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Pyron RA, Pirro S, Hains T, Colston TJ, Myers EA, O'Connell KA, Beamer DA. The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia). Biodivers Genomes 2024; 2024:10.56179/001c.116891. [PMID: 38725637 PMCID: PMC11081450 DOI: 10.56179/001c.116891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14-130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, George Washington University
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
| | | | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- Committee on Evolutionary Biology, University of Chicago
| | | | - Edward A Myers
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
- Department of Herpetology, California Academy of Sciences
| | - Kyle A O'Connell
- Department of Biological Sciences, George Washington University
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
- Health Data and AI, Deloitte Consulting LLP
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University
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2
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Chavez DE, Hains T, Espinoza S, Wayne RK, Chaves J. Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs. J Hered 2024:esae017. [PMID: 38498380 DOI: 10.1093/jhered/esae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Indexed: 03/20/2024] Open
Abstract
Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
- School of Biology. Pontifical Catholic University of Ecuador, Av. 12 de Octubre, Quito 170901, Ecuador
- Arizona Cancer Evolution Center, The Biodesign Institute, Arizona State University, Tempe, AZ School of Life Sciences, Arizona State University, Tempe, AZ
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Illinois, Chicago 60637, USA
- Negaunee Integrative Research Center, The Field Museum, Illinois, Chicago, 60605, USA
- Grainger Bioinformatics Center, The Field Museum, Chicago, Illinois, Chicago, 60605, USA
| | - Sebastian Espinoza
- School of Medicine. Pontifical Catholic University of Ecuador, Av. 12 de Octubre, Quito 170901, Ecuador
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Jaime Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132-1722, USA
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3
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Eliason CM, Mellenthin LE, Hains T, McCullough JM, Pirro S, Andersen MJ, Hackett SJ. Genomic signatures of convergent shifts to plunge-diving behavior in birds. Commun Biol 2023; 6:1011. [PMID: 37875535 PMCID: PMC10598022 DOI: 10.1038/s42003-023-05359-z] [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: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of convergence at broad phylogenetic scales remains a key challenge in biology. Kingfishers (Aves: Alcedinidae) are a cosmopolitan avian radiation with diverse colors, diets, and feeding behaviors-including the archetypal plunge-dive into water. Given the sensory and locomotor challenges associated with air-water transitions, kingfishers offer a powerful opportunity to explore the effects of convergent behaviors on the evolution of genomes and phenotypes, as well as direct comparisons between continental and island lineages. Here, we use whole-genome sequencing of 30 diverse kingfisher species to identify the genomic signatures associated with convergent feeding behaviors. We show that species with smaller ranges (i.e., on islands) have experienced stronger demographic fluctuations than those on continents, and that these differences have influenced the dynamics of molecular evolution. Comparative genomic analyses reveal positive selection and genomic convergence in brain and dietary genes in plunge-divers. These findings enhance our understanding of the connections between genotype and phenotype in a diverse avian radiation.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA.
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA.
| | - Lauren E Mellenthin
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Taylor Hains
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Shannon J Hackett
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
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4
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Capurucho JMG, Hains T, Pirro S, Bates J, Hackett S. The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves). Biodivers Genomes 2023; 2023:10.56179/001c.74632. [PMID: 37153853 PMCID: PMC10162776 DOI: 10.56179/001c.74632] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We present the complete genome sequences of 19 species of snipes from 7 genera. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
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Affiliation(s)
- João Marcos G Capurucho
- Coordenação de Biodiversidade, Field Museum of Natural History
- Committee on Evolutionary Biology, Instituto Nacional de Pesquisas da Amazônia
| | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago, Committee on Evolutionary Biology
| | | | - John Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
| | - Shannon Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
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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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Eliason CM, Cooper JC, Hackett SJ, Zahnle E, Pequeño Saco TZ, Maddox JD, Hains T, Hauber ME, Bates JM. Interspecific hybridization explains rapid gorget colour divergence in Heliodoxa hummingbirds (Aves: Trochilidae). R Soc Open Sci 2023; 10:221603. [PMID: 36866078 PMCID: PMC9974296 DOI: 10.1098/rsos.221603] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Hybridization is a known source of morphological, functional and communicative signal novelty in many organisms. Although diverse mechanisms of established novel ornamentation have been identified in natural populations, we lack an understanding of hybridization effects across levels of biological scales and upon phylogenies. Hummingbirds display diverse structural colours resulting from coherent light scattering by feather nanostructures. Given the complex relationship between feather nanostructures and the colours they produce, intermediate coloration does not necessarily imply intermediate nanostructures. Here, we characterize nanostructural, ecological and genetic inputs in a distinctive Heliodoxa hummingbird from the foothills of eastern Peru. Genetically, this individual is closely allied with Heliodoxa branickii and Heliodoxa gularis, but it is not identical to either when nuclear data are assessed. Elevated interspecific heterozygosity further suggests it is a hybrid backcross to H. branickii. Electron microscopy and spectrophotometry of this unique individual reveal key nanostructural differences underlying its distinct gorget colour, confirmed by optical modelling. Phylogenetic comparative analysis suggests that the observed gorget coloration divergence from both parentals to this individual would take 6.6-10 My to evolve at the current rate within a single hummingbird lineage. These results emphasize the mosaic nature of hybridization and suggest that hybridization may contribute to the structural colour diversity found across hummingbirds.
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Affiliation(s)
- Chad M. Eliason
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Jacob C. Cooper
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66044, USA
- Directora de Monitoreo y Evaluacion de Recursos Naturales del Territorio, Plataforma digital única del Estado Peruano, Iquitos, Perú
| | - Shannon J. Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Erica Zahnle
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66044, USA
| | - Tatiana Z. Pequeño Saco
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Iquitos, Perú
| | - Joseph Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Iquitos, Perú
| | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Mark E. Hauber
- Department of Evolution, Ecology, and Behaviour, School at Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - John M. Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
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7
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Hains T, Pirro S, Bates JM, Hackett SJ. The Complete Genome Sequence of Conuropsis carolinensis, the Carolina Parakeet. Biodivers Genomes 2022; 2022:10.56179/001c.66227. [PMID: 36632172 PMCID: PMC9830951 DOI: 10.56179/001c.66227] [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] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Carolina Parakeet (Conuropsis carolinensis) is an extinct species of parrot that was native to the eastern, midwest, and plains regions of the United States. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR21023482) and assembled genome (JAOBYI000000000).
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Affiliation(s)
- Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- Committee on Evolutionary Biology, University of Chicago
| | | | - John M Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
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8
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Eliason CM, Hains T, McCullough J, Andersen MJ, Hackett SJ. Genomic novelty within a "great speciator" revealed by a high-quality reference genome of the collared kingfisher (Todiramphus chloris collaris). G3 (Bethesda) 2022; 12:jkac260. [PMID: 36156134 PMCID: PMC9635628 DOI: 10.1093/g3journal/jkac260] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin's finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr's "great speciators," the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL 60605, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Taylor Hains
- Department of Ecology and Evolution, Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jenna McCullough
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael J Andersen
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
- Department of Ecology and Evolution, Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
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9
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Hains T, Pirro S, O'Neill K, Valez J, Speed N, Clubb S, Oleksyk T, Bates J, Hackett S. The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves). Biodivers Genomes 2022; 2022:10.56179/001c.40338. [PMID: 36405343 PMCID: PMC9671223 DOI: 10.56179/001c.40338] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
We present the complete genome sequences of 94 species of parrots from 40 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.
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Affiliation(s)
- Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
| | | | | | - Jafet Valez
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service
| | - Nancy Speed
- Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc
| | - Susan Clubb
- Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc
| | - Taras Oleksyk
- Department of Biological Sciences, Oakland University
| | - John Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
| | - Shannon Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
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10
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Chavez DE, Gronau I, Hains T, Dikow RB, Frandsen PB, Figueiró HV, Garcez FS, Tchaicka L, de Paula RC, Rodrigues FHG, Jorge RSP, Lima ES, Songsasen N, Johnson WE, Eizirik E, Koepfli KP, Wayne RK. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids. Proc Natl Acad Sci U S A 2022; 119:e2205986119. [PMID: 35969758 PMCID: PMC9407222 DOI: 10.1073/pnas.2205986119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.
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Affiliation(s)
- Daniel E. Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya 46150, Israel
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Henrique V. Figueiró
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Fabrício S. Garcez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Ligia Tchaicka
- Rede de Biodiversidade e Biotecnologia da Amazônia, Curso de Pós-Graduação em Recursos Aquáticos e Pesca, Universidade Estadual do Maranhão, São Luis, 2016-8100, Brazil
| | - Rogério C. de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, 12952-011, Atibaia, Brazil
| | - Flávio H. G. Rodrigues
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo S. P. Jorge
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado, Instituto Chico Mendes de Conservação da Biodiversidade, Brasilia, 70670-350, Brazil
| | - Edson S. Lima
- Private address, Nova Xavantina, MT, 78690-000, Brazil
| | - Nucharin Songsasen
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Warren E. Johnson
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, 12945-010, Brazil
- Instituto Nacional de Ciência e Tecnologia em Ecologia Evolução Conservação da Biodiverside, Universidade Federal de GoiásGoiânia, 74690-900, Brazil
| | - Klaus-Peter Koepfli
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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11
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Hains T, Pirro S, Bates J, Hackett S. The Complete Genome Sequence of Cyanopsitta spixii, the Spix's Macaw. Biodivers Genomes 2022; 2022:10.56179/001c.37839. [PMID: 36467626 PMCID: PMC9718372 DOI: 10.56179/001c.37839] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Spix's Macaw (Cyanopsitta spixii) is a critically endangered parrot that was once endemic to Brazil. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR15037507) and Assembly (GCA_024336845).
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Affiliation(s)
- Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
| | | | - John Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
| | - Shannon Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
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12
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Kolchanova S, Komissarov A, Kliver S, Mazo-Vargas A, Afanador Y, Velez-Valentín J, de la Rosa RV, Castro-Marquez S, Rivera-Colon I, Majeske AJ, Wolfsberger WW, Hains T, Corvelo A, Martinez-Cruzado JC, Glenn TC, Robinson O, Koepfli KP, Oleksyk TK. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles. Genes (Basel) 2021; 12:608. [PMID: 33924228 PMCID: PMC8074781 DOI: 10.3390/genes12040608] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/10/2023] Open
Abstract
Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.
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Affiliation(s)
- Sofiia Kolchanova
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Alexey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 191002 St. Petersburg, Russia;
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 664033 Novosibirsk, Russia;
| | - Anyi Mazo-Vargas
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Yashira Afanador
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Jafet Velez-Valentín
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande 00745, Puerto Rico;
| | - Ricardo Valentín de la Rosa
- The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo 00613, Puerto Rico;
| | - Stephanie Castro-Marquez
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
| | - Israel Rivera-Colon
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Audrey J. Majeske
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
| | - Walter W. Wolfsberger
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
- Department of Biology, Uzhhorod National University, 88000 Uzhhorod, Ukraine
| | - Taylor Hains
- Terra Wildlife Genomics, Washington, DC 20009, USA;
- Environmental Science and Policy, Johns Hopkins University, Washington, DC 20036, USA
| | | | - Juan-Carlos Martinez-Cruzado
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Travis C. Glenn
- Department of Environmental Health, The University of Georgia, Athens, GA 30602, USA;
| | | | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia;
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Taras K. Oleksyk
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
- Department of Biology, Uzhhorod National University, 88000 Uzhhorod, Ukraine
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13
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Chavez DE, Gronau I, Hains T, Kliver S, Koepfli KP, Wayne RK. Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). Sci Rep 2019; 9:8329. [PMID: 31171819 PMCID: PMC6554312 DOI: 10.1038/s41598-019-44772-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 12/02/2022] Open
Abstract
Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya, 46150, Israel
| | - Taylor Hains
- Environmental Science and Policy, Johns Hopkins University, Washington, D.C., 20036, USA
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Novosibirsk, 630090, Russian Federation
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., 20008, USA
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
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