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McComish BJ, Charleston MA, Parks M, Baroni C, Salvatore MC, Li R, Zhang G, Millar CD, Holland BR, Lambert DM. Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time. Genome Biol Evol 2024; 16:evae017. [PMID: 38412309 PMCID: PMC10972684 DOI: 10.1093/gbe/evae017] [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: 04/05/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.
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Affiliation(s)
- Bennet J McComish
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | | | - Matthew Parks
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034, USA
| | - Carlo Baroni
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Maria Cristina Salvatore
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Ruiqiang Li
- Novogene Bioinformatics Technology Co. Ltd., Beijing 100083, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - David M Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
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Ward AJ, Lambert DM, Butterly D, O'Byrne JJ, McGrath V, Lynch SA. Genetic services survey-experience of people with rare diseases and their families accessing genetic services in the Irish Republic. J Community Genet 2023; 14:583-592. [PMID: 37632685 PMCID: PMC10725380 DOI: 10.1007/s12687-023-00664-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023] Open
Abstract
Irish Health Service objectives state that patients with rare diseases should have timely access to genomic diagnostics with appropriate pre and post-test counselling. However, waiting times for clinical genetics outpatient appointments, during the study period, were up to two years as staffing levels remain low. A targeted public online survey was conducted in January 2022 to capture the experiences of Rare Disease families trying to access genetic testing and clinical genetic clinics in the Irish Republic. Irish patients experience significant waiting times to access clinical genetic services and self-report anxiety and stress, related to delayed access to diagnosis, clarity around recurrence risk and follow-up management. This negatively impacts personal decisions around family planning, education and employment and has a significant impact on family members seeking clarity on their own risk. Mainstream genetic testing activity is significant. Families report concern over the competency of health care professionals arranging and delivering genetic results and delays in accessing clinical genetics expertise to take them through the clinical implications. Timely access to clinical genetics expertise is important to ensure families with rare diseases have an appropriate understanding of the medical and reproductive implications of a genetic diagnosis and access to relevant care pathways. A national framework to develop competency in genomic literacy for health-care professionals including a national genetic test directory may be beneficial. Clinical genetics teams require ongoing support and investment to ensure the delivery of a safe and effective service for Irish families with rare diseases.
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Affiliation(s)
- A J Ward
- University College Dublin, School of Medicine, Dublin, Ireland
| | - D M Lambert
- University College Dublin, School of Medicine, Dublin, Ireland
| | - D Butterly
- University College Dublin, School of Medicine, Dublin, Ireland
| | - J J O'Byrne
- University College Dublin, School of Medicine, Dublin, Ireland
- Mater Misericordiae University Hospital, National Centre for Inherited Metabolic Disorders, Dublin, Ireland
- Trinity College Dublin, School of Medicine, Dublin, Ireland
| | - V McGrath
- Rare Diseases Ireland, Dublin, Ireland
| | - S A Lynch
- University College Dublin, School of Medicine, Dublin, Ireland.
- Children's Health Ireland (CHI) at Crumlin, Clinical Genetics, Dublin, Ireland.
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Lambert DM. Editorial. Theor Biol Forum 2023; 116:9-11. [PMID: 37638477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
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Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J, Kennedy R, Winch P, Pappin M, Wales T, Bates W“B, Hamilton S, Whyman N, van Holst Pellekaan S, McAllister PJ, Taçon PS, Curnoe D, Li R, Millar C, Subramanian S, Willerslev E, Malaspinas AS, Sikora M, Lambert DM. Ancient nuclear genomes enable repatriation of Indigenous human remains. Sci Adv 2018; 4:eaau5064. [PMID: 30585290 PMCID: PMC6300400 DOI: 10.1126/sciadv.aau5064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.
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Affiliation(s)
- Joanne L. Wright
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Sally Wasef
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Tim H. Heupink
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Belgium
| | - Michael C. Westaway
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Colin Pardoe
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | | | - Michael Young
- Barkandji/Paakantyi Elder, Red Cliffs, VIC, Australia
| | - Trish Johnson
- Barkandji/Paakantyi Elder, Pooncarie, NSW, Australia
| | - Joan Slade
- Ngiyampaa Elder, Ivanhoe, NSW, Australia
| | | | - Patsy Winch
- Mutthi Mutthi Elder, Balranald, NSW, Australia
| | - Mary Pappin
- Mutthi Mutthi Elder, Broken Hill, NSW, Australia
| | - Tapij Wales
- Thanynakwith Elder, Napranum, QLD, Australia
| | | | | | | | - Sheila van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - Paul S.C. Taçon
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Paleontology, Geobiology and Earth Archives Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sankar Subramanian
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (M.S.); (D.M.L.)
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Corresponding author. (M.S.); (D.M.L.)
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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Affiliation(s)
- David M Lambert
- George Evelyn Hutchinson Laboratory, Department of Zoology, University of the Witwatersrand, Jan Smuts Avenue, Johannesburg, South Africa
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Smith CA, Farlie PG, Davidson NM, Roeszler KN, Hirst C, Oshlack A, Lambert DM. Limb patterning genes and heterochronic development of the emu wing bud. EvoDevo 2016; 7:26. [PMID: 28031782 PMCID: PMC5168868 DOI: 10.1186/s13227-016-0063-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/01/2016] [Indexed: 01/08/2023] Open
Abstract
Background The forelimb of the flightless emu is a vestigial structure, with greatly reduced wing elements and digit loss. To explore the molecular and cellular mechanisms associated with the evolution of vestigial wings and loss of flight in the emu, key limb patterning genes were examined in developing embryos. Methods Limb development was compared in emu versus chicken embryos. Immunostaining for cell proliferation markers was used to analyze growth of the emu forelimb and hindlimb buds. Expression patterns of limb patterning genes were studied, using whole-mount in situ hybridization (for mRNA localization) and RNA-seq (for mRNA expression levels). Results The forelimb of the emu embryo showed heterochronic development compared to that in the chicken, with the forelimb bud being retarded in its development. Early outgrowth of the emu forelimb bud is characterized by a lower level of cell proliferation compared the hindlimb bud, as assessed by PH3 immunostaining. In contrast, there were no obvious differences in apoptosis in forelimb versus hindlimb buds (cleaved caspase 3 staining). Most key patterning genes were expressed in emu forelimb buds similarly to that observed in the chicken, but with smaller expression domains. However, expression of Sonic Hedgehog (Shh) mRNA, which is central to anterior–posterior axis development, was delayed in the emu forelimb bud relative to other patterning genes. Regulators of Shh expression, Gli3 and HoxD13, also showed altered expression levels in the emu forelimb bud. Conclusions These data reveal heterochronic but otherwise normal expression of most patterning genes in the emu vestigial forelimb. Delayed Shh expression may be related to the small and vestigial structure of the emu forelimb bud. However, the genetic mechanism driving retarded emu wing development is likely to rest within the forelimb field of the lateral plate mesoderm, predating the expression of patterning genes. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0063-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Craig A Smith
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800 Australia
| | - Peter G Farlie
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052 Australia
| | - Nadia M Davidson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052 Australia
| | - Kelly N Roeszler
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052 Australia
| | - Claire Hirst
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800 Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052 Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111 Australia
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Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 2016; 538:238-242. [PMID: 27654910 PMCID: PMC5164938 DOI: 10.1038/nature19792] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Luca Pagani
- Estonian Biocentre, Tartu, Estonia.,Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniel John Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Evelyn Jagoda
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Mörseburg
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Anders Eriksson
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Florian Clemente
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, Estonia.,Department of Psychology, University of Auckland, Auckland, 1142, New Zealand.,Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, California 94143, USA
| | - Alexia Cardona
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Melissa A Wilson Sayres
- School of Life Sciences, Tempe, AZ, 85287 USA.,Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA
| | - Sarah Kaewert
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Inchley
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Christiana L Scheib
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | | | - Monika Karmin
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Guy S Jacobs
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK
| | - Tiago Antao
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Florin Mircea Iliescu
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | | | | | - Lehti Saag
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Denmark
| | - Michael C Westaway
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - David M Lambert
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania
| | | | - Dilbar Dalimova
- Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan
| | | | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA.,School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic
| | - Larisa D Damba
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, Russia.,Anthony Nolan, London, United Kingdom
| | | | - Olga Utevska
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Nicolas Brucato
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Thierry Letellier
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nikolay A Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Vedrana Skaro
- Genos, DNA laboratory, Zagreb, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | | | - Dragan Primorac
- St. Catherine Speciality Hospital, Zabok, Croatia.,Eberly College of Science, The Pennsylvania State University, University Park, PA, USA.,University of Split, Medical School, Split, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Christina A Eichstaedt
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany
| | - Daria V Lichman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Alexandra Karunas
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Natalya Ekomasova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Damir Marjanović
- Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina.,Institute for Anthropological Researches, Zagreb, Croatia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | | | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Andres Metspalu
- Department of Zoology, University of Cambridge, Cambridge, UK.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Mikhail Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.,Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Pascale Gerbault
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Matthew Leavesley
- Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea.,College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia
| | | | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia
| | | | - Toomas Kivisild
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Estonian Biocentre, Tartu, Estonia
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9
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Heupink TH, Subramanian S, Wright JL, Endicott P, Westaway MC, Huynen L, Parson W, Millar CD, Willerslev E, Lambert DM. Ancient mtDNA sequences from the First Australians revisited. Proc Natl Acad Sci U S A 2016; 113:6892-7. [PMID: 27274055 PMCID: PMC4922152 DOI: 10.1073/pnas.1521066113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.
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Affiliation(s)
- Tim H Heupink
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Joanne L Wright
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Phillip Endicott
- Department of Zoology, Oxford University, Oxford OX1 2JD, United Kingdom
| | | | - Leon Huynen
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA 16801
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, University of Copenhagen, 1017 Copenhagen, Denmark
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia;
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10
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Song G, Zhang R, DuBay SG, Qu Y, Dong L, Wang W, Zhang Y, Lambert DM, Lei F. East Asian allopatry and north Eurasian sympatry in Long-tailed Tit lineages despite similar population dynamics during the late Pleistocene. ZOOL SCR 2015. [DOI: 10.1111/zsc.12148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Center for Developmental Biology; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Shane G. DuBay
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Life Sciences Section; Integrative Research Center; Field Museum of Natural History; Chicago IL 60605 USA
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Wenjuan Wang
- Center for Watershed Ecology; Institute of Life Science; Nanchang University; Nanchang 330031 China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - David M. Lambert
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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11
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Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130381. [PMID: 25487332 DOI: 10.1098/rstb.2013.0381] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Affiliation(s)
- M Parks
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - S Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - C Baroni
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - M C Salvatore
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - G Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, Republic of China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - C D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
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12
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Huynen L, Lambert DM. A Concentrated Hydrochloric Acid-based Method for Complete Recovery of DNA from Bone. J Forensic Sci 2015; 60:1553-7. [PMID: 26250052 DOI: 10.1111/1556-4029.12846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 09/07/2014] [Revised: 11/02/2014] [Accepted: 11/05/2014] [Indexed: 12/17/2022]
Abstract
The successful extraction of DNA from historical or ancient animal bone is important for the analysis of discriminating genetic markers. Methods used currently rely on the digestion of bone with EDTA and proteinase K, followed by purification with phenol/chloroform and silica bed binding. We have developed a simple concentrated hydrochloric acid-based method that precludes the use of phenol/chloroform purification and can lead to a several-fold increase in DNA yield when compared to other commonly used methods. Concentrated hydrochloric acid was shown to dissolve most of the undigested bone and allowed the efficient recovery of DNA fragments <100 bases in length. This method should prove useful for the recovery of DNAs from highly degraded animal bone, such as that found in historical or ancient samples.
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Affiliation(s)
- Leon Huynen
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Qld, 4111, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Qld, 4111, Australia
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13
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Subramanian S, Mohandesan E, Millar CD, Lambert DM. Distance-dependent patterns of molecular divergences in Tuatara mitogenomes. Sci Rep 2015; 5:8703. [PMID: 25731894 PMCID: PMC4346810 DOI: 10.1038/srep08703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/02/2015] [Indexed: 01/21/2023] Open
Abstract
Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
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Affiliation(s)
- Sankar Subramanian
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
| | - Elmira Mohandesan
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private 92019, Auckland, New Zealand
| | - David M Lambert
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
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14
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Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SYW, Burt DW, Ponting CP, Jarvis ED, Gilbert MTP, Yang H, Wang J, Lambert DM, Wang J, Zhang G. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 2014; 3:27. [PMID: 25671092 PMCID: PMC4322438 DOI: 10.1186/2047-217x-3-27] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/06/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. RESULTS Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. CONCLUSIONS Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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Affiliation(s)
- Cai Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Yong Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jianwen Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Lesheng Kong
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Haofu Hu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Hailin Pan
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Luohao Xu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yuan Deng
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Qiye Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Lijun Jin
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Hao Yu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yan Chen
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Binghang Liu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Linfeng Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shiping Liu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yan Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yongshan Lang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jinquan Xia
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Weiming He
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Qiong Shi
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sankar Subramanian
- />Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia
| | - Craig D Millar
- />Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Stephen Meader
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Chris M Rands
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Matthew K Fujita
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
- />Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Matthew J Greenwold
- />Department of Biological Sciences, University of South Carolina, Columbia, SC USA
| | - Todd A Castoe
- />Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA
- />Biology Department, University of Texas Arlington, Arlington, TX 76016 USA
| | - David D Pollock
- />Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA
| | - Wanjun Gu
- />Research Centre of Learning Sciences, Southeast University, Nanjing, 210096 China
| | - Kiwoong Nam
- />Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden
- />Bioinformatics Research Centre (BiRC), Aarhus University, C.F.Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Hans Ellegren
- />Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden
| | - Simon YW Ho
- />School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus Midlothian, Edinburgh, EH25 9RG UK
| | - Chris P Ponting
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Erich D Jarvis
- />Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC27710 USA
| | - M Thomas P Gilbert
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- />Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia
| | - Huanming Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Jian Wang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - David M Lambert
- />Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia
| | - Jun Wang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
- />Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- />Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China
- />Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100 Denmark
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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014; 346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Citation(s) in RCA: 1095] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
| | - Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andre J Aberer
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Bo Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Benoit Nabholz
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Claudia C Weber
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jianwen Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Nitish Narula
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ganesh Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Volodymyr Zavidovych
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Bhanu Rekepalli
- Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bent Lindow
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA
| | - David Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Richard E Green
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maria Paula Cruz Schneider
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil
| | - Francisco Prosdocimi
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - José Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Amhed Missael Vargas Velazquez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bent Petersen
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Ponten
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - An Pas
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Tom Bailey
- Dubai Falcon Hospital, Dubai, United Arab Emirates
| | - Paul Scofield
- Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia
| | - Amy C Driskell
- Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Zijun Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yongli Zeng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenyu Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Binghang Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiong Yinqi
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuemei Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Michael Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA
| | - Jon Fjeldsa
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Warren Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Stephen O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - John McCormack
- Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Dave Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany
| | - David P Mindell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wang Jun
- BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Heupink TH, van Grouw H, Lambert DM. The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred. BMC Evol Biol 2014; 14:136. [PMID: 25027719 PMCID: PMC4099497 DOI: 10.1186/1471-2148-14-136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/18/2014] [Indexed: 11/11/2022] Open
Abstract
Background The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors’ remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred. Results We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire. Conclusions The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.
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Affiliation(s)
- Tim H Heupink
- Environmental Futures Research Institute, Griffith University, Nathan, Australia.
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Huynen L, Suzuki T, Ogura T, Watanabe Y, Millar CD, Hofreiter M, Smith C, Mirmoeini S, Lambert DM. Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes). BMC Evol Biol 2014; 14:75. [PMID: 24885927 PMCID: PMC4101845 DOI: 10.1186/1471-2148-14-75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022] Open
Abstract
Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. Conclusions The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David M Lambert
- Environmental Futures Centre, Griffith University, 170 Kessels Road, Nathan Qld 4111, Australia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chambers GK, Curtis C, Millar CD, Huynen L, Lambert DM. DNA fingerprinting in zoology: past, present, future. Investig Genet 2014; 5:3. [PMID: 24490906 PMCID: PMC3909909 DOI: 10.1186/2041-2223-5-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/19/2013] [Indexed: 01/07/2023]
Abstract
In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work.
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Affiliation(s)
| | | | | | | | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia.
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Kapanda CN, Poupaert JH, Lambert DM. Insight into the medicinal chemistry of the endocannabinoid hydrolase inhibitors. Curr Med Chem 2014; 20:1824-46. [PMID: 23410152 DOI: 10.2174/09298673113209990108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 01/07/2013] [Accepted: 02/13/2013] [Indexed: 11/22/2022]
Abstract
Endocannabinoid hydrolases are nowadays increasingly considered as potential therapeutic targets for treating several pathological states. So far, numerous classes of endocannabinoid hydrolase inhibitors have been described. We herein review the medicinal chemistry of these inhibitors with a particular emphasis on the basis of their design, chemical structure, structure-activity relationships, and inhibition mechanisms.
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Affiliation(s)
- C N Kapanda
- Medicinal Chemistry, Cannabinoid and Endocannabinoid Research Group, B1.73.10, Louvain Drug Research Institute (LDRI), Université catholique de Louvain, 73 avenue E. Mounier B-1200 Bruxelles, Belgium
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Abstract
Penguins are a remarkable group of birds, with the 18 extant species living in diverse climatic zones from the tropics to Antarctica. The timing of the origin of these extant penguins remains controversial. Previous studies based on DNA sequences and fossil records have suggested widely differing times for the origin of the group. This has given rise to widely differing biogeographic narratives about their evolution. To resolve this problem, we sequenced five introns from 11 species representing all genera of living penguins. Using these data and other available DNA sequences, together with the ages of multiple penguin fossils to calibrate the molecular clock, we estimated the age of the most recent common ancestor of extant penguins to be 20.4 Myr (17.0-23.8 Myr). This time is half of the previous estimates based on molecular sequence data. Our results suggest that most of the major groups of extant penguins diverged 11-16 Ma. This overlaps with the sharp decline in Antarctic temperatures that began approximately 12 Ma, suggesting a possible relationship between climate change and penguin evolution.
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Abstract
Tuatara are the sister taxon to the Squamata (including lizards and snakes) and are regarded as the most distinctive surviving reptilian genus. They are currently inhabits on offshore islands around New Zealand and have been recognized as a species in need of active conservation management. In this study, we report a total number of five nearly complete mitochondrial genomes, which were sequenced by Sanger and Next Generation DNA sequencing methods. Our phylogenomic analysis revealed distinct clustering of tuatara populations from the north and south islands of New Zealand.
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Affiliation(s)
- Elmira Mohandesan
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland , Auckland , New Zealand and
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Shepherd LD, Tennyson AJD, Lambert DM. Using ancient DNA to enhance museum collections: a case study of rare kiwi (Apteryxspp.) specimens. J R Soc N Z 2013. [DOI: 10.1080/03036758.2012.732585] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
In contrast to molecular rates for neutral mitochondrial sequences, rates for constrained sites (including nonsynonymous sites, D-loop, and RNA) in the mitochondrial genome are known to vary with the time frame used for their estimation. Here, we examined this issue for the nuclear genomes using single-nucleotide polymorphisms (SNPs) from six complete human genomes of individuals belonging to different populations. We observed a strong time-dependent distribution of nonsynonymous SNPs (nSNPs) in highly constrained genes. Typically, the proportion of young nSNPs specific to a single population was found to be up to three times higher than that of the ancient nSNPs shared between diverse human populations. In contrast, this trend disappeared, and a uniform distribution of young and old nSNPs was observed in genes under relaxed selective constraints. This suggests that because mutations in constrained genes are highly deleterious, they are removed over time, resulting in a relative overabundance of young nSNPs. In contrast, mutations in genes under relaxed constraints are nearly neutral, which leads to similar proportions of young and old SNPs. These results could be useful to researchers aiming to select appropriate genes or genomic regions for estimating evolutionary rates and species or population divergence times.
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McCallum J, Hall S, Lissone I, Anderson J, Huynen L, Lambert DM. Highly informative ancient DNA 'snippets' for New Zealand moa. PLoS One 2013; 8:e50732. [PMID: 23341875 PMCID: PMC3547012 DOI: 10.1371/journal.pone.0050732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. METHODOLOGY/PRINCIPAL FINDINGS By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. CONCLUSIONS/SIGNIFICANCE Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.
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Affiliation(s)
- Jonathan McCallum
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Samantha Hall
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Iman Lissone
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Jennifer Anderson
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
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Shepherd LD, Worthy TH, Tennyson AJD, Scofield RP, Ramstad KM, Lambert DM. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp.) and a recently extinct lineage of spotted kiwi. PLoS One 2012; 7:e42384. [PMID: 22876319 PMCID: PMC3410920 DOI: 10.1371/journal.pone.0042384] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/04/2012] [Indexed: 11/18/2022] Open
Abstract
The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.
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Affiliation(s)
- Lara D Shepherd
- Allan Wilson Centre, Massey University, Auckland, New Zealand.
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Abstract
During the summer months, Adélie penguins represent the dominant biomass of terrestrial Antarctica. Literally millions of individuals nest in ice-free areas around the coast of the continent. Hence, these modern populations of Adélie penguins have often been championed as an ideal biological indicator of ecological and environmental changes that we currently face. In addition, Adélie penguins show an extraordinary record of sub-fossil remains, dating back to the late Pleistocene. At this time, temperatures were much lower than now. Hence, this species offers unique long-term information, at both the genomic and ecological levels, about how a species has responded to climate change over more than 40 000 years.
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Affiliation(s)
- Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, New Zealand
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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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Heupink TH, van den Hoff J, Lambert DM. King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times. Biol Lett 2012; 8:586-9. [PMID: 22357937 DOI: 10.1098/rsbl.2012.0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.
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Affiliation(s)
- Tim H Heupink
- Environmental Futures Centre and Australian Rivers Institute, Griffith University, Nathan, Australia
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Abstract
Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, whereas a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. Although the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9–15 times higher than that estimated using the human–chimpanzee pair, in contrast, the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous to synonymous sites estimated using intra- and interspecific comparisons vary up to nine times, which corroborates our results independent of calibration times.
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Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Romero IG, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 2011; 334:94-8. [PMID: 21940856 PMCID: PMC3991479 DOI: 10.1126/science.1211177] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
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Affiliation(s)
- Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Xiaosen Guo
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Wang
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kirk E. Lohmueller
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Skotte
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stinus Lindgreen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Thibaut Jombart
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Toomas Kivisild
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Weiwei Zhai
- Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
| | - Anders Eriksson
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Silvana Tridico
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Ene Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Kasper Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - María C. Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - J. Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Avenida Universidad s/n Chamilpa 62210, Cuernavaca, Morelos, Mexico
| | - Craig Muller
- Goldfields Land and Sea Council Aboriginal Corporation, 14 Throssell Street, Kalgoorlie, Western Australia 6430, Australia
| | - Joe Dortch
- Archaeology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Agata Wesolowska
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Monika Karmin
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Lucy A. Weinert
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Bo Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuaishuai Tai
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Fei Xiao
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Japan
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, 3000 Bern 9, Switzerland
| | - Aashish R. Jha
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Université de Toulouse (Paul Sabatier)–CNRS UMR 5288, 31073 Toulouse Cedex 3, France
| | - Peter de Knijff
- Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Andrea B Migliano
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
- Department of Anthropology, University College London, London WC1E 6BT, UK
| | | | - Karsten Kristiansen
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland 4111, Australia
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Forster
- Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, UK
- Institute for Forensic Genetics, D-48161 Münster, Germany
| | | | - Olaf Nehlich
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Bunce
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Michael Richards
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anders Krogh
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Marta M. Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Francois Balloux
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Richard Villems
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
- Estonian Academy of Sciences, 6 Kohtu Street, 10130 Tallinn, Estonia
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jun Wang
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
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Abstract
While flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochrome c oxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA-based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.
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Affiliation(s)
- John Waugh
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Natural Sciences, Massey University, Private Bag 102 904, NSMC, Auckland, New Zealand.
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Abstract
Feather cloaks ("kakahu"), particularly those adorned with kiwi feathers, are treasured items or "taonga" to the Māori people of "Aotearoa"/New Zealand. They are considered iconic expression of Māori culture. Despite their status, much of our knowledge of the materials used to construct cloaks, the provenance of cloaks, and the origins of cloak making itself, has been lost. We used ancient DNA methods to recover mitochondrial DNA sequences from 849 feather samples taken from 109 cloaks. We show that almost all (>99%) of the cloaks were constructed using feathers from North Island brown kiwi. Molecular sexing of nuclear DNA recovered from 92 feather cloak samples also revealed that the sex ratio of birds deviated from a ratio of 1:1 observed in reference populations. Additionally, we constructed a database of 185 mitochondrial control region DNA sequences of kiwi feathers comprising samples collected from 26 North Island locations together with data available from the literature. Genetic subdivision (G(ST)), nucleotide subdivision (N(ST)) and Spatial Analysis of Molecular Variants (SAMOVA) analyses revealed high levels of genetic structuring in North Island brown kiwi. Together with sequence data from previously studied ancient and modern kiwi samples, we were able to determine the geographic provenance of 847 cloak feathers from 108 cloaks. A surprising proportion (15%) of cloaks were found to contain feathers from different geographic locations, providing evidence of kiwi trading among Māori tribes or organized hunting trips into other tribal areas. Our data also suggest that the east of the North Island of New Zealand was the most prolific of all kiwi cloak making areas, with over 50% of all cloaks analyzed originating from this region. Similar molecular approaches have the potential to discover a wealth of lost information from artifacts of endemic cultures worldwide.
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Affiliation(s)
- K Hartnup
- Institute of Natural Sciences, Massey University, Auckland, New Zealand
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Abstract
Background The King Island Emu (Dromaius ater) of Australia is one of several extinct emu taxa whose taxonomic relationship to the modern Emu (D. novaehollandiae) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu. Methodology and Results We investigated the evolutionary relationships between the King Island and modern Emu by the recovery of both nuclear and mitochondrial DNA sequences from sub-fossil remains. The complete mitochondrial control (1,094 bp) and cytochrome c oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu. Conclusions These data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled.
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Affiliation(s)
- Tim H. Heupink
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
- * E-mail:
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35
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Subramanian S, Huynen L, Millar CD, Lambert DM. Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi. BMC Evol Biol 2010; 10:387. [PMID: 21156082 PMCID: PMC3009673 DOI: 10.1186/1471-2148-10-387] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 12/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. RESULTS Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. CONCLUSIONS The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.
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Affiliation(s)
- Sankar Subramanian
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - David M Lambert
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
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Labar G, Wouters J, Lambert DM. A review on the monoacylglycerol lipase: at the interface between fat and endocannabinoid signalling. Curr Med Chem 2010; 17:2588-607. [PMID: 20491633 DOI: 10.2174/092986710791859414] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 05/18/2010] [Indexed: 11/22/2022]
Abstract
Together with anandamide, 2-arachidonoylglycerol (2-AG) constitutes one of the main representatives of a family of endogenous lipids known as endocannabinoids. These act by binding to CB(1) and CB(2) cannabinoid receptors, the molecular target of the psychoactive compound Delta(9)-THC, both in the periphery and in the central nervous system, where they behave as retrograde messengers to modulate synaptic transmission. These last years, evidence has accumulated to demonstrate the lead role played by the monoacylglycerol lipase (MAGL) in the regulation of 2-arachidonoylglycerol (2-AG) levels. Considering the numerous physiological functions played by this endocannabinoid, MAGL is now considered a promising target for therapeutics, as inhibitors of this enzyme could reveal useful for the treatment of pain and inflammatory disorders, as well as in cancer research, among others. Here we review the milestones that punctuated MAGL history, from its discovery to recent advances in the field of inhibitors development. An emphasis is given on the recent elucidation of the tridimensional structure of the enzyme, which could offer new opportunities for rational drug design.
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Affiliation(s)
- G Labar
- Université Catholique de Louvain, Louvain Drug Research Institute, Cannabinoid and Endocannabinoid Research Group, Pharmaceutical Chemistry Dpt, Avenue E. Mounier, 73.40, 1200 Brussels, Belgium
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Lambert DM. It is the nature of the world in which we currently live. J Oral Maxillofac Surg 2010; 68:708-9. [PMID: 20171498 DOI: 10.1016/j.joms.2009.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 11/04/2009] [Indexed: 12/01/2022]
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Lambert DM, Shepherd LD, Huynen L, Beans-Picón G, Walter GH, Millar CD. The molecular ecology of the extinct New Zealand Huia. PLoS One 2009; 4:e8019. [PMID: 19946368 PMCID: PMC2777306 DOI: 10.1371/journal.pone.0008019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 10/19/2009] [Indexed: 11/29/2022] Open
Abstract
The extinct Huia (Heteralocha acutirostris) of New Zealand represents the most extreme example of beak dimorphism known in birds. We used a combination of nuclear genotyping methods, molecular sexing, and morphometric analyses of museum specimens collected in the late 19(th) and early 20(th) centuries to quantify the sexual dimorphism and population structure of this extraordinary species. We report that the classical description of Huia as having distinctive sex-linked morphologies is not universally correct. Four Huia, sexed as females had short beaks and, on this basis, were indistinguishable from males. Hence, we suggest it is likely that Huia males and females were indistinguishable as juveniles and that the well-known beak dimorphism is the result of differential beak growth rates in males and females. Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. In addition, using mitochondrial hypervariable region sequences, and likely mutation rates and generation times, we estimated that the census population size of Huia was moderately high. We conclude that the social organization and limited powers of flight did not result in a highly structured population.
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Affiliation(s)
- David M Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia.
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Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM. High mitogenomic evolutionary rates and time dependency. Trends Genet 2009; 25:482-6. [PMID: 19836098 DOI: 10.1016/j.tig.2009.09.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 12/18/2022]
Abstract
Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.
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Affiliation(s)
- Sankar Subramanian
- Griffith School of Environment, Griffith University, 170 Kessels Road, Nathan, Qld 4111, Australia
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Cani PD, Possemiers S, Van de Wiele T, Guiot Y, Everard A, Rottier O, Geurts L, Naslain D, Neyrinck A, Lambert DM, Muccioli GG, Delzenne NM. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut 2009; 58:1091-103. [PMID: 19240062 PMCID: PMC2702831 DOI: 10.1136/gut.2008.165886] [Citation(s) in RCA: 1740] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Obese and diabetic mice display enhanced intestinal permeability and metabolic endotoxaemia that participate in the occurrence of metabolic disorders. Our recent data support the idea that a selective increase of Bifidobacterium spp. reduces the impact of high-fat diet-induced metabolic endotoxaemia and inflammatory disorders. Here, we hypothesised that prebiotic modulation of gut microbiota lowers intestinal permeability, by a mechanism involving glucagon-like peptide-2 (GLP-2) thereby improving inflammation and metabolic disorders during obesity and diabetes. METHODS Study 1: ob/ob mice (Ob-CT) were treated with either prebiotic (Ob-Pre) or non-prebiotic carbohydrates as control (Ob-Cell). Study 2: Ob-CT and Ob-Pre mice were treated with GLP-2 antagonist or saline. Study 3: Ob-CT mice were treated with a GLP-2 agonist or saline. We assessed changes in the gut microbiota, intestinal permeability, gut peptides, intestinal epithelial tight-junction proteins ZO-1 and occludin (qPCR and immunohistochemistry), hepatic and systemic inflammation. RESULTS Prebiotic-treated mice exhibited a lower plasma lipopolysaccharide (LPS) and cytokines, and a decreased hepatic expression of inflammatory and oxidative stress markers. This decreased inflammatory tone was associated with a lower intestinal permeability and improved tight-junction integrity compared to controls. Prebiotic increased the endogenous intestinotrophic proglucagon-derived peptide (GLP-2) production whereas the GLP-2 antagonist abolished most of the prebiotic effects. Finally, pharmacological GLP-2 treatment decreased gut permeability, systemic and hepatic inflammatory phenotype associated with obesity to a similar extent as that observed following prebiotic-induced changes in gut microbiota. CONCLUSION We found that a selective gut microbiota change controls and increases endogenous GLP-2 production, and consequently improves gut barrier functions by a GLP-2-dependent mechanism, contributing to the improvement of gut barrier functions during obesity and diabetes.
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Affiliation(s)
- P D Cani
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium.
| | - S Possemiers
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - T Van de Wiele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Y Guiot
- Department of Pathology, Université catholique de Louvain, Brussels, Belgium
| | - A Everard
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - O Rottier
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - L Geurts
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - D Naslain
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium,Medicinal Chemistry and Radiopharmacy Unit, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - A Neyrinck
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - D M Lambert
- Medicinal Chemistry and Radiopharmacy Unit, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - G G Muccioli
- Laboratory of Chemical and Physico-chemical Analysis of Drugs (CHAM), Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - N M Delzenne
- Unit of Pharmacokinetics, Metabolism, Nutrition and Toxicology, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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Seabrook-Davison M, Huynen L, Lambert DM, Brunton DH. Ancient DNA resolves identity and phylogeny of New Zealand's extinct and living quail (Coturnix sp.). PLoS One 2009; 4:e6400. [PMID: 19636374 PMCID: PMC2712072 DOI: 10.1371/journal.pone.0006400] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 06/23/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. METHODOLOGY/PRINCIPAL FINDINGS Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. CONCLUSION/SIGNIFICANCE Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.
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Affiliation(s)
- Mark Seabrook-Davison
- Ecology and Conservation Group, Institute of Natural Sciences, Massey University, Auckland, New Zealand.
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Hay JM, Sarre SD, Lambert DM, Allendorf FW, Daugherty CH. Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9952-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Millar CD, Dodd A, Anderson J, Gibb GC, Ritchie PA, Baroni C, Woodhams MD, Hendy MD, Lambert DM. Mutation and evolutionary rates in adélie penguins from the antarctic. PLoS Genet 2008; 4:e1000209. [PMID: 18833304 PMCID: PMC2546446 DOI: 10.1371/journal.pgen.1000209] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 08/25/2008] [Indexed: 12/15/2022] Open
Abstract
Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (micro) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29-0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.
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Affiliation(s)
- Craig D. Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Dodd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Jennifer Anderson
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Gillian C. Gibb
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Peter A. Ritchie
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Carlo Baroni
- Dipartmento Scienze della Terra, Università di Pisa, Pisa, Italy
- Consiglio Nazionale Ricerche, Centro Studio Geologia Strutturale, Pisa, Italy
| | - Michael D. Woodhams
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - Michael D. Hendy
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - David M. Lambert
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
- * E-mail:
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Lawrence HA, Taylor GA, Crockett DE, Millar CD, Lambert DM. New genetic approach to detecting individuals of rare and endangered species. Conserv Biol 2008; 22:1267-1276. [PMID: 18717692 DOI: 10.1111/j.1523-1739.2008.01021.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Many rare and endangered species are difficult to locate, observe, and study. Consequently, many individuals, breeding pairs, and even populations of such species could remain undetected. Genetic markers can potentially be used to detect the existence of undiscovered individuals and populations, and we propose a method to do so that requires 3 conditions. First, sampling of the known population(s) of the target species must be comprehensive. Second, the species must display a reasonable level of philopatry and genetic structuring. Third, individuals must be able to be caught outside of breeding locations (e.g., at courtship or feeding areas, in flight), and the level of recapture must be reasonably high. We applied our method to the Chatham Island Taiko (Pterodroma magentae), one of the world's most endangered seabirds. We sequenced the Taiko mitochondrial cytochrome b gene and both copies of a fragment of the duplicated domain I of the control region. Twenty-one haplotypes were revealed, including 4 (19%) not found in birds at known burrows. These results suggest there are more burrow groups yet to be located. The species is a pelagic gadfly petrel that inhabits land only in the breeding season during which it is nocturnal and nests in burrows. Taiko burrows are situated in dense forest in a remote area of Chatham Island, and are consequently difficult to locate and study. It is important that all Taiko burrows be discovered to enable monitoring and protection of the birds from exotic predators.
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Affiliation(s)
- Hayley A Lawrence
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Albany, Private Bag 102904, NSMC, Auckland, New Zealand
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Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM. New developments in ancient genomics. Trends Ecol Evol 2008; 23:386-93. [PMID: 18501471 DOI: 10.1016/j.tree.2008.04.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 03/27/2008] [Accepted: 04/04/2008] [Indexed: 11/29/2022]
Abstract
Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.
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Affiliation(s)
- Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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Lawrence HA, Taylor GA, Millar CD, Lambert DM. High mitochondrial and nuclear genetic diversity in one of the world’s most endangered seabirds, the Chatham Island Taiko (Pterodroma magentae). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9471-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wallace VCJ, Segerdahl AR, Lambert DM, Vandevoorde S, Blackbeard J, Pheby T, Hasnie F, Rice ASC. The effect of the palmitoylethanolamide analogue, palmitoylallylamide (L-29) on pain behaviour in rodent models of neuropathy. Br J Pharmacol 2007; 151:1117-28. [PMID: 17558434 PMCID: PMC2042941 DOI: 10.1038/sj.bjp.0707326] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND PURPOSE Cannabinoids are associated with analgesia in acute and chronic pain states. A spectrum of central cannabinoid (CB(1)) receptor-mediated motor and psychotropic side effects limit their therapeutic potential. Here, we investigate the analgesic effect of the palmitoylethanolamide (PEA) analogue, palmitoylallylamide (L-29), which via inhibition of fatty acid amide hydrolase (FAAH) may potentiate endocannabinoids thereby avoiding psychotropic side effects. EXPERIMENTAL APPROACH The in vivo analysis of the effect of L-29 on measures of pain behaviour in three rat models of neuropathic pain. KEY RESULTS Systemically administered L-29 (10 mg kg(-1)) reduced hypersensitivity to mechanical and thermal stimuli in the partial sciatic nerve injury (PSNI) model of neuropathic pain; and mechanical hypersensitivity in a model of antiretroviral (ddC)-associated hypersensitivity and a model of varicella zoster virus (VZV)-associated hypersensitivity. The effects of L-29 were comparable to those of gabapentin (50 mg kg(-1)). The CB(1) receptor antagonist SR141716a (1 mg kg(-1)) and the CB(2) receptor antagonist SR144528 (1 mg kg(-1)) reduced the effect of L-29 on hypersensitivity in the PSNI and ddC models, but not in the VZV model. The peroxisome proliferator-activated receptor-alpha antagonist, MK-886 (1 mg kg(-1)), partially attenuated the effect of L-29 on hypersensitivity in the PSNI model. L-29 (10 mg kg(-1)) significantly attenuated thigmotactic behaviour in the open field arena without effect on locomotor activity. CONCLUSIONS AND IMPLICATIONS L-29 produces analgesia in a range of neuropathic pain models. This presents L-29 as a novel analgesic compound that may target the endogenous cannabinoid system while avoiding undesirable side effects associated with direct cannabinoid receptor activation.
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Affiliation(s)
- V C J Wallace
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
| | - A R Segerdahl
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
| | - D M Lambert
- Unite de Chimie Pharmaceutique et de Radiopharmacie, Universite Catholique de Louvain, Avenue Mounier Brussels, Belgium
| | - S Vandevoorde
- Unite de Chimie Pharmaceutique et de Radiopharmacie, Universite Catholique de Louvain, Avenue Mounier Brussels, Belgium
| | - J Blackbeard
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
| | - T Pheby
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
| | - F Hasnie
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
| | - A S C Rice
- Pain Research Group, Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus London, UK
- Author for correspondence:
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Labar G, Vliet FV, Wouters J, Lambert DM. A MBP-FAAH fusion protein as a tool to produce human and rat fatty acid amide hydrolase: expression and pharmacological comparison. Amino Acids 2007; 34:127-33. [PMID: 17476568 DOI: 10.1007/s00726-007-0540-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 02/23/2007] [Indexed: 11/30/2022]
Abstract
Fatty acid amide hydrolase (FAAH), a membrane-anchored enzyme responsible for the termination of endocannabinoid signalling, is an attractive target for treating conditions such as pain and anxiety. Inhibitors of the enzyme, optimized using rodent FAAH, are known but their pharmacology and medicinal chemistry properties on the human FAAH are missing. Therefore recombinant human enzyme would represent a powerful tool to evaluate new drug candidates. However, the production of high amounts of enzyme is hampered by the known refractiveness of FAAH to overexpression. Here, we report the successful overexpression of rat and human FAAH as a fusion to the E. coli maltose-binding protein, retaining catalytic properties of native FAAH. Several known FAAH inhibitors were tested and differences in their potencies toward the human and rat FAAH were found, underscoring the importance of using a human FAAH in the development of inhibitors.
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Affiliation(s)
- G Labar
- Unité de Chimie pharmaceutique et de Radiopharmacie, Ecole de Pharmacie, Faculté de Médecine, Université catholique de Louvain, Bruxelles, Belgium
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Shepherd LD, Lambert DM. The relationships and origins of the New Zealand wattlebirds (Passeriformes, Callaeatidae) from DNA sequence analyses. Mol Phylogenet Evol 2006; 43:480-92. [PMID: 17369056 DOI: 10.1016/j.ympev.2006.12.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 09/12/2006] [Accepted: 12/09/2006] [Indexed: 11/21/2022]
Abstract
The monophyly of the endemic New Zealand wattlebirds (Callaeatidae) was examined through the sequencing of nuclear RAG-1 and c-mos genes and comparison to other passerine sequences. The New Zealand wattlebirds were strongly supported to be monophyletic and were nested within Corvida. An estimate for the time of divergence of the New Zealand wattlebirds indicated that the ancestors of this family arrived via transoceanic dispersal after the separation of New Zealand from Gondwana. Long branches separated the three New Zealand wattlebird genera from one another and relationships among them were unresolved, even in analyses including a further 1.5 kb of mitochondrial DNA sequences. However, most of the analyses supported either a basally diverging huia or kokako.
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Affiliation(s)
- Lara D Shepherd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
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