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Byerly PA, Chesser RT, Fleischer RC, McInerney N, Przelomska NAS, Leberg PL. Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic. Integr Comp Biol 2022; 62:1838-1848. [PMID: 35781565 DOI: 10.1093/icb/icac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.
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Affiliation(s)
- Paige A Byerly
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - R Terry Chesser
- Eastern Ecological Science Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708, USA.,National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Nancy McInerney
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Natalia A S Przelomska
- National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA.,Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Paul L Leberg
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA
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Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E. Evidence for a duplicated mitochondrial region in Audubon's shearwater based on MinION sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:256-263. [PMID: 30043666 DOI: 10.1080/24701394.2018.1484116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.
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Affiliation(s)
- Lucas Torres
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France.,b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
| | | | - Catherine Zanchetta
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - R Terry Chesser
- e USGS Patuxent Wildlife Research Center , National Museum of Natural History, Smithsonian Institution , Washington , DC , USA
| | - Maxime Manno
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Cécile Donnadieu
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Vincent Bretagnolle
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France
| | - Eric Pante
- b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
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Munilla I, Genovart M, Paiva VH, Velando A. Colony Foundation in an Oceanic Seabird. PLoS One 2016; 11:e0147222. [PMID: 26909694 PMCID: PMC4766187 DOI: 10.1371/journal.pone.0147222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022] Open
Abstract
Seabirds are colonial vertebrates that despite their great potential for long-range dispersal and colonization are reluctant to establish in novel locations, often recruiting close to their natal colony. The foundation of colonies is therefore a rare event in most seabird species and little is known about the colonization process in this group. The Cory’s shearwater (Calonectris diomedea) is a pelagic seabird that has recently established three new colonies in Galicia (NE Atlantic) thus expanding its distribution range 500 km northwards. This study aimed to describe the establishment and early progress of the new Galician populations and to determine the genetic and morphometric characteristics of the individuals participating in these foundation events. Using 10 microsatellite loci, we tested the predictions supported by different seabird colonization models. Possibly three groups of non-breeders, adding up to around 200 birds, started visiting the Galician colonies in the mid 2000’s and some of them eventually laid eggs and reproduced, thus establishing new breeding colonies. The Galician populations showed a high genetic diversity and a frequency of private alleles similar to or even higher than some of the large historical populations. Most individuals were assigned to several Atlantic populations and a few (if any) to Mediterranean colonies. Our study suggests that a large and admixed population is settling in Galicia, in agreement with predictions from island metapopulation models of colonization. Multiple source colonies imply that some birds colonizing Galicia were dispersing from very distant colonies (> 1500 km). Long-distance colonizations undertaken by relatively large and admixed groups of colonizers can help to explain the low levels of genetic structure over vast areas that are characteristic of most oceanic seabird species.
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Affiliation(s)
- Ignacio Munilla
- Departamento de Botánica, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
- * E-mail: (AV); (IM)
| | - Meritxell Genovart
- Departamento de Botánica, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Vitor H. Paiva
- Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Alberto Velando
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, Galicia, Spain
- * E-mail: (AV); (IM)
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Rayfield B, Pelletier D, Dumitru M, Cardille JA, Gonzalez A. Multipurpose habitat networks for short‐range and long‐range connectivity: a new method combining graph and circuit connectivity. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12470] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bronwyn Rayfield
- Department of Biology McGill University 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - David Pelletier
- Department of Natural Resource Sciences and McGill School of Environment McGill University 21111 Lakeshore Road, Sainte Anne de Bellevue Montreal QC H9X 3V9 Canada
| | - Maria Dumitru
- Department of Biology McGill University 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - Jeffrey A. Cardille
- Department of Natural Resource Sciences and McGill School of Environment McGill University 21111 Lakeshore Road, Sainte Anne de Bellevue Montreal QC H9X 3V9 Canada
| | - Andrew Gonzalez
- Department of Biology McGill University 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
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