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Kessler AE, Santos MA, Flatz R, Batbayar N, Natsagdorj T, Batsuuri D, Bidashko FG, Galbadrakh N, Goroshko O, Khrokov VV, Unenbat T, Vagner II, Wang M, Smith CI. Mitochondrial Divergence between Western and Eastern Great Bustards: Implications for Conservation and Species Status. J Hered 2018; 109:641-652. [PMID: 29917081 DOI: 10.1093/jhered/esy025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/01/2018] [Indexed: 11/13/2022] Open
Abstract
The great bustard is the heaviest bird capable of flight and an iconic species of the Eurasian steppe. Populations of both currently recognized subspecies are highly fragmented and critically small in Asia. We used DNA sequence data from the mitochondrial cytochrome b gene and the mitochondrial control region to estimate the degree of mitochondrial differentiation and rates of female gene flow between the subspecies. We obtained genetic samples from 51 individuals of Otis tarda dybowskii representing multiple populations, including the first samples from Kazakhstan and Mongolia and samples from near the Altai Mountains, the proposed geographic divide between the subspecies, allowing for better characterization of the boundary between the 2 subspecies. We compared these with existing sequence data (n = 66) from Otis tarda tarda. Our results suggest, though do not conclusively prove, that O. t. dybowskii and O. t. tarda may be distinct species. The geographic distribution of haplotypes, phylogenetic analysis, analyses of molecular variance, and coalescent estimation of divergence time and female migration rates indicate that O. t. tarda and O. t. dybowskii are highly differentiated in the mitochondrial genome, have been isolated for approximately 1.4 million years, and exchange much less than 1 female migrant per generation. Our findings indicate that the 2 forms should at least be recognized and managed as separate evolutionary units. Populations in Xinjiang, China and Khövsgöl and Bulgan, Mongolia exhibited the highest levels of genetic diversity and should be prioritized in conservation planning.
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Affiliation(s)
| | | | - Ramona Flatz
- Department of Biology, Willamette University, Salem, OR
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center of Mongolia, Ulaanbaatar, Mongolia
| | - Tseveenmyadag Natsagdorj
- Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Dashnyam Batsuuri
- Department of Environment & Biodiversity, HSESC, Oyu Tolgoi LLC, Ulaanbaatar, Mongolia
| | | | | | - Oleg Goroshko
- Daursky State Nature Biosphere Reserve, Chita, Russia.,Institute of Nature Resources, Ecology and Cryology, Russian Academy of Sciences, Chita, Russia
| | - Valery V Khrokov
- Association for the Conservation of Biodiversity in Kazakhstan, Astana, Kazakhstan
| | | | - Ivan I Vagner
- Hunters' and Fishers' Society of Southern Kazakhstan Province, Shymkent, Kazakhstan
| | - Muyang Wang
- Key Laboratory of Biogeography and Bioresources in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Costa MC, Oliveira PRR, Davanço PV, de Camargo C, Laganaro NM, Azeredo RA, Simpson J, Silveira LF, Francisco MR. Recovering the Genetic Identity of an Extinct-in-the-Wild Species: The Puzzling Case of the Alagoas Curassow. PLoS One 2017; 12:e0169636. [PMID: 28056082 PMCID: PMC5215914 DOI: 10.1371/journal.pone.0169636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 12/16/2016] [Indexed: 01/18/2023] Open
Abstract
The conservation of many endangered taxa relies on hybrid identification, and when hybrids become morphologically indistinguishable from the parental species, the use of molecular markers can assign individual admixture levels. Here, we present the puzzling case of the extinct in the wild Alagoas Curassow (Pauxi mitu), whose captive population descends from only three individuals. Hybridization with the Razor-billed Curassow (P. tuberosa) began more than eight generations ago, and admixture uncertainty affects the whole population. We applied an analysis framework that combined morphological diagnostic traits, Bayesian clustering analyses using 14 microsatellite loci, and mtDNA haplotypes to assess the ancestry of all individuals that were alive from 2008 to 2012. Simulated data revealed that our microsatellites could accurately assign an individual a hybrid origin until the second backcross generation, which permitted us to identify a pure group among the older, but still reproductive animals. No wild species has ever survived such a severe bottleneck, followed by hybridization, and studying the recovery capability of the selected pure Alagoas Curassow group might provide valuable insights into biological conservation theory.
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Affiliation(s)
- Mariellen C. Costa
- Programa de Pós Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, Rod. Washington Luís, CEP, São Carlos, SP, Brazil
| | - Paulo R. R. Oliveira
- Programa de Pós Graduação em Diversidade Biológica e Conservação, Universidade Federal de São Carlos, campus de Sorocaba, Rod. João Leme dos Santos, CEP, Sorocaba, SP, Brazil
| | - Paulo V. Davanço
- Programa de Pós Graduação em Diversidade Biológica e Conservação, Universidade Federal de São Carlos, campus de Sorocaba, Rod. João Leme dos Santos, CEP, Sorocaba, SP, Brazil
| | - Crisley de Camargo
- Departamento de Ciências Ambientais, Universidade Federal de São Carlos, Campus de Sorocaba, Rod. João Leme dos Santos, CEP, Sorocaba, SP, Brazil
| | - Natasha M. Laganaro
- Programa de Pós Graduação em Diversidade Biológica e Conservação, Universidade Federal de São Carlos, campus de Sorocaba, Rod. João Leme dos Santos, CEP, Sorocaba, SP, Brazil
| | - Roberto A. Azeredo
- CRAX—Sociedade de Pesquisa do Manejo e da Reprodução da Fauna Silvestre, rua Jarbas Camargo, Chácara Campestre, Contagem, MG, Brazil
| | - James Simpson
- CRAX—Sociedade de Pesquisa do Manejo e da Reprodução da Fauna Silvestre, rua Jarbas Camargo, Chácara Campestre, Contagem, MG, Brazil
| | - Luis F. Silveira
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, CEP, São Paulo, SP, Brazil
| | - Mercival R. Francisco
- Departamento de Ciências Ambientais, Universidade Federal de São Carlos, Campus de Sorocaba, Rod. João Leme dos Santos, CEP, Sorocaba, SP, Brazil
- * E-mail:
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A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves). Mol Phylogenet Evol 2015; 92:155-64. [DOI: 10.1016/j.ympev.2015.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 05/19/2015] [Accepted: 06/11/2015] [Indexed: 01/22/2023]
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4
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Alvarez-Prada D, Ruiz-García M. Population genetics of the endangered Wattled Curassow (Crax globulosa, Cracidae, Aves) of the Colombian–Peruvian Amazon using DNA microsatellites and ND2 mitochondrial sequences. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2015. [DOI: 10.1080/01650521.2015.1048615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Yang C, Lian T, Wang QX, Huang Y, Xiao H. Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2487-91. [PMID: 26016878 DOI: 10.3109/19401736.2015.1033711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The structure of the mitochondrial DNA control region in the Relict Gull (Larus relictus) was predicted and compared with data from the National Center for Biotechnology Information (NCBI) on five other gulls. The results showed that the control regions of the six gulls comprise three domains. Sequences of CSB-1-like (domain I) and CSB-1 (domain III) in L. relictus have the highest similarity with those in the other five gulls. The insertion fragments are located in downstream domain I of L. ridibundus, L. brunnicephalus, and L. saundersi. Seven conserved sequence boxes (additional box, F-box, E-box, D-box, C-box, bird-similarity-box, and B-box) are located in domain II in all six gulls. It is suggested that the CSB-2/3 sequence, the origin of H-strand replication, and bidirectional light- and heavy-strand transcription promoters in domain III of L. relictus have some distinguishing features to those of other gulls. Some repeat units are contained in the 3' end of the control region in the five gulls; however, no repeat units are found in the sequence CAAACAACAAA in L. relictus. The distribution of nucleotide diversity analysis will provide the useful information on the selected DNA fragment within the control region for genetic analyses among gulls.
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Affiliation(s)
- Chao Yang
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
| | - Ting Lian
- b Department of Bioengineering , Xi'an Vocational and Technical College , Xi'an , China , and
| | - Qing-Xiong Wang
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
| | - Yuan Huang
- c College of Life Sciences, Shaanxi Normal University , Xi'an , China
| | - Hong Xiao
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
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Guo SS, Zhang GR, Guo XZ, Wei KJ, Yang RB, Wei QW. Genetic diversity and population structure of Schizopygopsis younghusbandi Regan in the Yarlung Tsangpo River inferred from mitochondrial DNA sequence analysis. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Sun K, Luo L, Zhang Z, Liu S, Feng J. Molecular characteristics and evolution of the mitochondrial control region in three genera (Hipposideridae: Hipposideros Aselliscus and Coelops) of leaf-nosed bats. ACTA ACUST UNITED AC 2013; 24:451-61. [PMID: 23406568 DOI: 10.3109/19401736.2013.766176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial control region (CR) was sequenced for three genera of Hipposideridae to give a detailed overview of its features. The CR of leaf-nosed bats (1288-1560 bp) was divided into three domains like that of other mammals. In addition to the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2, and CSB3) found in all species, a CSB1-like element was also detected in the conserved sequence blocks (CSB). Repeated motifs were examined in the ETAS of Aselliscus stoliczkanus (26 bp) and Hipposideros bicolor (80 bp) and were present in the CSB of all individuals (6, 8, 16, and 20 bp). Phylogenetic reconstructions using the CR sequences indicated that the phylogenetic relationships among Hipposideros species were consistent with the results of other molecular and phenetic analyses. Aselliscus and Coelops had a closer relationship. But the central domain could not be used for phylogenetic analyses at family and genus levels due to its high conservation.
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Affiliation(s)
- Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, China
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Barker FK, Benesh MK, Vandergon AJ, Lanyon SM. Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene. PLoS One 2012; 7:e46403. [PMID: 23071562 PMCID: PMC3465326 DOI: 10.1371/journal.pone.0046403] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/03/2012] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (Agelaius phoeniceus) and its close relative the tricolored blackbird (A. tricolor). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for A. phoeniceus. However, individual Sanger-read-length fragments (~600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.
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Affiliation(s)
- F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America.
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Verkuil YI, Piersma T, Baker AJ. A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes). Mol Phylogenet Evol 2010; 57:411-6. [DOI: 10.1016/j.ympev.2010.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/13/2010] [Accepted: 06/15/2010] [Indexed: 11/29/2022]
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10
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Prost S, Smirnov N, Fedorov VB, Sommer RS, Stiller M, Nagel D, Knapp M, Hofreiter M. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus. PLoS One 2010; 5:e10447. [PMID: 20523724 PMCID: PMC2877706 DOI: 10.1371/journal.pone.0010447] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 04/11/2010] [Indexed: 11/19/2022] Open
Abstract
Background Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. Results Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød) warming phase at 14.5 kyrs BP. Conclusion Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared lemmings would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.
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Affiliation(s)
- Stefan Prost
- Research Group Molecular Ecology, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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11
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Unexpectedly high genetic diversity of mtDNA control region through severe bottleneck in vulnerable albatross Phoebastria albatrus. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0011-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography. Mol Phylogenet Evol 2009; 53:923-34. [DOI: 10.1016/j.ympev.2009.08.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 08/12/2009] [Accepted: 08/18/2009] [Indexed: 11/18/2022]
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13
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Ksepka DT. Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status forGallinuloides wyomingensisand rallid affinities forAmitabha urbsinterdictensis. Cladistics 2009; 25:173-197. [DOI: 10.1111/j.1096-0031.2009.00250.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Pereira SL, Baker AJ, Wajntal A. Did increased taxon and character sampling really reveal novel intergeneric relationships in the Cracidae (Aves: Galliformes)? J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00512.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Calibration of a molecular clock in tits (Paridae)—Do nucleotide substitution rates of mitochondrial genes deviate from the 2% rule? Mol Phylogenet Evol 2007; 44:1-14. [DOI: 10.1016/j.ympev.2007.03.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 12/18/2006] [Accepted: 03/05/2007] [Indexed: 11/18/2022]
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16
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Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, Hedderson TAJ, Randi E, Pereira SL, Wakeling J. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 2006; 22:495-532. [DOI: 10.1111/j.1096-0031.2006.00120.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Pereira SL, Baker AJ. A Mitogenomic Timescale for Birds Detects Variable Phylogenetic Rates of Molecular Evolution and Refutes the Standard Molecular Clock. Mol Biol Evol 2006; 23:1731-40. [PMID: 16774978 DOI: 10.1093/molbev/msl038] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.
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Affiliation(s)
- Sergio L Pereira
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.
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Goricki S, Trontelj P. Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus. Gene 2006; 378:31-41. [PMID: 16764998 DOI: 10.1016/j.gene.2006.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The European cave salamander Proteus anguinus Laurenti 1768 is one of the best-known subterranean animals, yet its evolutionary history and systematic relationships remain enigmatic. This is the first comprehensive study on molecular evolution within the taxon, using an mtDNA segment containing the control region (CR) and adjacent sequences. Two to seven tandem repeats of 24-32 bp were found in the intergenic spacer region (VNTR1), and three, four or six repeats, 59-77 bp each, in the 3' end of the CR (VNTR2). Different molecular mechanisms account for VNTR2 formation in different lineages of Proteus. The overall CR variation was lower than that of the spacer region, the 3' end of the cytb gene, or the tRNA genes. Individual genes and the concatenated non-repetitive sequences produced similar, well resolved maximum likelihood, Bayesian inference and parsimony trees. The numbers of repeat elements as well as the genealogy of the VNTR2 repeat units were mostly inconsistent with the groupings of the non-repetitive sequences. Different degrees of repeat array homogenization were detected in all major groups. Orthology was established for the first and the second VNTR2 elements of some populations. These two copies may therefore be used for analyses at the population level. The pattern of CR sequence variation points to strong genetic isolation of hydrographically separated populations. Genetic separation of the major groups of populations is incongruent with the current division into subspecies.
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Affiliation(s)
- Spela Goricki
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
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Pereira SL, Baker AJ. A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol Phylogenet Evol 2005; 38:499-509. [PMID: 16112881 DOI: 10.1016/j.ympev.2005.07.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2005] [Revised: 06/23/2005] [Accepted: 07/12/2005] [Indexed: 10/25/2022]
Abstract
A recent molecular timescale for major lineages of the Galliformes indicated that Megapodiidae and possibly Cracidae, originated in the Cretaceous, while the remaining families originated in the Tertiary. This timescale was based on clock-like evolution in genetic and taxonomic partitions of mitochondrial ND2 and cyt b DNA sequences, and assumed that ordinal diversification of Galloanserae around 90 million years ago and imposed, whenever appropriate, minimum age constraints based on the fossil record. This approach is not ideal, as it did not account for uncertainty in estimating branch lengths and time, including the calibration time, and heterogeneity in the rate of DNA substitution among sites and in different lineages. Furthermore all the information available in the DNA sequences was not included, and may have been affected by stochastic error in individual gene partitions. Here, we present a follow-up analysis by estimating divergence times using a Bayesian framework that accounts for these possible sources of uncertainty. Our results based on combined and separate analyses of mitochondrial DNA sequences comprised of 1756 sites of 12S rDNA, ND2 and cyt b indicated that (1) Megapodiidae and Cracidae, and likely Odontophoridae, originated in the Cretaceous; (2) estimates based on concatenated genes are less affected by stochastic error among sites and less influenced by the phylogenetic signals of individual gene partitions, which are unequally distributed along the phylogenetic tree; and (3) the use of only an external molecular calibration results in lower estimation of most ingroup node ages. We also point out that galliform fossils may not be as useful for point calibrations as was previously suggested, but instead may be better employed as priors for the estimation of node ages under a Bayesian approach.
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Affiliation(s)
- Sergio L Pereira
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ont., Canada M5S 2C6.
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Grau ET, Pereira SL, Silveira LF, Höfling E, Wajntal A. Molecular phylogenetics and biogeography of Neotropical piping guans (Aves: Galliformes): Pipile Bonaparte, 1856 is synonym of Aburria Reichenbach, 1853. Mol Phylogenet Evol 2005; 35:637-45. [PMID: 15878132 DOI: 10.1016/j.ympev.2004.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2004] [Revised: 12/01/2004] [Accepted: 12/06/2004] [Indexed: 11/27/2022]
Abstract
The Cracidae are Neotropical galliform birds with 11 genera currently recognized. To investigate the questioned validity of Pipile Bonaparte, 1856 and the monotypic Aburria Reichenbach, 1853 as separate genera, we gathered data from 2727 bp of mitochondrial DNA (cytochrome b, ND2 and control region) and 151 osteological characters. Our phylogenetic analyses of DNA sequences indicated that Aburria aburri is embedded within Pipile. Also, genetic distances between Aburria and any Pipile species are equivalent to the distances estimated for other congeneric cracid species, which genus status is not doubtful. Although the osteological characters do not have phylogenetic signal to solve the phylogenetic relationships at species level, five synapomorphies were found for Aburria and Pipile. Therefore, we suggest that Pipile should be merged with Aburria, which is the oldest described genus. We estimated that speciation in this group occurred in the Plio-Pleistocene, concordant with other birds, primates and rodents that have similar geographic distribution, and proposed a diversification hypothesis based on the occurrence of sea transgressions and the formation of the Amazon Lagoon. Therefore, we conclude that these palaeogeographic events may have contributed to Neotropical taxa diversification to a greater extent than previously suspected.
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Affiliation(s)
- Erwin T Grau
- Departamento de Biologia, Universidade de São Paulo, Caixa Postal 11461, CEP 05422-970, São Paulo, Brazil
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