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Oswald JA, Smith BT, Allen JM, Guralnick RP, Steadman DW, LeFebvre MJ. Changes in parrot diversity after human arrival to the Caribbean. Proc Natl Acad Sci U S A 2023; 120:e2301128120. [PMID: 37748079 PMCID: PMC10576146 DOI: 10.1073/pnas.2301128120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/31/2023] [Indexed: 09/27/2023] Open
Abstract
Humans did not arrive on most of the world's islands until relatively recently, making islands favorable places for disentangling the timing and magnitude of natural and anthropogenic impacts on species diversity and distributions. Here, we focus on Amazona parrots in the Caribbean, which have close relationships with humans (e.g., as pets as well as sources of meat and colorful feathers). Caribbean parrots also have substantial fossil and archaeological records that span the Holocene. We leverage this exemplary record to showcase how combining ancient and modern DNA, along with radiometric dating, can shed light on diversification and extinction dynamics and answer long-standing questions about the magnitude of human impacts in the region. Our results reveal a striking loss of parrot diversity, much of which took place during human occupation of the islands. The most widespread species, the Cuban Parrot, exhibits interisland divergences throughout the Pleistocene. Within this radiation, we identified an extinct, genetically distinct lineage that survived on the Turks and Caicos until Indigenous human settlement of the islands. We also found that the narrowly distributed Hispaniolan Parrot had a natural range that once included The Bahamas; it thus became "endemic" to Hispaniola during the late Holocene. The Hispaniolan Parrot also likely was introduced by Indigenous people to Grand Turk and Montserrat, two islands where it is now also extirpated. Our research demonstrates that genetic information spanning paleontological, archaeological, and modern contexts is essential to understand the role of humans in altering the diversity and distribution of biota.
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Affiliation(s)
- Jessica A. Oswald
- US Fish and Wildlife Service, National Fish and Wildlife Forensic Laboratory, Ashland, OR97520
- Department of Biology, University of Nevada, Reno, Reno, NV89557
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY10024
| | - Julie M. Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA24061
| | - Robert P. Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL32611
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL32611
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots. Nat Commun 2022; 13:944. [PMID: 35177601 PMCID: PMC8854603 DOI: 10.1038/s41467-022-28585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots. Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.
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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change. Genomics 2021; 113:3430-3438. [PMID: 34400239 DOI: 10.1016/j.ygeno.2021.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 01/15/2023]
Abstract
We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.
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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] [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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Russello M, Amato G, DeSalle R, Knapp M. Conservation Genetics and Genomics. Genes (Basel) 2020; 11:genes11030318. [PMID: 32192054 PMCID: PMC7140847 DOI: 10.3390/genes11030318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Michael Russello
- Department of Biology, The University of British Columbia, 3247 University Way, FIP346, Kelowna, BC V1V 1V7, Canada;
| | - George Amato
- Conservation Genomics, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024-5102, USA;
- Correspondence:
| | - Robert DeSalle
- Conservation Genomics, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024-5102, USA;
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand;
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