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Billerman SM, Walsh J. Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions. Mol Ecol Resour 2019; 19:1115-1130. [PMID: 31336408 DOI: 10.1111/1755-0998.13066] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high-throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.
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Affiliation(s)
- Shawn M Billerman
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Abstract
De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In 2016, a special committee of the International Union for the Conservation of Nature (IUCN) published a set of guidelines for de-extinction practice, establishing the first detailed description of de-extinction; yet incoherencies in published literature persist. There are even several problems with the IUCN definition. Here I present a comprehensive definition of de-extinction practice and rationale that expounds and reconciles the biological and ecological inconsistencies in the IUCN definition. This new definition brings together the practices of reintroduction and ecological replacement with de-extinction efforts that employ breeding strategies to recover unique extinct phenotypes into a single “de-extinction” discipline. An accurate understanding of de-extinction and biotechnology segregates the restoration of certain species into a new classification of endangerment, removing them from the purview of de-extinction and into the arena of species’ recovery. I term these species as “evolutionarily torpid species”; a term to apply to species falsely considered extinct, which in fact persist in the form of cryopreserved tissues and cultured cells. For the first time in published literature, all currently active de-extinction breeding programs are reviewed and their progress presented. Lastly, I review and scrutinize various topics pertaining to de-extinction in light of the growing body of peer-reviewed literature published since de-extinction breeding programs gained public attention in 2013.
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Novak BJ, Estes JA, Shaw HE, Novak EV, Shapiro B. Experimental Investigation of the Dietary Ecology of the Extinct Passenger Pigeon, Ectopistes migratorius. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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Soares AER, Novak BJ, Haile J, Heupink TH, Fjeldså J, Gilbert MTP, Poinar H, Church GM, Shapiro B. Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. BMC Evol Biol 2016; 16:230. [PMID: 27782796 PMCID: PMC5080718 DOI: 10.1186/s12862-016-0800-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. RESULTS We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. CONCLUSIONS Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.
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Affiliation(s)
- André E. R. Soares
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
| | - Ben J. Novak
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
- Revive & Restore, The Long Now Foundation, San Francisco, CA 94123 USA
| | - James Haile
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tim H. Heupink
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road QLD 4111, Nathan, Australia
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 L9 Canada
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115 USA
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
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Hykin SM, Bi K, McGuire JA. Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing. PLoS One 2015; 10:e0141579. [PMID: 26505622 PMCID: PMC4623518 DOI: 10.1371/journal.pone.0141579] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/09/2015] [Indexed: 01/23/2023] Open
Abstract
For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens—particularly for use in phylogenetic analyses—has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis.
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Affiliation(s)
- Sarah M. Hykin
- Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America
- * E-mail: (SMH); (KB)
| | - Ke Bi
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America
- * E-mail: (SMH); (KB)
| | - Jimmy A. McGuire
- Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, California, United States of America
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