1
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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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2
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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3
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Greig K, Rawlence NJ. The Contribution of Kurī (Polynesian Dog) to the Ecological Impacts of the Human Settlement of Aotearoa New Zealand. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.757988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The pre-human Aotearoa New Zealand fauna was dominated by avian and reptilian species. Prior to first human settlement by East Polynesian colonists, the top predators were two giant raptorial birds. Aside from humans themselves, colonisation also resulted in the simultaneous introduction of two novel mammalian predators into this naive ecosystem, the kiore (Pacific rat) and kurī (Polynesian dog). While the ecological impacts of kiore are relatively well understood, those of kurī are difficult to assess, and as such kurī have frequently been disregarded as having any meaningful impact on New Zealand’s biodiversity. Here we use the archaeological and palaeoecological record to reassess the potential impacts of kurī on this ecosystem. We argue that far from being confined to villages, kurī could have had a significant widespread but relatively localised impact on New Zealand’s avian, reptilian and marine mammal (seals and sea lions) fauna as a novel predator of medium-sized species. In this way, kurī potentially amplified the already significant impacts of Polynesian colonists and their descendants on New Zealand’s ecosystem, prior to European arrival. As such, kurī should be included in models of human impact in addition to over-hunting, environmental modification and predation by kiore.
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4
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Hahn EE, Alexander MR, Grealy A, Stiller J, Gardiner DM, Holleley CE. Unlocking inaccessible historical genomes preserved in formalin. Mol Ecol Resour 2021; 22:2130-2147. [PMID: 34549888 DOI: 10.1111/1755-0998.13505] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/27/2022]
Abstract
Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
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Affiliation(s)
- Erin E Hahn
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Marina R Alexander
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Alicia Grealy
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Jiri Stiller
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Clare E Holleley
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
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5
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Eliason CM, Clarke JA. Cassowary gloss and a novel form of structural color in birds. SCIENCE ADVANCES 2020; 6:eaba0187. [PMID: 32426504 PMCID: PMC7220335 DOI: 10.1126/sciadv.aba0187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
One of the two lineages of extant birds resulting from its deepest split, Palaeognathae, has been reported not to exhibit structural coloration in feathers, affecting inferences of ancestral coloration mechanisms in extant birds. Structural coloration in facial skin and eggshells has been shown in this lineage, but has not been reported in feathers. We present the first evidence for two distinct mechanisms of structural color in palaeognath feathers. One extinct volant clade, Lithornithidae, shows evidence of elongate melanin-containing organelles uniquely associated with glossy/iridescent color, a structural color mechanism found in fossil outgroups and neognath birds. We also demonstrate a structural basis for the exceptional gloss in extant cassowary feathers. We propose gloss as an intermediate phenotype between matte and iridescent plumage, conferred by a thick and smooth feather rachis. Rachis-based structural color has not been previously investigated. The new data illuminate the relationships between avian melanin-based coloration and feather structure.
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Affiliation(s)
- Chad M. Eliason
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL, USA
- Jackson School of Geosciences and Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Julia A. Clarke
- Jackson School of Geosciences and Integrative Biology, University of Texas at Austin, Austin, TX, USA
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6
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Abstract
Mobile devices for on-field DNA analysis have been used for medical diagnostics
at the point-of-care, forensic investigations and environmental surveys, but
still have to be validated for ancient DNA studies. We report here on a mobile
laboratory that we setup using commercially available devices, including a
compact real-time PCR machine, and describe procedures to perform DNA extraction
and analysis from a variety of archeological samples within 4 hours. The process
is carried out on 50 mg samples that are identified at the species level using
custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated
the potential of this approach in museums lacking facilities for DNA studies by
analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3
deposits), and also performed experiments during an excavation campaign at the
Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples
only yielded DNA for the extinct steppe bison (Bison priscus),
whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta
crocuta spelaea) DNA together, for some of them, with DNA for the
European bison sister species/subspecies (Bison
schoetensacki/Bb1-X), thus highlighting the cave hyena diet.
Roc-en-Pail Bovinae bone and tooth samples also contained DNA
for the Bison schoetensacki/Bb1-X clade, and
Cervidae bone samples only yielded reindeer
(Rangifer tarandus) DNA. Subsequent DNA sequencing analyses
confirmed that correct species identification had been achieved using our TaqMan
assays, hence validating these assays for future studies. We conclude that our
approach enables the rapid genetic characterization of tens of millennia-old
archeological samples and is expected to be useful for the on-site screening of
museums and freshly excavated samples for DNA content. Because our mobile
laboratory is made up of commercially available instruments, this approach is
easily accessible to other investigators.
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7
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A novel method to optimise the utility of underused moulted plumulaceous feather samples for genetic analysis in bird conservation. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01117-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Non-invasive sampling methods are increasingly being used in conservation research as they reduce or eliminate the stress and disturbance resulting from invasive sampling of blood or tissue. Here we present a protocol optimised for obtaining usable genetic material from moulted plumulaceous feather samples. The combination of simple alterations to a ‘user-developed’ method, comprised of increased incubation time and modification of temperature and volume of DNA elution buffer, are outlined to increase DNA yield and significantly increase DNA concentration (W = 81, p < 0.01, Cohens’s d = 0.89). We also demonstrate that the use of a primerless polymerase chain reaction (PCR) technique increases DNA quality and amplification success when used prior to PCR reactions targeting avian mitochondrial DNA (mtDNA). A small amplicon strategy proved effective for mtDNA amplification using PCR, targeting three overlapping 314–359 bp regions of the cytochrome oxidase I barcoding region which, when combined, aligned with target-species reference sequences. We provide evidence that samples collected non-invasively in the field and kept in non-optimal conditions for DNA extraction can be used effectively to sequence a 650 bp region of mtDNA for genetic analysis.
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8
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Tsai WLE, Schedl ME, Maley JM, McCormack JE. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol Ecol Resour 2019; 20:1220-1227. [PMID: 31478338 DOI: 10.1111/1755-0998.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
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Affiliation(s)
- Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Margaret E Schedl
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California.,Biology Department, Occidental College, Los Angeles, California
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9
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Abstract
DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using either silica column or organic methods.
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Affiliation(s)
- Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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10
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Development of a sensitive and specific qPCR method to detect duck and goose DNA in meat and feathers. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3165-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Koczur LM, Williford D, DeYoung RW, Ballard BM. Bringing back the dead: Genetic data from avian carcasses. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lianne M. Koczur
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Bart M. Ballard
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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12
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Cole TL, Wood JR. The ancient DNA revolution: the latest era in unearthing New Zealand’s faunal history. NEW ZEALAND JOURNAL OF ZOOLOGY 2017. [DOI: 10.1080/03014223.2017.1376690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Theresa L. Cole
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
| | - Jamie R. Wood
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
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13
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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14
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Grosser S, Rawlence NJ, Anderson CNK, Smith IWG, Scofield RP, Waters JM. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins. Proc Biol Sci 2017; 283:rspb.2015.2879. [PMID: 26842575 DOI: 10.1098/rspb.2015.2879] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.
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Affiliation(s)
- Stefanie Grosser
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Ian W G Smith
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
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15
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Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens. Proc Biol Sci 2016; 282:20150015. [PMID: 25972464 DOI: 10.1098/rspb.2015.0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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16
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Rawlence NJ, Paul Scofield R, Spencer HG, Lalas C, Easton LJ, Tennyson AJD, Adams M, Pasquet E, Fraser C, Waters JM, Kennedy M. Genetic and morphological evidence for two species ofLeucocarboshag (Aves, Pelecaniformes, Phalacrocoracidae) from southern South Island of New Zealand. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12376] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas J. Rawlence
- Allan Wilson Centre; Department of Zoology; University of Otago; 340 Great King Street Dunedin New Zealand
| | | | - Hamish G. Spencer
- Allan Wilson Centre; Department of Zoology; University of Otago; 340 Great King Street Dunedin New Zealand
| | - Chris Lalas
- Department of Marine Science; University of Otago; 310 Castle Street Dunedin New Zealand
| | - Luke J. Easton
- Allan Wilson Centre; Department of Zoology; University of Otago; 340 Great King Street Dunedin New Zealand
| | | | - Mark Adams
- Bird Group; Natural History Museum; Akeman Street Tring Hertfordshire UK
| | - Eric Pasquet
- Collections d'Oiseaux; Musèum National d'Histoire Naturelle; 57 Rue Cuvier Paris France
| | - Cody Fraser
- Otago Museum; 419 Great King Street Dunedin New Zealand
| | - Jonathan M. Waters
- Allan Wilson Centre; Department of Zoology; University of Otago; 340 Great King Street Dunedin New Zealand
| | - Martyn Kennedy
- Allan Wilson Centre; Department of Zoology; University of Otago; 340 Great King Street Dunedin New Zealand
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17
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Huynen L, Lambert DM. Complex species status for extinct moa (Aves: Dinornithiformes) from the genus Euryapteryx. PLoS One 2014; 9:e90212. [PMID: 24594991 PMCID: PMC3940832 DOI: 10.1371/journal.pone.0090212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 01/29/2014] [Indexed: 11/25/2022] Open
Abstract
The exact species status of New Zealand's extinct moa remains unknown. In particular, moa belonging to the genus Euryapteryx have been difficult to classify. We use the DNA barcoding sequence on a range of Euryapteryx samples in an attempt to resolve the species status for this genus. We obtained mitochondrial control region and the barcoding region from Cytochrome Oxidase Subunit I (COI) from a number of new moa samples and use available sequences from previous moa phylogenies and eggshell data to try and clarify the species status of Euryapteryx. Using the COI barcoding region we show that species status in Euryapteryx is complex with no clear separation between various individuals. Eggshell, soil, and bone data suggests that a Euryapteryx subspecies likely exists on New Zealand's North Island and can be characterized by a single mitochondrial control region SNP. COI divergences between Euryapteryx individuals from the south of New Zealand's South Island and those from the Far North of the North Island exceed 1.6% and are likely to represent separate species. Individuals from other areas of New Zealand were unable to be clearly separated based on COI differences possibly as a result of repeated hybridisation events. Despite the accuracy of the COI barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus Euryapteryx, COI barcoding fails to provide a clear result, possibly as a consequence of repeated hybridisation events between these moa. A single control region SNP was identified however that segregates with the two general morphological variants determined for Euryapteryx; a smaller subspecies restricted to the North Island of New Zealand, and a larger subspecies, found on both New Zealand's North and South Island.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - David M Lambert
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
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18
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19
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Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013; 8:e56301. [PMID: 23437111 PMCID: PMC3577829 DOI: 10.1371/journal.pone.0056301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022] Open
Abstract
The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum and Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chiou-Ju Yao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail:
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Wood JR, Wilmshurst JM, Wagstaff SJ, Worthy TH, Rawlence NJ, Cooper A. High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus). PLoS One 2012; 7:e40025. [PMID: 22768206 PMCID: PMC3386916 DOI: 10.1371/journal.pone.0040025] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/30/2012] [Indexed: 11/23/2022] Open
Abstract
Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand’s largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 14C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.
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Affiliation(s)
- Jamie R Wood
- Landcare Research, Lincoln, Canterbury, New Zealand.
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Huynen L, Millar CD, Lambert DM. Resurrecting ancient animal genomes: the extinct moa and more. Bioessays 2012; 34:661-9. [PMID: 22674514 DOI: 10.1002/bies.201200040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
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Worthy TH, Scofield RP. Twenty-first century advances in knowledge of the biology of moa (Aves: Dinornithiformes): a new morphological analysis and moa diagnoses revised. NEW ZEALAND JOURNAL OF ZOOLOGY 2012. [DOI: 10.1080/03014223.2012.665060] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using either silica-column or organic methods.
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Affiliation(s)
- Paula F Campos
- Natural History Museum of Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
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Olsen ME, Bengtsson CF, Bertelsen MF, Willerslev E, Gilbert MTP. DNA from keratinous tissue. Ann Anat 2012; 194:31-5. [DOI: 10.1016/j.aanat.2011.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/10/2011] [Accepted: 03/10/2011] [Indexed: 10/18/2022]
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Speller CF, Nicholas GP, Yang DY. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations. INVESTIGATIVE GENETICS 2011; 2:16. [PMID: 21794178 PMCID: PMC3199791 DOI: 10.1186/2041-2223-2-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/28/2011] [Indexed: 12/01/2022]
Abstract
Background The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. Results By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardea herodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. Conclusions By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.
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Affiliation(s)
- Camilla F Speller
- Centre for Forensic Research, Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand. Ann Anat 2011; 194:36-51. [PMID: 21596537 DOI: 10.1016/j.aanat.2011.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/23/2022]
Abstract
The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.
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Allentoft ME, Oskam C, Houston J, Hale ML, Gilbert MTP, Rasmussen M, Spencer P, Jacomb C, Willerslev E, Holdaway RN, Bunce M. Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and prospects. PLoS One 2011; 6:e16670. [PMID: 21304955 PMCID: PMC3031614 DOI: 10.1371/journal.pone.0016670] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 12/31/2010] [Indexed: 11/19/2022] Open
Abstract
We present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the ‘shotgun’ reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36–70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600–5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (MEA); (MB)
| | - Charlotte Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Jayne Houston
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M. Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Peter Spencer
- Wildlife Identification Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Christopher Jacomb
- Southern Pacific Archaeological Research, Department of Anthropology, University of Otago, Dunedin, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Palaecol Research Ltd, Christchurch, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- * E-mail: (MEA); (MB)
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Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, Olsen ME, Bengtsson C, Miller GH, Schwenninger JL, Jacomb C, Walter R, Baynes A, Dortch J, Parker-Pearson M, Gilbert MTP, Holdaway RN, Willerslev E, Bunce M. Fossil avian eggshell preserves ancient DNA. Proc Biol Sci 2010; 277:1991-2000. [PMID: 20219731 DOI: 10.1098/rspb.2009.2019] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.
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Affiliation(s)
- Charlotte L Oskam
- Ancient DNA Laboratory, School of Biological Sciences, Murdoch University, Perth, Western Australia, Australia
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