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Setti PG, Deon GA, Zeni Dos Santos R, Goes CAG, Garnero ADV, Gunski RJ, de Oliveira EHC, Porto-Foresti F, de Freitas TRO, Silva FAO, Liehr T, Utsunomia R, Kretschmer R, de Bello Cioffi M. Evolution of bird sex chromosomes: a cytogenomic approach in Palaeognathae species. BMC Ecol Evol 2024; 24:51. [PMID: 38654159 PMCID: PMC11036779 DOI: 10.1186/s12862-024-02230-5] [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: 12/07/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa). RESULTS From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu's sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats. CONCLUSION The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.
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Affiliation(s)
- Príncia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | | | | | - Analía Del Valle Garnero
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - Fábio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | | | - Fábio Augusto Oliveira Silva
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, 07747, Jena, Germany.
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, 96.010-610, Pelotas, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
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Westbury MV, De Cahsan B, Shepherd LD, Holdaway RN, Duchene DA, Lorenzen ED. Genomic insights into the evolutionary relationships and demographic history of kiwi. PLoS One 2022; 17:e0266430. [PMID: 36215252 PMCID: PMC9550048 DOI: 10.1371/journal.pone.0266430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
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Affiliation(s)
- Michael V. Westbury
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MVW); (EDL)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Richard N. Holdaway
- Palaecol Research Ltd, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | | | - Eline D. Lorenzen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MVW); (EDL)
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3
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Yazdi HP, Silva WTAF, Suh A. Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes. Genes (Basel) 2020; 11:E1153. [PMID: 33007827 PMCID: PMC7601716 DOI: 10.3390/genes11101153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023] Open
Abstract
The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.
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Affiliation(s)
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK;
- Department of Organismal Biology—Systematic Biology, Uppsala University, SE-752 36 Uppsala, Sweden
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4
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Bailleul R, Curantz C, Desmarquet-Trin Dinh C, Hidalgo M, Touboul J, Manceau M. Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning. PLoS Biol 2019; 17:e3000448. [PMID: 31577791 PMCID: PMC6791559 DOI: 10.1371/journal.pbio.3000448] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 10/14/2019] [Accepted: 09/04/2019] [Indexed: 01/22/2023] Open
Abstract
The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds. A survey of plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins shows that their formation depends on a species-specific prepattern in the embryo and demonstrates that universal mechanisms govern the timely emergence of natural patterns in birds.
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Affiliation(s)
- Richard Bailleul
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- Sorbonne Université, UPMC Univ Paris 06, Laboratoire Jacques-Louis Lions, Paris, France
| | - Camille Curantz
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- Sorbonne Université, UPMC Univ Paris 06, Laboratoire Jacques-Louis Lions, Paris, France
| | - Carole Desmarquet-Trin Dinh
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
| | - Magdalena Hidalgo
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
| | - Jonathan Touboul
- Department of Mathematics and Volen National Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail: (MM); (JT)
| | - Marie Manceau
- Center for Interdisciplinary Research in Biology, CNRS UMR7241, INSERM U1050, Collège de France, Paris Sciences et Lettres University, Paris, France
- * E-mail: (MM); (JT)
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5
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Le Duc D, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, Ongyerth M, Bitarello BD, Schiöth HB, Hofreiter M, Stadler PF, Prüfer K, Lambert D, Kelso J, Schöneberg T. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol 2015; 16:147. [PMID: 26201466 PMCID: PMC4511969 DOI: 10.1186/s13059-015-0711-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [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: 02/13/2015] [Accepted: 07/01/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. RESULTS We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. CONCLUSIONS The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.
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Affiliation(s)
- Diana Le Duc
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Arunkumar Krishnan
- Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden.
| | - Markus Sällman Almén
- Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden.
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, 4111, Australia.
| | - Sonja J Prohaska
- Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany.
| | - Matthias Ongyerth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, 05508-090, Brazil.
| | - Helgi B Schiöth
- Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Box 593, Husargatan 3, Uppsala, 751 24, Sweden.
| | - Michael Hofreiter
- Adaptive Evolutionary Genomics, Institute for Biochemistry and Biology, University Potsdam, Potsdam, 14469, Germany.
| | - Peter F Stadler
- Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany.
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - David Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, 4111, Australia.
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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6
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Ramstad KM, Colbourne RM, Robertson HA, Allendorf FW, Daugherty CH. Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii). Proc Biol Sci 2013; 280:20130576. [PMID: 23677342 PMCID: PMC3673049 DOI: 10.1098/rspb.2013.0576] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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] [Received: 03/05/2013] [Accepted: 04/16/2013] [Indexed: 01/24/2023] Open
Abstract
We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D'Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D'Urville birds among extant LSK. The Ne/NC ratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size.
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Affiliation(s)
- Kristina M. Ramstad
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Rogan M. Colbourne
- Department of Conservation, Research and Development Group, PO Box 10-420, Wellington, New Zealand
| | - Hugh A. Robertson
- Department of Conservation, Research and Development Group, PO Box 10-420, Wellington, New Zealand
| | - Fred W. Allendorf
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Charles H. Daugherty
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
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Weiser EL, Grueber CE, Jamieson IG. Simulating retention of rare alleles in small populations to assess management options for species with different life histories. Conserv Biol 2013; 27:335-344. [PMID: 23330669 DOI: 10.1111/cobi.12011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 08/11/2012] [Indexed: 06/01/2023]
Abstract
Preserving allelic diversity is important because it provides the capacity for adaptation and thus enables long-term population viability. Allele retention is difficult to predict in animals with overlapping generations, so we used a new computer model to simulate retention of rare alleles in small populations of 3 species with contrasting life-history traits: North Island Brown Kiwi (Apteryx mantelli; monogamous, long-lived), North Island Robins (Petroica longipes; monogamous, short-lived), and red deer (Cervus elaphus; polygynous, moderate lifespan). We simulated closed populations under various demographic scenarios and assessed the amounts of artificial immigration needed to achieve a goal of retaining 90% of selectively neutral rare alleles (frequency in the source population = 0.05) after 10 generations. The number of immigrants per generation required to meet the genetic goal ranged from 11 to 30, and there were key similarities and differences among species. None of the species met the genetic goal without immigration, and red deer lost the most allelic diversity due to reproductive skew among polygynous males. However, red deer required only a moderate rate of immigration relative to the other species to meet the genetic goal because nonterritorial breeders had a high turnover. Conversely, North Island Brown Kiwi needed the most immigration because the long lifespan of locally produced territorial breeders prevented a large proportion of immigrants from recruiting. In all species, the amount of immigration needed generally decreased with an increase in carrying capacity, survival, or reproductive output and increased as individual variation in reproductive success increased, indicating the importance of accurately quantifying these parameters to predict the effects of management. Overall, retaining rare alleles in a small, isolated population requires substantial investment of management effort. Use of simulations to explore strategies optimized for the populations in question will help maximize the value of this effort..
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Affiliation(s)
- Emily L Weiser
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
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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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10
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Wood JR, Wilmshurst JM, Wagstaff SJ, Worthy TH, Rawlence NJ, Cooper A. High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus). PLoS One 2012; 7:e40025. [PMID: 22768206 PMCID: PMC3386916 DOI: 10.1371/journal.pone.0040025] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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: 03/30/2012] [Accepted: 05/30/2012] [Indexed: 11/23/2022] Open
Abstract
Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand’s largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 14C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.
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Affiliation(s)
- Jamie R Wood
- Landcare Research, Lincoln, Canterbury, New Zealand.
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11
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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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12
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Steiger SS, Fidler AE, Kempenaers B. Evidence for increased olfactory receptor gene repertoire size in two nocturnal bird species with well-developed olfactory ability. BMC Evol Biol 2009; 9:117. [PMID: 19467156 PMCID: PMC2701422 DOI: 10.1186/1471-2148-9-117] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [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: 10/21/2008] [Accepted: 05/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In vertebrates, the molecular basis of the sense of smell is encoded by members of a large gene family, namely olfactory receptor (OR) genes. Both the total number of OR genes and the proportion of intact OR genes in a genome may indicate the importance of the sense of smell for an animal. There is behavioral, physiological, and anatomical evidence that some bird species, in particular nocturnal birds, have a well developed sense of smell. Therefore, we hypothesized that nocturnal birds with good olfactory abilities have evolved (i) more OR genes and (ii) more intact OR genes than closely related and presumably less 'olfaction-dependent' day-active avian taxa. RESULTS We used both non-radioactive Southern hybridization and PCR with degenerate primers to investigate whether two nocturnal bird species that are known to rely on olfactory cues, the brown kiwi (Apteryx australis) and the kakapo (Strigops habroptilus), have evolved a larger OR gene repertoire than their day-active, closest living relatives (for kiwi the emu Dromaius novaehollandiae, rhea Rhea americana, and ostrich Struthio camelus and for kakapo the kaka Nestor meridionalis and kea Nestor notabilis). We show that the nocturnal birds did not have a significantly higher proportion of intact OR genes. However, the estimated total number of OR genes was larger in the two nocturnal birds than in their relatives. CONCLUSION Our results suggest that ecological niche adaptations such as daily activity patterns may have shaped avian OR gene repertoires.
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Affiliation(s)
- Silke S Steiger
- Department of Behavioural Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany
| | - Andrew E Fidler
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson 7042, New Zealand
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max-Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany
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13
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Harshman J, Braun EL, Braun MJ, Huddleston CJ, Bowie RCK, Chojnowski JL, Hackett SJ, Han KL, Kimball RT, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Steppan SJ, Witt CC, Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proc Natl Acad Sci U S A 2008; 105:13462-7. [PMID: 18765814 PMCID: PMC2533212 DOI: 10.1073/pnas.0803242105] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [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] [Received: 04/02/2008] [Indexed: 11/18/2022] Open
Abstract
Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.
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Affiliation(s)
- John Harshman
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
- 4869 Pepperwood Way, San Jose, CA 95124
| | - Edward L. Braun
- Department of Zoology, University of Florida, Gainesville, FL 32611
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
| | - Rauri C. K. Bowie
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720
- Department of Science and Technology/National Resource Foundation Centre of Excellence at the Percy FitzPatrick Institute, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
| | | | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
| | - Kin-Lan Han
- Department of Zoology, University of Florida, Gainesville, FL 32611
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742
| | | | - Ben D. Marks
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
| | - Kathleen J. Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202
| | - Sushma Reddy
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306; and
| | - Christopher C. Witt
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131
| | - Tamaki Yuri
- Department of Zoology, University of Florida, Gainesville, FL 32611
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
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14
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Tsuda Y, Nishida-Umehara C, Ishijima J, Yamada K, Matsuda Y. Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds. Chromosoma 2007; 116:159-73. [PMID: 17219176 DOI: 10.1007/s00412-006-0088-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [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: 07/03/2006] [Revised: 10/07/2006] [Accepted: 10/29/2006] [Indexed: 11/26/2022]
Abstract
To clarify the process of avian sex chromosome differentiation in palaeognathous birds, we performed molecular and cytogenetic characterization of W chromosome-specific repetitive DNA sequences for elegant crested tinamou (Eudromia elegans, Tinamiformes) and constructed comparative cytogenetic maps of the Z and W chromosomes with nine chicken Z-linked gene homologues for E. elegans and ostrich (Struthio camelus, Struthioniformes). A novel family of W-specific repetitive sequences isolated from E. elegans was found to be composed of guanine- and cytosine-rich 293-bp elements that were tandemly arrayed in the genome as satellite DNA. No nucleotide sequence homologies were found for the Struthioniformes and neognathous birds. The comparative cytogenetic maps of the Z and W chromosomes of E. elegans and S. camelus revealed that there are partial deletions in the proximal regions of the W chromosomes in the two species, and the W chromosome is more differentiated in E. elegans than in S. camelus. These results suggest that a deletion firstly occurred in the proximal region close to the centromere of the acrocentric proto-W chromosome and advanced toward the distal region. In E. elegans, the W-specific repeated sequence elements were amplified site-specifically after deletion of a large part of the W chromosome occurred.
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Affiliation(s)
- Yayoi Tsuda
- Laboratory of Cytogenetics, Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, North 10 West 8, Sapporo 060-0810, Japan
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15
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Affiliation(s)
- Jonathan M Waters
- Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand.
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16
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Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SYW, Hansen AJ, Willerslev E. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 2005; 172:733-41. [PMID: 16299392 PMCID: PMC1456239 DOI: 10.1534/genetics.105.049718] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [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: 01/12/2023] Open
Abstract
To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine --> guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine --> adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.
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Affiliation(s)
- Jonas Binladen
- Ancient DNA and Evolution Group, Centre for Ancient Genetics, Niels Bohr Institute, University of Copenhagen, Denmark
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17
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Abstract
The tinamid bird Nothura maculosa, along with other species of the order Tinamiformes and all of the existent ratites, form the infraclass Paleognathae, the most primitive living birds. Previous work has shown that in all studied Neognathae, the ZW pair shows strictly localized recombination in a very short pseudoautosomal region, while in paleognath birds, the ZW pairs have mostly free recombination. The present observations show that the ZW pair of N. maculosa has a recombination pattern departing from both neognaths and other Paleognath birds, as there is a single crossover but occurring at random points along a significant part of the long arm of the W chromosome. This recombination pattern agrees with the presence of intercalary and terminal heterochromatin in the W chromosome, suggesting an exceptional, additional step of recombination suppression.
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Affiliation(s)
- M I Pigozzi
- CIR, Facultad de Medicina, Buenos Aires, Argentina
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18
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Baker AJ, Huynen LJ, Haddrath O, Millar CD, Lambert DM. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand. Proc Natl Acad Sci U S A 2005; 102:8257-62. [PMID: 15928096 PMCID: PMC1149408 DOI: 10.1073/pnas.0409435102] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [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] [Received: 12/17/2004] [Accepted: 04/04/2005] [Indexed: 11/18/2022] Open
Abstract
The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximately 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.
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Affiliation(s)
- Allan J Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6.
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19
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Abstract
Until a few hundred years ago, New Zealand hosted several species of flightless ratite birds, collectively known as the moa. We have used mitochondrial sequence data for Dinornis, the largest of the moa, and new coalescent approaches to estimate its population size prior to human arrival ca. 1000-6000 years BP. We show that, as little as 1000 years ago, Dinornis numbered between 300,000 and 1.4 million and that the standing population of all moa species was ca. 3-12 million. This estimate is an order of magnitude larger than the accepted population estimate (ca. 159,000) for all moa species at the arrival of humans and suggests that moa numbers had already declined prior to human settlement.
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Affiliation(s)
- Neil J Gemmell
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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20
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Abstract
A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.
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Affiliation(s)
- D M Lambert
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, Auckland, New Zealand.
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21
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Shetty S, Kirby P, Zarkower D, Graves JAM. DMRT1 in a ratite bird: evidence for a role in sex determination and discovery of a putative regulatory element. Cytogenet Genome Res 2004; 99:245-51. [PMID: 12900571 DOI: 10.1159/000071600] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [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: 07/09/2002] [Accepted: 01/02/2003] [Indexed: 11/19/2022] Open
Abstract
Unlike mammals, birds have a ZZ male/ZW female sex-determining system. In most birds, the Z is large and gene rich, whereas the W is small and heterochromatic, but the ancient group of ratite birds are characterized by sex chromosomes that are virtually homomorphic. Any gene differentially present on the ratite Z and W is therefore a strong candidate for a sex-determining role. We have cloned part of the candidate bird sex-determining gene DMRT1 from the emu, a ratite bird, and have shown that it is expressed during the stages of development corresponding to gonadal differentiation in the chicken. The gene maps to the distal region of the Z short arm and is absent from the large W chromosome. Because most sequences on the emu W chromosome are shared with the Z, the Z-specific location constitutes strong evidence that differential dosage of DMRT1 is involved in sex determination in all birds. The sequence of emu DMRT1 has 88% homology with chicken DMRT1 and 65% with human DMRT1. Unexpectedly, an unexpressed 270-bp region in intron 3 of emu DMRT1 showed 90% homology with a sequence in the corresponding intron of human DMRT1. This extraordinarily high conservation across 300 million years of evolution suggests an important function, perhaps involved in control of DMRT1 expression and vertebrate sex determination.
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Affiliation(s)
- S Shetty
- Department of Genetics, La Trobe University, Bundoora, Victoria, Australia
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22
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Bunce M, Worthy TH, Ford T, Hoppitt W, Willerslev E, Drummond A, Cooper A. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 2003; 425:172-5. [PMID: 12968178 DOI: 10.1038/nature01871] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [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: 03/06/2003] [Accepted: 06/23/2003] [Indexed: 11/08/2022]
Abstract
The ratite moa (Aves; Dinornithiformes) were massive graviportal browsers weighing up to 250 kg (ref. 1) that dominated the New Zealand biota until their extinction approximately 500 yr ago. Despite an extensive Quaternary fossil record, moa taxonomy remains problematic and currently 11 species are recognized. Three Dinornis species were found throughout New Zealand and differed markedly in size (1-2 m height at back) and mass (from approximately 34 to 242 kg). Surprisingly, ancient mitochondrial DNA sequences show that the three species were genetically indistinguishable within each island, but formed separate North and South Island clades. Here we show, using the first sex-linked nuclear sequences from an extinct species, that on each island the three morphological forms actually represent just one species, whose size varied markedly according to sex and habitat. The largest females in this example of extreme reversed sexual size dimorphism were about 280% the weight and 150% the height of the largest males, which is unprecedented among birds and terrestrial mammals. The combination of molecular and palaeontological data highlights the difficulties of analysing extinct groups, even those with detailed fossil records.
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Affiliation(s)
- Michael Bunce
- Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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23
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Huynen L, Millar CD, Scofield RP, Lambert DM. Nuclear DNA sequences detect species limits in ancient moa. Nature 2003; 425:175-8. [PMID: 12968179 DOI: 10.1038/nature01838] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [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: 03/14/2003] [Accepted: 06/03/2003] [Indexed: 11/09/2022]
Abstract
Ancient DNA studies have typically used multi-copy mitochondrial DNA sequences. This is largely because single-locus nuclear genes have been difficult to recover from sub-fossil material, restricting the scope of ancient DNA research. Here, we have isolated single-locus nuclear DNA markers to assign the sex of 115 extinct moa and, in combination with a mitochondrial DNA phylogeny, tested competing hypotheses about the specific status of moa taxa. Moa were large ratite birds that showed extreme size variation both within and among species. For some taxa, this large variation was hypothesized to represent sexual dimorphism, while for others it was argued to reflect the existence of different species. Our results show that moa were characterized by extreme reverse sexual dimorphism and as a result we have been able to clarify the number of moa species. For example, we show that the three recognized 'species' of Dinornis comprised only two monophyletic groups and that two of these 'species' comprised individuals of one sex only. This study also illustrates that single-locus nuclear DNA sequences can be consistently recovered from ancient material.
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Affiliation(s)
- L Huynen
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, Auckland, New Zealand
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24
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Abstract
DNA-based sex tests now exist for many avian species. However, none of these tests are widely applicable to ratites. We present DNA sequence data for a locus that is W chromosome-linked in the kiwi, ostrich, cassowary, rhea, and emu. At the amino acid level, this sequence has significant homology to X-linked genes in platyfish and Caenorhabditis elegans. Polymerase chain reaction (PCR) primers designed to this locus allow the assignment of sex in all species of living ratites.
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Affiliation(s)
- Leon Huynen
- Institute of Molecular BioSciences and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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25
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Haddrath O, Baker AJ. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc Biol Sci 2001; 268:939-45. [PMID: 11370967 PMCID: PMC1088691 DOI: 10.1098/rspb.2001.1587] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.7] [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: 11/12/2022] Open
Abstract
The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.
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Affiliation(s)
- O Haddrath
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada.
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26
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Grützner F, Zend-Ajusch E, Stout K, Munsche S, Niveleau A, Nanda I, Schmid M, Haaf T. Chicken microchromosomes are hypermethylated and can be identified by specific painting probes. Cytogenet Cell Genet 2001; 93:265-9. [PMID: 11528124 DOI: 10.1159/000056996] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microdissection of single chicken microchromosomes (MICs) followed by degenerate oligonucleotide-primed (DOP) PCR allows the rapid generation of MIC-specific DNA libraries. Since some libraries derived from a single (or a few) chromosome(s) label the entire MIC fraction, the majority of chicken MICs share repetitive DNA sequences that are not found on the macrochromosomes. In evolutionarily distant bird species, MICs are invariably hypermethylated. Methylcytosine staining provides additional in situ evidence for the high gene content of MICs and strong compartmentalization of avian genomes.
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Affiliation(s)
- F Grützner
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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27
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Nishida-Umehara C, Fujiwara A, Ogawa A, Mizuno S, Abe S, Yoshida MC. Differentiation of Z and W chromosomes revealed by replication banding and FISH mapping of sex-chromosome-linked DNA markers in the cassowary (Aves, Ratitae). Chromosome Res 2000; 7:635-40. [PMID: 10628664 DOI: 10.1023/a:1009236103013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [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: 11/12/2022]
Abstract
We identified sex chromosomes of the double-wattled cassowary (Casuarius casuarius) by a replication banding method. The acrocentric Z chromosome, the fifth largest pair in males and slightly smaller W chromosome show no sign of heterochromatinization and share a nearly identical banding pattern in the distal half of the long arm. These chromosomes were further characterized by FISH with three probes linked either to Z or W chromosome in most avian species examined thus far. Contrary to the situation in the chicken, we obtained positive signals with Z-specific ZOV3 and W-specific EEO.6 in the distal region of both Z and W chromosomes. However, IREBP signals localized to the proximal half of the Z chromosome were not detected on the W chromosome. Thus, structural rearrangements such as deletions and inversions might have been the initial step of W chromosome differentiation from an ancestral homomorphic pair in this species.
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Affiliation(s)
- C Nishida-Umehara
- Chromosome Research Unit, Faculty of Science, Hokkaido University, Sapporo, Japan
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Taylor EL, Vercoe P, Cockrem J, Groth D, Wetherall JD, Martin GB. Isolation and characterization of microsatellite loci in the emu, Dromaius novaehollandiae, and cross-species amplification within Ratitae. Mol Ecol 1999; 8:1963-4. [PMID: 10620242 DOI: 10.1046/j.1365-294x.1999.00778-4.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- E L Taylor
- Department of Molecular Genetics, School of Biomedical Sciences, Curtin University, Bentley, Western Australia.
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