairbairn CW, Harrigan RJ, McCormack JE, Alfaro ME, Smith TB, Bay RA. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered 2024; 115:317-325. [PMID: 38401156 PMCID: PMC11081134 DOI: 10.1093/jhered/esae008] [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: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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Affiliation(s)
- Whitney L E Tsai
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Kimball L Garrett
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States
| | - Ryan S Terrill
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, 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
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Ryan J Harrigan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA 95616, United States
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2
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Tinsman JC, Gruppi C, Bossu CM, Prigge TL, Harrigan RJ, Zaunbrecher V, Koepfli KP, LeBreton M, Njabo K, Wenda C, Xing S, Abernethy K, Ades G, Akeredolu E, Andrew IB, Barrett TA, Bernáthová I, Černá Bolfíková B, Diffo JL, Difouo Fopa G, Ebong LE, Godwill I, Koumba Pambo AF, Labuschagne K, Nwobegahay Mbekem J, Momboua BR, Mousset Moumbolou CL, Ntie S, Rose-Jeffreys E, Simo FT, Sundar K, Swiacká M, Takuo JM, Talla VNK, Tamoufe U, Dingle C, Ruegg K, Bonebrake TC, Smith TB. Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia. Science 2023; 382:1282-1286. [PMID: 38096373 DOI: 10.1126/science.adi5066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
The white-bellied pangolin (Phataginus tricuspis) is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.
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Affiliation(s)
- Jen C Tinsman
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- National Fish and Wildlife Forensic Laboratory, US Fish and Wildlife Service, Ashland, OR, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
| | - Cristian Gruppi
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Tracey-Leigh Prigge
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Virginia Zaunbrecher
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Matthew LeBreton
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Mosaic, Yaoundé, Cameroon
- International Institute for Tropical Agriculture, Yaoundé, Cameroon
| | - Kevin Njabo
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cheng Wenda
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuang Xing
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Katharine Abernethy
- Institut de Recherche en Ecologie Tropicale, Centre National de la Recherche Scientifique et Technologique, Libreville, Gabon
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Gary Ades
- Fauna Conservation Department, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | | | - Imuzei B Andrew
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Taneisha A Barrett
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Iva Bernáthová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | | | - Ghislain Difouo Fopa
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Biology and Animal Physiology, University of Yaoundé I, Yaoundé, Cameroon
| | - Lionel Esong Ebong
- Department of Ecology and Nature Management, School of Earth Sciences and Environmental Engineering, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Ichu Godwill
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Starkville, MS, USA
| | | | - Kim Labuschagne
- South African National Biodiversity Institute, Pretoria, South Africa
| | | | - Brice R Momboua
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Carla L Mousset Moumbolou
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
- Pangolin Conservation Network, Libreville, Gabon
| | - Stephan Ntie
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | | | - Franklin T Simo
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- Department of Biology and Animal Physiology, University of Yaoundé I, Yaoundé, Cameroon
| | - Keerthana Sundar
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
| | - Markéta Swiacká
- Department of Spatial Sciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jean Michel Takuo
- International Institute for Tropical Agriculture, Yaoundé, Cameroon
- Metabiota Cameroon Ltd, Yaoundé, Cameroon
| | - Valery N K Talla
- Département de Biologie des Organismes, Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Applied Biology and Ecology, Faculty of Science, University of Dschang, Dschang, Cameroon
| | | | - Caroline Dingle
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Timothy C Bonebrake
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Pangolin Specialist Group, IUCN Species Survival Commission, London, UK
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, Los Angeles, CA, USA
- Congo Basin Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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3
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Gruppi C, Sanzenbacher P, Balekjian K, Hagar R, Hagen S, Rayne C, Schweizer TM, Bossu CM, Cooper D, Dietsch T, Smith TB, Ruegg K, Harrigan RJ. Genetic identification of avian samples recovered from solar energy installations. PLoS One 2023; 18:e0289949. [PMID: 37672506 PMCID: PMC10482291 DOI: 10.1371/journal.pone.0289949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/30/2023] [Indexed: 09/08/2023] Open
Abstract
Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots"-known to be of avian origin but not readily assignable to species via morphology-may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.
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Affiliation(s)
- Cristian Gruppi
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Peter Sanzenbacher
- U.S. Fish and Wildlife Service, Palm Springs, California, United States of America
| | - Karina Balekjian
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rachel Hagar
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Sierra Hagen
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Christine Rayne
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Teia M. Schweizer
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Christen M. Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Daniel Cooper
- Resource Conservation District, Santa Monica Mountains, Topanga, California, United States of America
| | - Thomas Dietsch
- U.S. Fish and Wildlife Service, Carlsbad, California, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
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4
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Freedman AH, Harrigan RJ, Zhen Y, Hamilton AM, Smith TB. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol Ecol 2023; 32:2287-2300. [PMID: 36718952 DOI: 10.1111/mec.16867] [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: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan J Harrigan
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Ying Zhen
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Alison M Hamilton
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Thomas B Smith
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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5
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Houck ML, Koepfli KP, Hains T, Khan R, Charter SJ, Fronczek JA, Misuraca AC, Kliver S, Perelman PL, Beklemisheva V, Graphodatsky A, Luo SJ, O'Brien SJ, Lim NTL, Chin JSC, Guerra V, Tamazian G, Omer A, Weisz D, Kaemmerer K, Sturgeon G, Gaspard J, Hahn A, McDonough M, Garcia-Treviño I, Gentry J, Coke RL, Janecka JE, Harrigan RJ, Tinsman J, Smith TB, Aiden EL, Dudchenko O. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Res 2023; 31:13. [PMID: 37043058 DOI: 10.1007/s10577-023-09722-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 04/13/2023]
Abstract
We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.
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Affiliation(s)
- Marlys L Houck
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA.
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA.
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA.
- Computer Technologies Laboratory, ITMO University, 197101, St. Petersburg, Russia.
| | - Taylor Hains
- Committee On Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suellen J Charter
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Julie A Fronczek
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Ann C Misuraca
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, 1353, Copenhagen, Denmark
| | - Polina L Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Violetta Beklemisheva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Computer Technologies Laboratory, ITMO University, 197101, St. Petersburg, Russia
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33004, USA
| | - Norman T-L Lim
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, 637616, Singapore
| | - Jason S C Chin
- Taipei Zoo, No. 30 Sec. 2 Xinguang Rd., Taipei, 11656, Taiwan
| | - Vanessa Guerra
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Gaik Tamazian
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | - Alicia Hahn
- Pittsburgh Zoo & Aquarium, PA, 15206, Pittsburgh, USA
| | | | | | - Jordan Gentry
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX, 78212, USA
| | - Rob L Coke
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX, 78212, USA
| | - Jan E Janecka
- Department of Biological Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University, Pittsburgh, PA, 15282, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
| | - Jen Tinsman
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Center for Theoretical and Biological Physics, Rice University, Houston, TX, 77030, USA.
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6
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Zhen Y, Dongmo MAK, Harrigan RJ, Ruegg K, Fu Q, Hanna R, Bonebrake TC, Smith TB. Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly. Evolution 2023:7086034. [PMID: 36964759 DOI: 10.1093/evolut/qpad052] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 03/26/2023]
Abstract
Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly Bicyclus dorothea originating from rainforest and ecotone habitats in Cameroon under common garden conditions. We also sampled wild-caught butterflies from forest and ecotone sites and used RADseq to explore genome-wide population differentiation. We found differences in the level of phenotypic plasticity across habitats. Specifically, ecotone populations exhibited greater sensitivity in wing eyespot features with variable development temperatures relative to rainforest populations. Known adaptive roles of wing eyespots in Bicyclus species suggest that this morphological plasticity is likely under divergent selection across environmental gradients. However, we found no distinct population structure of genome-wide variation between habitats, suggesting high levels of ongoing gene flow between habitats is homogenizing most parts of the genome.
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Affiliation(s)
- Ying Zhen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Michel A K Dongmo
- International Institute of Tropical Agriculture, Yaoundé, Cameroon
- Laboratory of Parasitology and Ecology, University of Yaoundé I, Faculty of Science, Yaoundé, Cameroon
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA 90095, USA
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Qi Fu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rachid Hanna
- International Institute of Tropical Agriculture, Yaoundé, Cameroon
| | - Timothy C Bonebrake
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Thomas B Smith
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E Young Drive East, Los Angeles, CA 90095, USA
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7
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Shaffer HB, Toffelmier E, Corbett-Detig RB, Escalona M, Erickson B, Fiedler P, Gold M, Harrigan RJ, Hodges S, Luckau TK, Miller C, Oliveira DR, Shaffer KE, Shapiro B, Sork VL, Wang IJ. Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project. J Hered 2022; 113:577-588. [PMID: 35395669 DOI: 10.1093/jhered/esac020] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 12/16/2022] Open
Abstract
The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Russ B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bjorn Erickson
- U.S. Fish and Wildlife Service, Sacramento, CA 95825, USA
| | - Peggy Fiedler
- Natural Reserve System, Office of the President, University of California, Oakland, CA 94607, USA
| | - Mark Gold
- California Natural Resources Agency, 1416 Ninth Street, Suite 1311, Sacramento, CA 95814, USA
| | - Ryan J Harrigan
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Center for Tropical Research, Institute for Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Scott Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Tara K Luckau
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Daniel R Oliveira
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Kevin E Shaffer
- California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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8
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Alvarado AH, Bossu CM, Harrigan RJ, Bay RA, Nelson ARP, Smith TB, Ruegg KC. Genotype‐environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence. Evol Appl 2022; 15:1390-1407. [PMID: 36187181 PMCID: PMC9488676 DOI: 10.1111/eva.13444] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/04/2022] [Indexed: 12/01/2022] Open
Abstract
Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.
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Affiliation(s)
- Allison H. Alvarado
- Biology Department California State University Channel Islands Camarillo CA USA
| | - Christen M. Bossu
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Biology Colorado State University Fort Collins CO USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
| | - Rachael A. Bay
- Department of Evolution and Ecology University of California Davis CA USA
| | | | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins CO USA
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9
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Brown JI, Harrigan RJ, Lavretsky P. Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex. Mol Ecol 2022; 31:2578-2593. [PMID: 35263000 DOI: 10.1111/mec.16423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Ryan J Harrigan
- Center for Tropical Research, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA, 90095, U.S.A
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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10
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecol Appl 2021; 31:e02379. [PMID: 34013632 DOI: 10.5281/zenodo.4516670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/27/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California, 90089, USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California, 91009, USA
| | - Dannise V Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri, 65201, USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Melisa G Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, 90089, USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Teia M Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Tiara N Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Emma A Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ana E Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Sarah K Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Miroslava N Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
- Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Michael N Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
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11
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecol Appl 2021; 31:e02379. [PMID: 34013632 PMCID: PMC9297316 DOI: 10.1002/eap.2379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/15/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California 90089 USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Emily E. Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Fabian D. Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91009 USA
| | - Dannise V. Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri 65201 USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Melisa G. Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Teia M. Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523 USA
| | - Tiara N. Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington 98195 USA
| | - Emma A. Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ana E. Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Sarah K. Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor 16911 Indonesia
| | - Miroslava N. Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
- Biological Sciences, University of Southern California, Los Angeles, California 90089 USA
| | - N. Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Michael N. Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
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12
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Abstract
Coccidioidomycosis is an infectious disease of humans and other mammals that has seen a recent increase in occurrence in the southwestern United States, particularly in California. A rise in cases and risk to public health can serve as the impetus to apply newly developed methods that can quickly and accurately predict future caseloads. The recursive and Hawkes point process models with various triggering functions were fit to the data and their goodness of fit evaluated and compared. Although the point process models were largely similar in their fit to the data, the recursive point process model offered a slightly superior fit. We explored forecasting the spread of coccidioidomycosis in California from December 2002 to December 2017 using this recursive model, and we separated the training and testing portions of the data and achieved a root mean squared error of just 3.62 cases/week.
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Affiliation(s)
- Jiajia Wang
- Department of Statistics, University of California, Los Angeles, CA 92521, USA;
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 92521, USA;
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13
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Smith TB, Fuller TL, Zhen Y, Zaunbrecher V, Thomassen HA, Njabo K, Anthony NM, Gonder MK, Buermann W, Larison B, Ruegg K, Harrigan RJ. Genomic vulnerability and socio-economic threats under climate change in an African rainforest bird. Evol Appl 2021; 14:1239-1247. [PMID: 34025764 PMCID: PMC8127712 DOI: 10.1111/eva.13193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 01/28/2023] Open
Abstract
Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way, understanding future genomic and environmental relationships can help guide management decisions, such as where to establish new protected areas where populations might be buffered from high temperatures or major changes in rainfall. However, climate warming is only one of many anthropogenic threats one must consider in rapidly developing parts of the world. In Central Africa, deforestation, mining, and infrastructure development are accelerating population declines of rainforest species. Here we investigate multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (Andropadus virens). We examine current climate and genomic variation in order to explore the association between genome and environment under future climate conditions. Specifically, we estimate Genomic Vulnerability, defined as the mismatch between current and predicted future genomic variation based on genotype-environment relationships modeled across contemporary populations. We do so while considering other anthropogenic impacts. We find that coastal and central Cameroon populations will require the greatest shifts in adaptive genomic variation, because both climate and land use in these areas are predicted to change dramatically. In contrast, in the more northern forest-savanna ecotones, genomic shifts required to keep pace with climate will be more moderate, and other anthropogenic impacts are expected to be comparatively low in magnitude. While an analysis of diverse taxa will be necessary for making comprehensive conservation decisions, the species-specific results presented illustrate how evolutionary genomics and other anthropogenic threats may be mapped and used to inform mitigation efforts. To this end, we present an integrated conceptual model demonstrating how the approach for a single species can be expanded to many taxonomically diverse species.
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Affiliation(s)
- Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Trevon L. Fuller
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
| | - Ying Zhen
- Zhejiang Provincial Laboratory of Life Sciences and BiomedicineKey Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhouChina
- Institute of BiologyWestlake Institute for Advanced StudyHangzhouChina
| | - Virginia Zaunbrecher
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
| | | | - Kevin Njabo
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
| | - Nicola M. Anthony
- Department of Biological SciencesUniversity of New OrleansNew OrleansLAUSA
| | | | | | - Brenda Larison
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Ryan J. Harrigan
- Center for Tropical ResearchInstitute of the Environment & SustainabilityUniversity of California Los AngelesLos AngelesCAUSA
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14
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Ruegg KC, Harrigan RJ, Saracco JF, Smith TB, Taylor CM. A genoscape-network model for conservation prioritization in a migratory bird. Conserv Biol 2020; 34:1482-1491. [PMID: 32391608 DOI: 10.1111/cobi.13536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Migratory animals are declining worldwide and coordinated conservation efforts are needed to reverse current trends. We devised a novel genoscape-network model that combines genetic analyses with species distribution modeling and demographic data to overcome challenges with conceptualizing alternative risk factors in migratory species across their full annual cycle. We applied our method to the long distance, Neotropical migratory bird, Wilson's Warbler (Cardellina pusilla). Despite a lack of data from some wintering locations, we demonstrated how the results can be used to help prioritize conservation of breeding and wintering areas. For example, we showed that when genetic, demographic, and network modeling results were considered together it became clear that conservation recommendations will differ depending on whether the goal is to preserve unique genetic lineages or the largest number of birds per unit area. More specifically, if preservation of genetic lineages is the goal, then limited resources should be focused on preserving habitat in the California Sierra, Basin Rockies, or Coastal California, where the 3 most vulnerable genetic lineages breed, or in western Mexico, where 2 of the 3 most vulnerable lineages overwinter. Alternatively, if preservation of the largest number of individuals per unit area is the goal, then limited conservation dollars should be placed in the Pacific Northwest or Central America, where densities are estimated to be the highest. Overall, our results demonstrated the utility of adopting a genetically based network model for integrating multiple types of data across vast geographic scales and better inform conservation decision-making for migratory animals.
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Affiliation(s)
- Kristen C Ruegg
- Biology Department, Colorado State University, 251 W. Pitkins St, Fort Collins, CO, 80521, U.S.A
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
| | - James F Saracco
- The Institute for Bird Populations, PO Box 1346, Point Reyes Station, CA, 94956, U.S.A
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, U.S.A
| | - Caz M Taylor
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs Center, New Orleans, LA, 70118, U.S.A
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15
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Affiliation(s)
- Junhyung Park
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam W. Chaffee
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ryan J. Harrigan
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
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16
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Morgan K, Mboumba JF, Ntie S, Mickala P, Miller CA, Zhen Y, Harrigan RJ, Le Underwood V, Ruegg K, Fokam EB, Tasse Taboue GC, Sesink Clee PR, Fuller T, Smith TB, Anthony NM. Precipitation and vegetation shape patterns of genomic and craniometric variation in the central African rodent Praomys misonnei. Proc Biol Sci 2020; 287:20200449. [PMID: 32635865 DOI: 10.1098/rspb.2020.0449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Predicting species' capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute reservoirs of standing variation, increasing the capacity for future adaptation. Here, we map patterns of environmentally associated genomic and craniometric variation in the central African rodent Praomys misonnei to identify areas with the greatest turnover in genomic composition. We also project patterns of environmentally associated genomic variation under future climate change scenarios to determine where populations may be under the greatest pressure to adapt. While precipitation gradients influence both genomic and craniometric variation, vegetation structure is also an important determinant of craniometric variation. Areas of elevated environmentally associated genomic and craniometric variation overlap with zones of rapid ecological transition underlining their importance as reservoirs of evolutionary potential. We also find that populations in the Sanaga river basin, central Cameroon and coastal Gabon are likely to be under the greatest pressure from climate change. Lastly, we make specific conservation recommendations on how to protect zones of high evolutionary potential and identify areas where populations may be the most susceptible to climate change.
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Affiliation(s)
- Katy Morgan
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Jean-François Mboumba
- Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Stephan Ntie
- Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Patrick Mickala
- Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Courtney A Miller
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Ying Zhen
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J Harrigan
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Vinh Le Underwood
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Kristen Ruegg
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Eric B Fokam
- Department of Zoology and Animal Physiology, University of Buea, Buea, Cameroon
| | | | | | - Trevon Fuller
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Thomas B Smith
- Centre for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Nicola M Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
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17
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Kelly JD, Park J, Harrigan RJ, Hoff NA, Lee SD, Wannier R, Selo B, Mossoko M, Njoloko B, Okitolonda-Wemakoy E, Mbala-Kingebeni P, Rutherford GW, Smith TB, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Rimoin AW, Schoenberg FP. Real-time predictions of the 2018-2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models. Epidemics 2019; 28:100354. [PMID: 31395373 PMCID: PMC7358183 DOI: 10.1016/j.epidem.2019.100354] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
As of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihoods of people already suffering from civil strife and armed conflict, relatively simple mathematical models and their short-term predictions have the potential to inform Ebola response efforts in real time. We applied recently developed non-parametrically estimated Hawkes point processes to model the expected cumulative case count using daily case counts from May 3, 2018, to June 16, 2019, initially reported by the Ministry of Health of DRC and later confirmed in World Health Organization situation reports. We generated probabilistic estimates of the ongoing EVD outbreak in DRC extending both before and after June 16, 2019, and evaluated their accuracy by comparing forecasted vs. actual outbreak sizes, out-of-sample log-likelihood scores and the error per day in the median forecast. The median estimated outbreak sizes for the prospective thee-, six-, and nine-week projections made using data up to June 16, 2019, were, respectively, 2317 (95% PI: 2222, 2464); 2440 (95% PI: 2250, 2790); and 2544 (95% PI: 2273, 3205). The nine-week projection experienced some degradation with a daily error in the median forecast of 6.73 cases, while the six- and three-week projections were more reliable, with corresponding errors of 4.96 and 4.85 cases per day, respectively. Our findings suggest the Hawkes point process may serve as an easily-applied statistical model to predict EVD outbreak trajectories in near real-time to better inform decision-making and resource allocation during Ebola response efforts.
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Affiliation(s)
- J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA; F.I. Proctor Foundation, University of California, San Francisco, CA USA.
| | - Junhyung Park
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Nicole A Hoff
- Department of Epidemiology, University of California, Los Angeles, CA, USA
| | - Sarita D Lee
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Rae Wannier
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | | | | | | | | | - George W Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | | | | | - Anne W Rimoin
- Department of Epidemiology, University of California, Los Angeles, CA, USA
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18
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Heppenheimer E, Harrigan RJ, Rutledge LY, Koepfli KP, DeCandia AL, Brzeski KE, Benson JF, Wheeldon T, Patterson BR, Kays R, Hohenlohe PA, von Holdt BM. Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status. Genes (Basel) 2018; 9:genes9120606. [PMID: 30518163 PMCID: PMC6316216 DOI: 10.3390/genes9120606] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 10/15/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 01/22/2023] Open
Abstract
The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.
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Affiliation(s)
- Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
| | - Linda Y Rutledge
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
- Biology Department, Trent University, Peterborough, ON K9L 1Z8, Canada.
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA.
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Alexandra L DeCandia
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Kristin E Brzeski
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - John F Benson
- School of Natural Resources, University of Nebraska, Lincoln, NE 68583, USA.
| | - Tyler Wheeldon
- Environmental & Life Sciences, Trent University, Peterborough, ON K9L 0G2, Canada.
- Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON K9L 0G2, Canada.
| | - Brent R Patterson
- Environmental & Life Sciences, Trent University, Peterborough, ON K9L 0G2, Canada.
- Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON K9L 0G2, Canada.
| | - Roland Kays
- North Carolina Museum of Natural Sciences and Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27601, USA.
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Bridgett M von Holdt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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19
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Bay RA, Harrigan RJ, Buermann W, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Response to Comment on "Genomic signals of selection predict climate-driven population declines in a migratory bird". Science 2018; 361:361/6401/eaat7279. [PMID: 30072513 DOI: 10.1126/science.aat7956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/05/2018] [Indexed: 11/02/2022]
Abstract
Fitzpatrick et al discuss issues that they had with analyses and interpretation in our recent manuscript on genomic correlates of climate in yellow warblers. We provide evidence that our findings would not change with different analysis and maintain that our study represents a promising direction for integrating the potential for climate adaptation as one of many tools in conservation management.
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Affiliation(s)
- Rachael A Bay
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA. .,Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ryan J Harrigan
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Wolfgang Buermann
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Vinh Le Underwood
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH 43210, USA
| | - Thomas B Smith
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kristen Ruegg
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
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20
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Affiliation(s)
| | - Joshua Seth Gordon
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ryan J. Harrigan
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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21
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Ruegg K, Bay RA, Anderson EC, Saracco JF, Harrigan RJ, Whitfield M, Paxton EH, Smith TB. Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecol Lett 2018; 21:1085-1096. [DOI: 10.1111/ele.12977] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/11/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Kristen Ruegg
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; Santa Cruz CA 95060 USA
| | - Rachael A. Bay
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Evolution and Ecology; University of California Davis; One Shields Ave Davis CA 95616 USA
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
| | - Eric C. Anderson
- Department of Evolution and Ecology; University of California Davis; One Shields Ave Davis CA 95616 USA
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
| | - James F. Saracco
- The Institute for Bird Populations; PO Box 1346 Point Reyes Station CA 94956 USA
| | - Ryan J. Harrigan
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
| | - Mary Whitfield
- Southern Sierra Research Station; P.O. Box 1316 Weldon CA 932883 USA
| | - Eben H. Paxton
- U.S. Geological Survey Pacific Island Ecosystems Research Center; Hawaii Volcano National Park; HI 96718
| | - Thomas B. Smith
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 USA
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22
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Ringler E, Szipl G, Harrigan RJ, Bartl-Binder P, Mangione R, Ringler M. Hierarchical decision-making balances current and future reproductive success. Mol Ecol 2018; 27:2289-2301. [PMID: 29633409 PMCID: PMC5969290 DOI: 10.1111/mec.14583] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 12/01/2017] [Revised: 01/28/2018] [Accepted: 02/23/2018] [Indexed: 11/27/2022]
Abstract
Parental decisions in animals are often context‐dependent and shaped by fitness trade‐offs between parents and offspring. For example, the selection of breeding habitats can considerably impact the fitness of both offspring and parents, and therefore, parents should carefully weigh the costs and benefits of available options for their current and future reproductive success. Here, we show that resource‐use preferences are shaped by a trade‐off between parental effort and offspring safety in a tadpole‐transporting frog. In a large‐scale in situ experiment, we investigated decision strategies across an entire population of poison frogs that distribute their tadpoles across multiple water bodies. Pool use followed a dynamic and sequential selection process, and transportation became more efficient over time. Our results point to a complex suite of environmental variables that are considered during offspring deposition, which necessitates a highly dynamic and flexible decision‐making process in tadpole‐transporting frogs.
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Affiliation(s)
- Eva Ringler
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California.,Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria.,Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Georgine Szipl
- Core Facility KLF for Behaviour and Cognition, University of Vienna, Vienna, Austria
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, California
| | - Perta Bartl-Binder
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Rosanna Mangione
- Department of Integrative Zoology, University of Vienna, Vienna, Austria.,Haus des Meeres Aqua Terra Zoo GmbH, Vienna, Austria
| | - Max Ringler
- Department of Integrative Zoology, University of Vienna, Vienna, Austria.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California
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23
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Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 2018; 359:83-86. [PMID: 29302012 DOI: 10.1126/science.aan4380] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/16/2017] [Indexed: 01/18/2023]
Abstract
The ongoing loss of biodiversity caused by rapid climatic shifts requires accurate models for predicting species' responses. Despite evidence that evolutionary adaptation could mitigate climate change impacts, evolution is rarely integrated into predictive models. Integrating population genomics and environmental data, we identified genomic variation associated with climate across the breeding range of the migratory songbird, yellow warbler (Setophaga petechia). Populations requiring the greatest shifts in allele frequencies to keep pace with future climate change have experienced the largest population declines, suggesting that failure to adapt may have already negatively affected populations. Broadly, our study suggests that the integration of genomic adaptation can increase the accuracy of future species distribution models and ultimately guide more effective mitigation efforts.
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Affiliation(s)
- Rachael A Bay
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Vinh Le Underwood
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH 43210, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Kristen Ruegg
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
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24
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Nigenda-Morales SF, Harrigan RJ, Wayne RK. Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial. PeerJ 2018; 6:e4512. [PMID: 29607255 PMCID: PMC5877449 DOI: 10.7717/peerj.4512] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 02/09/2017] [Accepted: 02/25/2018] [Indexed: 01/08/2023] Open
Abstract
Phenotypic variation along environmental gradients can provide evidence suggesting local adaptation has shaped observed morphological disparities. These differences, in traits such as body and extremity size, as well as skin and coat pigmentation, may affect the overall fitness of individuals in their environments. The Virginia opossum (Didelphis virginiana) is a marsupial that shows phenotypic variation across its range, one that has recently expanded into temperate environments. It is unknown, however, whether the variation observed in the species fits adaptive ecogeographic patterns, or if phenotypic change is associated with any environmental factors. Using phenotypic measurements of over 300 museum specimens of Virginia opossum, collected throughout its distribution range, we applied regression analysis to determine if phenotypes change along a latitudinal gradient. Then, using predictors from remote-sensing databases and a random forest algorithm, we tested environmental models to find the most important variables driving the phenotypic variation. We found that despite the recent expansion into temperate environments, the phenotypic variation in the Virginia opossum follows a latitudinal gradient fitting three adaptive ecogeographic patterns codified under Bergmann's, Allen's and Gloger's rules. Temperature seasonality was an important predictor of body size variation, with larger opossums occurring at high latitudes with more seasonal environments. Annual mean temperature predicted important variation in extremity size, with smaller extremities found in northern populations. Finally, we found that precipitation and temperature seasonality as well as low temperatures were strong environmental predictors of skin and coat pigmentation variation; darker opossums are distributed at low latitudes in warmer environments with higher precipitation seasonality. These results indicate that the adaptive mechanisms underlying the variation in body size, extremity size and pigmentation are related to the resource seasonality, heat conservation, and pathogen-resistance hypotheses, respectively. Our findings suggest that marsupials may be highly susceptible to environmental changes, and in the case of the Virginia opossum, the drastic phenotypic evolution in northern populations may have arisen rapidly, facilitating the colonization of seasonal and colder habitats of temperate North America.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America.,National Laboratory of Genomics for Biodiversity, Center for Research and Advanced Studies, Irapuato, Guanajuato, Mexico
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
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25
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Tiee MS, Harrigan RJ, Thomassen HA, Smith TB. Ghosts of infections past: using archival samples to understand a century of monkeypox virus prevalence among host communities across space and time. R Soc Open Sci 2018; 5:171089. [PMID: 29410823 PMCID: PMC5792900 DOI: 10.1098/rsos.171089] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species (F. anerythrus, F. carruthersi, F. congicus, F. lemniscatus and F. pyrropus), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899-1993).
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Affiliation(s)
- Madeline S. Tiee
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Henri A. Thomassen
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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26
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Hendricks SA, Koblmüller S, Harrigan RJ, Leonard JA, Schweizer RM, Vonholdt BM, Kays R, Wayne RK. Defense of an expanded historical range for the Mexican wolf: A comment on Heffelfinger et al. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21336] [Citation(s) in RCA: 7] [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: 11/08/2022]
Affiliation(s)
- Sarah A. Hendricks
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies; University of Idaho; Moscow ID USA
| | - Stephan Koblmüller
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability; University of California; Los Angeles, 300 LaKretz Hall Los Angeles CA 90095 USA
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); 41092 Sevilla Spain
| | - Rena M. Schweizer
- Division of Biological Sciences; University of Montana; 32 Campus Dr. Missoula MT 59812 USA
| | - Bridgett M. Vonholdt
- Department of Ecology and Evolutionary Biology; Princeton University; M151 Guyot Hall Princeton NJ 08544 USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences; Biodiversity Lab; Raleigh NC 27601 USA
- Department of Forestry & Environmental Resources; North Carolina State University; Raleigh NC 27695 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; 610 Charles E. Young Drive East Los Angeles CA 90095 USA
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27
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Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, Smith TB. Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). Mol Ecol 2017; 26:4966-4977. [PMID: 28752944 DOI: 10.1111/mec.14270] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest-savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise FST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.
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Affiliation(s)
- Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Kristen C Ruegg
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Thomas C Ng
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sirena Lao
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
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28
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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
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29
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Locatelli S, Harrigan RJ, Sesink Clee PR, Mitchell MW, McKean KA, Smith TB, Gonder MK. Why Are Nigeria-Cameroon Chimpanzees (Pan troglodytes ellioti) Free of SIVcpz Infection? PLoS One 2016; 11:e0160788. [PMID: 27505066 PMCID: PMC4978404 DOI: 10.1371/journal.pone.0160788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/24/2016] [Indexed: 12/26/2022] Open
Abstract
Simian immunodeficiency virus (SIV) naturally infects two subspecies of chimpanzee: Pan troglodytes troglodytes from Central Africa (SIVcpzPtt) and P. t. schweinfurtii from East Africa (SIVcpzPts), but is absent in P. t. verus from West Africa and appears to be absent in P. t. ellioti inhabiting Nigeria and western Cameroon. One explanation for this pattern is that P. t. troglodytes and P. t schweinfurthii may have acquired SIVcpz after their divergence from P. t. verus and P. t. ellioti. However, all of the subspecies, except P. t. verus, still occasionally exchange migrants making the absence of SIVcpz in P. t. ellioti puzzling. Sampling of P. t. ellioti has been minimal to date, particularly along the banks of the Sanaga River, where its range abuts that of P. t. troglodytes. This study had three objectives. First, we extended the sampling of SIVcpz across the range of chimpanzees north of the Sanaga River to address whether under-sampling might account for the absence of evidence for SIVcpz infection in P. t. ellioti. Second, we investigated how environmental variation is associated with the spread and prevalence of SIVcpz in the two chimpanzee subspecies inhabiting Cameroon since environmental variation has been shown to contribute to their divergence from one another. Finally, we compared the prevalence and distribution of SIVcpz with that of Simian Foamy Virus (SFV) to examine the role of ecology and behavior in shaping the distribution of diseases in wild host populations. The dataset includes previously published results on SIVcpz infection and SFVcpz as well as newly collected data, and represents over 1000 chimpanzee fecal samples from 41 locations across Cameroon. Results revealed that none of the 181 P. t. ellioti fecal samples collected across the range of P. t. ellioti tested positive for SIVcpz. In addition, species distribution models suggest that environmental variation contributes to differences in the distribution and prevalence of SIVcpz and SFVcpz. The ecological niches of these two viruses are largely non-overlapping, although stronger statistical support for this conclusion will require more sampling. Overall this study demonstrates that SIVcpz infection is absent or very rare in P. t. ellioti, despite multiple opportunities for transmission. The reasons for its absence remain unclear, but might be explained by one or more factors, including environmental variation, viral competition, and/or local adaptation—all of which should be explored in greater detail through continued surveillance of this region.
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Affiliation(s)
- Sabrina Locatelli
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- * E-mail:
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Paul R. Sesink Clee
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Matthew W Mitchell
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Kurt A. McKean
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Mary Katherine Gonder
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
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Arias MC, Aulagnier S, Baerwald EF, Barclay RMR, Batista JS, Beasley RR, Bezerra RA, Blanc F, Bridge ES, Cabria MT, Caputo LI, Chen J, Chen JH, Chen Z, Chen CH, Chu P, Contina A, da Silva Carmo FM, de Carvalho LC, de Freitas Viana PM, de Macêdo JLV, de Menezes Yazbeck G, de Oliveira Teixeira Z, de Souza Araujo N, Dequigiovanni G, Ding S, Dos Santos PKF, Ernest HB, Feng YW, Formiga KM, Fournier-Chambrillon C, Françoso E, Fu Y, Gagne RB, Gaiotto FA, Gao TX, Ge H, Ge T, Gillet F, Gong Y, Gong HM, Guo Q, Guo L, Guo L, Harrigan RJ, He L, House CJ, Der Hsiao C, Huang R, Iyengar A, Jiang X, Jiang HL, Johnson TA, Jones KL, Kageyama PY, Kelly JF, Lam L, Lance SL, Li H, Li C, Li F, Li H, Li S, Li Y, Li M, Li M, Li F, Li WG, Li J, Li J, Li X, Liang K, Liang Y, Liao F, Liao L, Lin H, Lin H, Lin H, Lin Q, Liu H, Liu H, Liu L, Liu XQ, Liu P, Liu C, Liu X, Lopes MTG, Lu D, Luan MB, Luo W, Meng Z, Meng Z, Michaux JR, Némoz M, Pollinger JP, Qiao Y, Qu H, Ramos SLF, Le Roux S, Santiago LR, Shao X, Shen KN, Shen H, Shen H, Smith TB, Song DY, Sourp E, Sun Y, Tang H, Tang Q, Tong Y, van den Einden M, van Hoppe MJC, Veasey EA, Vial-Novella C, Wan L, Wang X, Wang Y, Wang Y, Wang Y, Wang R, Wang X, Wang R, Wang Q, Wang GD, Wang J, Wang D, Wang P, Wei XM, Wen Y, Wen H, Wu XP, Wu X, Xiang J, Xie Z, Xu Z, Xu P, Yang Z, Yang S, Yang S, Yin C, Yin S, Yin S, Yu Y, Yuan X, Yue GH, Zang GG, Zardoya R, Zhang LH, Zhang X, Zhang Y, Zhang G, di Zhang Y, Zhang H, Zhang G, Zhao J, Zhao C, Zhu F, Zhu H, Zhu S, Zou S. Microsatellite records for volume 8, issue 1. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0522-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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George TL, Harrigan RJ, LaManna JA, DeSante DF, Saracco JF, Smith TB. Persistent impacts of West Nile virus on North American bird populations. Proc Natl Acad Sci U S A 2015; 112:14290-4. [PMID: 26578774 PMCID: PMC4655513 DOI: 10.1073/pnas.1507747112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Since its introduction to North America in 1999, West Nile virus (WNV) has had devastating impacts on native host populations, but to date these impacts have been difficult to measure. Using a continental-scale dataset comprised of a quarter-million birds captured over nearly two decades and a recently developed model of WNV risk, we estimated the impact of this emergent disease on the survival of avian populations. We find that populations were negatively affected by WNV in 23 of the 49 species studied (47%). We distinguished two groups of species: those for which WNV negatively impacted survival only during initial spread of the disease (n = 11), and those that show no signs of recovery since disease introduction (n = 12). Results provide a novel example of the taxonomic breadth and persistent impacts of this wildlife disease on a continental scale. Phylogenetic analyses further identify groups (New World sparrows, finches, and vireos) disproportionally affected by temporary or persistent WNV effects, suggesting an evolutionary dimension of disease risk. Identifying the factors affecting the persistence of a disease across host species is critical to mitigating its effects, particularly in a world marked by rapid anthropogenic change.
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Affiliation(s)
- T Luke George
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095;
| | - Joseph A LaManna
- Department of Biology, Washington University, St. Louis, MO 63130
| | - David F DeSante
- The Institute for Bird Populations, Point Reyes Station, CA 94956
| | - James F Saracco
- The Institute for Bird Populations, Point Reyes Station, CA 94956
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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32
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Larison B, Harrigan RJ, Rubenstein DI, Smith TB. Concordance on zebra stripes is not black and white: response to comment by Caro & Stankowich (2015). R Soc Open Sci 2015; 2:150359. [PMID: 26473058 PMCID: PMC4593692 DOI: 10.1098/rsos.150359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Ryan J. Harrigan
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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33
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Larison B, Harrigan RJ, Thomassen HA, Rubenstein DI, Chan-Golston AM, Li E, Smith TB. How the zebra got its stripes: a problem with too many solutions. R Soc Open Sci 2015; 2:140452. [PMID: 26064590 PMCID: PMC4448797 DOI: 10.1098/rsos.140452] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/15/2014] [Indexed: 05/30/2023]
Abstract
The adaptive significance of zebra stripes has thus far eluded understanding. Many explanations have been suggested, including social cohesion, thermoregulation, predation evasion and avoidance of biting flies. Identifying the associations between phenotypic and environmental factors is essential for testing these hypotheses and substantiating existing experimental evidence. Plains zebra striping pattern varies regionally, from heavy black and white striping over the entire body in some areas to reduced stripe coverage with thinner and lighter stripes in others. We examined how well 29 environmental variables predict the variation in stripe characteristics of plains zebra across their range in Africa. In contrast to recent findings, we found no evidence that striping may have evolved to escape predators or avoid biting flies. Instead, we found that temperature successfully predicts a substantial amount of the stripe pattern variation observed in plains zebra. As this association between striping and temperature may be indicative of multiple biological processes, we suggest that the selective agents driving zebra striping are probably multifarious and complex.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Ryan J. Harrigan
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Henri A. Thomassen
- Institute for Evolution and Ecology, University of Tübingen, Building E, Floor 4, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Alec M. Chan-Golston
- Department of Mathematics, University of California, 520 Portola Plaza, Math Sciences Building 6363, Los Angeles, CA 90095, USA
| | - Elizabeth Li
- Department of Mathematics, University of California, 520 Portola Plaza, Math Sciences Building 6363, Los Angeles, CA 90095, USA
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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34
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Chasar A, Harrigan RJ, Holbrook KM, Dietsch TV, Fuller TL, Wikelski M, Smith TB. Spatial and Temporal Patterns of Frugivorous Hornbill Movements in Central Africa and their Implications for Rain Forest Conservation. Biotropica 2014. [DOI: 10.1111/btp.12160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony Chasar
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
| | - Ryan J. Harrigan
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
| | - Kimberly M. Holbrook
- The Nature Conservancy; 4245 North Fairfax Drive Suite 100 Arlington VA 22203 U.S.A
| | - Thomas V. Dietsch
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
- Migratory Bird Division; U. S. Fish and Wildlife Service; 2177 Salk Avenue, Suite 250 Carlsbad CA 92008 U.S.A
| | - Trevon L. Fuller
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
| | - Martin Wikelski
- Max-Planck Institute for Ornithology; Am Obstberg 1 78315 Radolfzell Germany
- Department of Biology; University of Konstanz; 78457 Konstanz Germany
| | - Thomas B. Smith
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 U.S.A
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Harrigan RJ, Thomassen HA, Buermann W, Smith TB. A continental risk assessment of West Nile virus under climate change. Glob Chang Biol 2014; 20:2417-2425. [PMID: 24574161 DOI: 10.1111/gcb.12534] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
Since first introduced to North America in 1999, West Nile virus (WNV) has spread rapidly across the continent, threatening wildlife populations and posing serious health risks to humans. While WNV incidence has been linked to environmental factors, particularly temperature and rainfall, little is known about how future climate change may affect the spread of the disease. Using available data on WNV infections in vectors and hosts collected from 2003-2011 and using a suite of 10 species distribution models, weighted according to their predictive performance, we modeled the incidence of WNV under current climate conditions at a continental scale. Models were found to accurately predict spatial patterns of WNV that were then used to examine how future climate may affect the spread of the disease. Predictions were accurate for cases of human WNV infection in the following year (2012), with areas reporting infections having significantly higher probability of presence as predicted by our models. Projected geographic distributions of WNV in North America under future climate for 2050 and 2080 show an expansion of suitable climate for the disease, driven by warmer temperatures and lower annual precipitation that will result in the exposure of new and naïve host populations to the virus with potentially serious consequences. Our risk assessment identifies current and future hotspots of West Nile virus where mitigation efforts should be focused and presents an important new approach for monitoring vector-borne disease under climate change.
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Affiliation(s)
- Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California, 90095, USA
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Harrigan RJ, Sedano R, Chasar AC, Chaves JA, Nguyen JT, Whitaker A, Smith TB. New host and lineage diversity of avian haemosporidia in the northern Andes. Evol Appl 2014; 7:799-811. [PMID: 25469161 PMCID: PMC4227860 DOI: 10.1111/eva.12176] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 10/15/2013] [Accepted: 03/25/2014] [Indexed: 12/22/2022] Open
Abstract
The northern Andes, with their steep elevational and climate gradients, are home to an exceptional diversity of flora and fauna, particularly rich in avian species that have adapted to divergent ecological conditions. With this diversity comes the opportunity for parasites to exploit a wide breadth of avian hosts. However, little research has focused on examining the patterns of prevalence and lineage diversity of avian parasites in the Andes. Here, we screened a total of 428 birds from 19 species (representing nine families) and identified 133 infections of avian haemosporidia (31%), including lineages of Plasmodium, Haemoproteus, and Leucocytozoon. We document a higher prevalence of haemosporidia at higher elevations and lower temperatures, as well as an overall high diversity of lineages in the northern Andes, including the first sequences of haemosporidians reported in hummingbirds (31 sequences found in 11 species within the family Trochilidae). Double infections were distinguished using PHASE, which enables the separation of distinct parasite lineages. Results suggest that the ecological heterogeneity of the northern Andes that has given rise to a rich diversity of avian hosts may also be particularly conducive to parasite diversification and specialization.
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Affiliation(s)
- Ryan J Harrigan
- Center for Tropical Research, Institute of the
Environment and Sustainability, University of CaliforniaLos Angeles, CA, USA
| | - Raul Sedano
- Escuela de Biología, Universidad Industrial de
SantanderBucaramanga, Colombia
| | - Anthony C Chasar
- Center for Tropical Research, Institute of the
Environment and Sustainability, University of CaliforniaLos Angeles, CA, USA
| | - Jaime A Chaves
- Department of Biology, University of MiamiCoral Gables, FL, USA
- Universidad San Francisco de Quito, USFQ, Colegio de
Ciencias Biológicas y Ambientales, y Extensión Galápagos, Campus
CumbayáCasilla, Ecuador
| | - Jennifer T Nguyen
- Department of Ecology and Evolutionary Biology,
University of CaliforniaLos Angeles, CA, USA
| | - Alexis Whitaker
- Department of Ecology and Evolutionary Biology,
University of CaliforniaLos Angeles, CA, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the
Environment and Sustainability, University of CaliforniaLos Angeles, CA, USA
- Department of Ecology and Evolutionary Biology,
University of CaliforniaLos Angeles, CA, USA
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Oakgrove KS, Harrigan RJ, Loiseau C, Guers S, Seppi B, Sehgal RNM. Distribution, diversity and drivers of blood-borne parasite co-infections in Alaskan bird populations. Int J Parasitol 2014; 44:717-27. [PMID: 25014331 DOI: 10.1016/j.ijpara.2014.04.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
Abstract
Avian species are commonly infected by multiple parasites, however few studies have investigated the environmental determinants of the prevalence of co-infection over a large scale. Here we believe that we report the first, detailed ecological study of the prevalence, diversity and co-infections of four avian blood-borne parasite genera: Plasmodium spp., Haemoproteus spp., Leucocytozoon spp. and Trypanosoma spp. We collected blood samples from 47 resident and migratory bird species across a latitudinal gradient in Alaska. From the patterns observed at collection sites, random forest models were used to provide evidence of associations between bioclimatic conditions and the prevalence of parasite co-infection distribution. Molecular screening revealed a higher prevalence of haematozoa (53%) in Alaska than previously reported. Leucocytozoons had the highest diversity, prevalence and prevalence of co-infection. Leucocytozoon prevalence (35%) positively correlated with Trypanosoma prevalence (11%), negatively correlated with Haemoproteus prevalence (14%) and had no correlation with Plasmodium prevalence (7%). We found temperature, precipitation and tree cover to be the primary environmental drivers that show a relationship with the prevalence of co-infection. The results provide insight into the impacts of bioclimatic drivers on parasite ecology and intra-host interactions, and have implications for the study of infectious diseases in rapidly changing environments.
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Affiliation(s)
- Khouanchy S Oakgrove
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Claire Loiseau
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA
| | - Sue Guers
- Alaska Songbird Institute, PO Box 82035, Fairbanks, AK 99708, USA
| | - Bruce Seppi
- Bureau of Land Management, Anchorage Field Office, 4700 BLM Road, Anchorage, AK 99507, USA
| | - Ravinder N M Sehgal
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA
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Larison B, Njabo KY, Chasar A, Fuller T, Harrigan RJ, Smith TB. Spillover of pH1N1 to swine in Cameroon: an investigation of risk factors. BMC Vet Res 2014; 10:55. [PMID: 24593895 PMCID: PMC4016523 DOI: 10.1186/1746-6148-10-55] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 02/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The 2009 pH1N1 influenza pandemic resulted in at least 18,500 deaths worldwide. While pH1N1 is now considered to be in a post-pandemic stage in humans it has nevertheless spilled back into swine in at least 20 countries. Understanding the factors that increase the risk of spillover events between swine and humans is essential to predicting and preventing future outbreaks. We assessed risk factors that may have led to spillover of pH1N1 from humans to swine in Cameroon, Central Africa. We sampled swine, domestic poultry and wild birds for influenza A virus at twelve sites in Cameroon from December 2009 while the pandemic was ongoing, to August 2012. At the same time we conducted point-count surveys to assess the abundance of domestic livestock and wild birds and assess interspecific contact rates. Random forest models were used to assess which variables were the best predictors of influenza in swine. RESULTS We found swine with either active pH1N1 infections or positive for influenza A at four of our 12 sites. Only one swine tested positive by competitive ELISA in 2011-2012. To date we have found pH1N1 only in the North and Extreme North regions of Cameroon (regions in Cameroon are administrative units similar to provinces), though half of our sites are in the Central and Western regions. Swine husbandry practices differ between the North and Extreme North regions where it is common practice in to let swine roam freely, and the Central and Western regions where swine are typically confined to pens. Random forest analyses revealed that the three best predictors of the presence of pH1N1 in swine were contact rates between free-ranging swine and domestic ducks, contact rates between free-ranging swine and wild Columbiformes, and contact rates between humans and ducks. Sites in which swine were allowed to range freely had closer contact with other species than did sites in which swine were kept penned. CONCLUSIONS Results suggest that the practice of allowing swine to roam freely is a significant risk factor for spillover of influenza from humans into swine populations.
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Affiliation(s)
- Brenda Larison
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, California 90095, USA
| | - Kevin Y Njabo
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Anthony Chasar
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Trevon Fuller
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, California 90095, USA
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, California 90095, USA
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Abstract
Nuclear sequence data, often from multiple loci, are increasingly being employed in analyses of population structure and history, yet there has been relatively little evaluation of methods for accurately and efficiently separating the alleles or haplotypes in heterozygous individuals. We compared the performance of a computational method of haplotype reconstruction and standard cloning methods using a highly variable intron (ornithine decarboxylase, intron 6) in three closely related species of dabbling ducks (genus Anas). Cloned sequences from 32 individuals were compared to results obtained from phase 2.1.1 . phase correctly identified haplotypes in 28 of 30 heterozygous individuals when the underlying model assumed no recombination. Haplotypes of the remaining two individuals were also inferred correctly except for unique polymorphisms, the phase of which was appropriately indicated as uncertain (phase probability = 0.5). For a larger set of 232 individuals, results were essentially identical regardless of the recombination model used and haplotypes for all 30 of the tested heterozygotes were correctly inferred, with the exception of uncertain phase for unique polymorphisms in one individual. In contrast, initial sequences of one clone per sample yielded accurate haplotype determination in only 26 of 30 individuals; polymerase chain reaction (PCR)/cloning errors resulting from misincorporation of individual nucleotides could be recognized and avoided by comparison to direct sequences, but errors due to PCR recombination resulted in incorrect haplotype reconstruction in four individuals. The accuracy of haplotypes reconstructed by phase, even when dealing with a relatively small number of samples and numerous variable sites, suggests broad utility of computational approaches for reducing the cost and improving the efficiency of data collection from nuclear sequence loci.
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Affiliation(s)
- Ryan J Harrigan
- Department of Biology, Boston University, 5 Cummington St., Boston, MA 02215, USA
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Smith TB, Harrigan RJ, Kirschel ANG, Buermann W, Saatchi S, Blumstein DT, de Kort SR, Slabbekoorn H. Predicting bird song from space. Evol Appl 2013; 6:865-74. [PMID: 24062797 PMCID: PMC3779089 DOI: 10.1111/eva.12072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 09/21/2012] [Accepted: 03/26/2013] [Indexed: 11/26/2022] Open
Abstract
Environmentally imposed selection pressures are well known to shape animal signals. Changes in these signals can result in recognition mismatches between individuals living in different habitats, leading to reproductive divergence and speciation. For example, numerous studies have shown that differences in avian song may be a potent prezygotic isolating mechanism. Typically, however, detailed studies of environmental pressures on variation in animal behavior have been conducted only at small spatial scales. Here, we use remote-sensing data to predict animal behavior, in this case, bird song, across vast spatial scales. We use remotely sensed data to predict the song characteristics of the little greenbul (Andropadus virens), a widely distributed African passerine, found across secondary and mature rainforest habitats and the rainforest-savanna ecotone. Satellite data that captured ecosystem structure and function explained up to 66% of the variation in song characteristics. Song differences observed across habitats, including those between human-altered and mature rainforest, have the potential to lead to reproductive divergence, and highlight the impacts that both natural and anthropogenic change may have on natural populations. Our approach offers a novel means to examine the ecological correlates of animal behavior across large geographic areas with potential applications to both evolutionary and conservation biology.
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Affiliation(s)
- Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles Los Angeles, CA, USA ; Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles Los Angeles, CA, USA
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41
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Loiseau C, Harrigan RJ, Bichet C, Julliard R, Garnier S, Lendvai AZ, Chastel O, Sorci G. Predictions of avian Plasmodium expansion under climate change. Sci Rep 2013; 3:1126. [PMID: 23350033 PMCID: PMC3553554 DOI: 10.1038/srep01126] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/19/2012] [Indexed: 11/24/2022] Open
Abstract
Vector-borne diseases are particularly responsive to changing environmental conditions. Diurnal temperature variation has been identified as a particularly important factor for the development of malaria parasites within vectors. Here, we conducted a survey across France, screening populations of the house sparrow (Passer domesticus) for malaria (Plasmodium relictum). We investigated whether variation in remotely-sensed environmental variables accounted for the spatial variation observed in prevalence and parasitemia. While prevalence was highly correlated to diurnal temperature range and other measures of temperature variation, environmental conditions could not predict spatial variation in parasitemia. Based on our empirical data, we mapped malaria distribution under climate change scenarios and predicted that Plasmodium occurrence will spread to regions in northern France, and that prevalence levels are likely to increase in locations where transmission already occurs. Our findings, based on remote sensing tools coupled with empirical data suggest that climatic change will significantly alter transmission of malaria parasites.
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Affiliation(s)
- Claire Loiseau
- Department of Biology, San Francisco State University, San Francisco, California 94132, USA.
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Loiseau C, Harrigan RJ, Cornel AJ, Guers SL, Dodge M, Marzec T, Carlson JS, Seppi B, Sehgal RNM. First evidence and predictions of Plasmodium transmission in Alaskan bird populations. PLoS One 2012; 7:e44729. [PMID: 23028595 PMCID: PMC3446979 DOI: 10.1371/journal.pone.0044729] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
The unprecedented rate of change in the Arctic climate is expected to have major impacts on the emergence of infectious diseases and host susceptibility to these diseases. It is predicted that malaria parasites will spread to both higher altitudes and latitudes with global warming. Here we show for the first time that avian Plasmodium transmission occurs in the North American Arctic. Over a latitudinal gradient in Alaska, from 61°N to 67°N, we collected blood samples of resident and migratory bird species. We found both residents and hatch year birds infected with Plasmodium as far north as 64°N, providing clear evidence that malaria transmission occurs in these climates. Based on our empirical data, we make the first projections of the habitat suitability for Plasmodium under a future-warming scenario in Alaska. These findings raise new concerns about the spread of malaria to naïve host populations.
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Affiliation(s)
- Claire Loiseau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America.
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43
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Abstract
Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist versus generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in Cameroon, highland forests in East Africa and fynbos in South Africa. We calculated the host specificity index of parasites to examine the range of hosts parasitized as a function of the habitat and investigated the phylogenetic relationships of parasites. First, using phylogenetic and ancestral reconstruction analyses, we found an evolutionary tendency for generalist malaria parasites to become specialists. The transition rate at which generalists become specialists was nearly four times as great as the rate at which specialists become generalists. We also found more specialist parasites and greater parasite diversity in African lowland rainforests as compared to the more climatically variable habitats of the fynbos and the highland forests. Thus, with environmental changes, we anticipate a change in the distribution of both specialist and generalist parasites with potential impacts on bird communities.
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Affiliation(s)
- Claire Loiseau
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
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Harrigan RJ, Thomassen HA, Buermann W, Cummings RF, Kahn ME, Smith TB. Economic conditions predict prevalence of West Nile virus. PLoS One 2010; 5:e15437. [PMID: 21103053 PMCID: PMC2980475 DOI: 10.1371/journal.pone.0015437] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 09/21/2010] [Indexed: 12/26/2022] Open
Abstract
Understanding the conditions underlying the proliferation of infectious diseases is crucial for mitigating future outbreaks. Since its arrival in North America in 1999, West Nile virus (WNV) has led to population-wide declines of bird species, morbidity and mortality of humans, and expenditures of millions of dollars on treatment and control. To understand the environmental conditions that best explain and predict WNV prevalence, we employed recently developed spatial modeling techniques in a recognized WNV hotspot, Orange County, California. Our models explained 85–95% of the variation of WNV prevalence in mosquito vectors, and WNV presence in secondary human hosts. Prevalence in both vectors and humans was best explained by economic variables, specifically per capita income, and by anthropogenic characteristics of the environment, particularly human population and neglected swimming pool density. While previous studies have shown associations between anthropogenic change and pathogen presence, results show that poorer economic conditions may act as a direct surrogate for environmental characteristics related to WNV prevalence. Low-income areas may be associated with higher prevalence for a number of reasons, including variations in property upkeep, microhabitat conditions conducive to viral amplification in both vectors and hosts, host community composition, and human behavioral responses related to differences in education or political participation. Results emphasize the importance and utility of including economic variables in mapping spatial risk assessments of disease.
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Affiliation(s)
- Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment, University of California Los Angeles, Los Angeles, California, United States of America.
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Sehgal RNM, Buermann W, Harrigan RJ, Bonneaud C, Loiseau C, Chasar A, Sepil I, Valkiūnas G, Iezhova T, Saatchi S, Smith TB. Spatially explicit predictions of blood parasites in a widely distributed African rainforest bird. Proc Biol Sci 2010; 278:1025-33. [PMID: 20880888 DOI: 10.1098/rspb.2010.1720] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Critical to the mitigation of parasitic vector-borne diseases is the development of accurate spatial predictions that integrate environmental conditions conducive to pathogen proliferation. Species of Plasmodium and Trypanosoma readily infect humans, and are also common in birds. Here, we develop predictive spatial models for the prevalence of these blood parasites in the olive sunbird (Cyanomitra olivacea). Since this species exhibits high natural parasite prevalence and occupies diverse habitats in tropical Africa, it represents a distinctive ecological model system for studying vector-borne pathogens. We used PCR and microscopy to screen for haematozoa from 28 sites in Central and West Africa. Species distribution models were constructed to associate ground-based and remotely sensed environmental variables with parasite presence. We then used machine-learning algorithm models to identify relationships between parasite prevalence and environmental predictors. Finally, predictive maps were generated by projecting model outputs to geographically unsampled areas. Results indicate that for Plasmodium spp., the maximum temperature of the warmest month was most important in predicting prevalence. For Trypanosoma spp., seasonal canopy moisture variability was the most important predictor. The models presented here visualize gradients of disease prevalence, identify pathogen hotspots and will be instrumental in studying the effects of ecological change on these and other pathogens.
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Affiliation(s)
- R N M Sehgal
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
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Kulikova IV, Drovetski SV, Gibson DD, Harrigan RJ, Rohwer S, Sorenson MD, Winker K, Zhuravlev YN, McCracken KG. Phylogeography of The Mallard (Anas Platyrhynchos): Hybridization, Dispersal, and Lineage Sorting Contribute to Complex Geographic Structure. ACTA ACUST UNITED AC 2005. [DOI: 10.1093/auk/122.3.949] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractPopulation genetic variation in Mallards (Anas platyrhynchos; n = 152) from Western Russia, North Asia, the Aleutian Islands, and mainland Alaska was investigated using 667 base pairs of the 5′-end of the mitochondrial DNA (mtDNA) control region. DNA sequencing revealed two clades that correspond to Avise et al.’s (1990) group A and B mtDNA haplotypes. Group A haplotypes (80.3%) were wide- spread in all localities from Western Russia to Alaska. Group B haplotypes (19.7%), by contrast, were found primarily in mainland Alaska, where they occurred at high frequency (77.4%), but they also occurred at low frequencies (declining east to west) in the Aleutian Islands (11.8%) and the Primorye region of North Asia (4.4%). Group B haplotypes were not observed in Western Russia or elsewhere in North Asia outside Primorye. Consequently, Mallards exhibited substantial genetic structure between Old World and New World (ΦST = 0.4112–0.4956) but possessed little genetic structure within the Old World continental area (ΦST = 0.0018). Nonetheless, when only group A haplotypes were included in the analysis, Mallards from the Aleutian Islands differed (albeit with low levels of divergence) from each of the other three sampled regions in the Old World and New World (ΦST = 0.0728–0.1461, P < 0.05). Mallards inhabit the Aleutian Islands year-round, so these insular populations may be isolated from Asian and North American populations that occur in the Aleutian Islands only during migration. Overall weak phylogeographic structure and low genetic differentiation within Asia, and between Asia and North America when only group A haplotypes were evaluated, is probably explained by large long-term population sizes and significant intra-continental dispersal. The coexistence and nonrandom distribution of two divergent mtDNA haplotype lineages in Alaska, the Aleutian Islands, and the Primorye region of North Asia, but not in Western Russia or elsewhere in North Asia, is consistent with historical and contemporary hybridization and incomplete sorting of A and B mtDNA haplotype lineages in Mallards and closely related species inhabiting the Old World and New World.
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Affiliation(s)
- Irina V. Kulikova
- Institute of Biology and Soil Science, Far East Branch, Russian Academy of Sciences, Vladivostok 690022, Russia
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
| | - Sergei V. Drovetski
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, Alaska 99508, USA
| | - Daniel D. Gibson
- University of Alaska Museum, 907 Yukon Drive, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
| | - Ryan J. Harrigan
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - Sievert Rohwer
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | | | - Kevin Winker
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
- University of Alaska Museum, 907 Yukon Drive, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
| | - Yuri N. Zhuravlev
- Institute of Biology and Soil Science, Far East Branch, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Kevin G. McCracken
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
- University of Alaska Museum, 907 Yukon Drive, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
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