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Arnaiz-Villena A, Ruiz-del-Valle V, Muñiz E, Palacio-Gruber J, Campos C, Gómez-Casado E, Villa JMM, Serrano-Vela I. Major Histocompatibility Complex Allele Persistence in Eurasia and America in the Genus Carduelis (Spinus) During Million Years. THE OPEN ORNITHOLOGY JOURNAL 2017; 10:92-104. [DOI: 10.2174/1874453201710010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 10/10/2023]
Abstract
Introduction:GenusCarduelis(Fringillidaefamily) includes goldfinches, siskins, redpolls, greenfinches and crossbills. Many of the species classified within this genus and other related genera have been grouped by using molecular systematics and the mitochondrial cytochrome b (mt cyt b) gene. According to this, the Eurasian siskin (C. spinus)is the only one extant direct ancestor of several North American finches; North American / South American radiations may have been originated by Eurasian siskin (or extinct relative). In the present work, we aim to perform a study of transpecies and transcontinental analyses of MHC (Major Histocompatibility Complex) Class I alleles in several genusCarduelis/Spinusspecies in order to draw evolutionary conclusions in several wild bird species belonging to the genusCarduelis / Spinus.Materials and Methods:Blood was taken from worldwide wild bird species. Passerine phylogeny was done after analysing mtDNA with Maximun Likelihood and Bayesian dendrograms. Major histocompatibility complex alleles were obtained by standard DNA cloning and sequencing.Results:We found two matches between MHC-I DNA alleles from different South American siskins at DNA level. Also, it was observed that the Eurasian siskin shares a protein with pine siskin and another with three South American siskins. Eight South American siskins species also share the same MHC protein. In addition, studied songbirds MHC class I intron 2 is longer than that ofGallus gallus.Conclusion:We have drawn the following conclusions: 1) We present the first direct evidence that “Minimal Essential MHC” does not exist for birds; one of its main definition characters,i.e.: small intron size does not hold for songbirds. 2) We also report that MHC genes transpecies evolution exist in birds by showing also for the first time that worldwide bird species keep the same MHC protein and DNA alleles. 3) New evidences on MHC alleles conservation from EurasianCarduelis spinus(most ancient) to South American siskins (most recent) during million years support that Eurasian siskin is the parental species for American GenusCarduelis (Spinus)species. It is uncertain whether Eurasian siskin (or extant relative) had initially an Holoartic distribution, including America.
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Wang E, Van Wijk RE, Braun MS, Wink M. Gene flow and genetic drift contribute to high genetic diversity with low phylogeographical structure in European hoopoes (Upupa epops). Mol Phylogenet Evol 2017; 113:113-125. [PMID: 28533084 DOI: 10.1016/j.ympev.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 10/19/2022]
Abstract
The Hoopoe (Upupa epops epops) breeds widely in Eurasia and most populations migrate to Africa during the boreal winter. To date, data regarding its phylogeography in Europe are missing. In this study, we investigated the phylogeography and population genetics of Hoopoes by means of mitochondrial DNA (mtDNA) sequencing as well as microsatellite genotyping. Our analyses revealed 32 haplotypes in the cytochrome c oxidase subunit I (COI) (269 individuals) and 50 haplotypes in cytochrome b (cyt b) (233 individuals). Analyses of mtDNA clearly demonstrated that the bulk of variance (98.23%) could be attributed to inner-population variance. Thus, the low frequency single nucleotide substitutions resulted in "star-like" haplotype networks without define geographical structure. Hoopoes clearly experienced a bottleneck followed by sudden expansion, as was also apparent from tests on the unimodal mismatch, Bayesian skyline plot, significant negative neutrality tests as well as bottleneck signals. These tests pointed to strong demographic fluctuations in the hoopoe populations. GENELAND, DAPC and STRUCTURE analyses of microsatellites along with their corresponding Fst values suggested that current genetic restriction separates birds from Armenia from the remaining populations. Except for hoopoes from Armenia, all the European populations exhibited an admixed phylogeographic pattern. We conclude that this genetic panmixia might be a consequence of a combination of historical events (e.g. repeated colonizations and retreatments from northern habitats during the Pleistocene and a sudden postglacial expansion) and current processes (e.g. long-distance migration, immigration or population recruitments).
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Affiliation(s)
- Erjia Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120 Heidelberg, Germany
| | - Rien E Van Wijk
- Swiss Ornithological Institute, Department of Bird Migration, Seerose 1, 6204 Sempach, Switzerland; University of Zurich, Department of Evolutionary Biology and Environmental Studies, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Markus Santhosh Braun
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120 Heidelberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120 Heidelberg, Germany.
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Cibois A, Thibault JC, Bonillo C, Filardi CE, Pasquet E. Phylogeny and biogeography of the imperial pigeons (Aves: Columbidae) in the Pacific Ocean. Mol Phylogenet Evol 2017; 110:19-26. [PMID: 28249741 DOI: 10.1016/j.ympev.2017.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/16/2017] [Accepted: 02/24/2017] [Indexed: 11/28/2022]
Abstract
We reconstruct the phylogeny of imperial pigeons (genus Ducula) using mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. The divergence time analysis suggests that the basal divergences within Ducula occurred more recently than in the fruit doves (genus Ptilinopus), a group that is also well diversified in Oceania. The imperial pigeons colonized the Melanesian region several times independently, and the diversification within this region led to several species in sympatry, in particular in the Bismarck archipelago. Central Polynesia was also colonized several times, first by a lineage during the Miocene that led to the large D. latrans, sister to the New Caledonian endemic D. goliath, then more recently by the widespread D. pacifica, during the Pleistocene. The phylogenetic pattern obtained with the extant Ducula species showed that the Eastern Polynesian endemics do not form a monophyletic group, with the Pacific Imperial Pigeon D. pacifica sister species with good support to the Polynesian Imperial Pigeon D. aurorae. However, the impact of recent anthropic extinctions has been important for the imperial pigeons, more than for the smaller fruit doves, suggesting that several Ducula lineages might be missing today.
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Affiliation(s)
- Alice Cibois
- Natural History Museum of Geneva, Department of Mammalogy and Ornithology, CP 6434, CH 1211 Geneva 6, Switzerland.
| | - Jean-Claude Thibault
- UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 51, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Céline Bonillo
- UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 51, 57 rue Cuvier, F-75231 Paris Cedex 05, France; UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle, CP 26, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | | | - Eric Pasquet
- UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 51, 57 rue Cuvier, F-75231 Paris Cedex 05, France; UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle, CP 26, 57 rue Cuvier, F-75231 Paris Cedex 05, France
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Contrasting egg recognition between European and Asian populations of tree sparrows (Passer montanus). Behav Processes 2016; 125:85-8. [DOI: 10.1016/j.beproc.2016.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/11/2016] [Accepted: 02/16/2016] [Indexed: 11/24/2022]
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Cramer ERA, Laskemoen T, Stensrud E, Rowe M, Haas F, Lifjeld JT, Saetre GP, Johnsen A. Morphology-function relationships and repeatability in the sperm of Passer sparrows. J Morphol 2014; 276:370-7. [PMID: 25427840 DOI: 10.1002/jmor.20346] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/14/2014] [Accepted: 11/08/2014] [Indexed: 11/11/2022]
Abstract
Sperm performance is likely to be an important determinant of male reproductive success, especially when females copulate with multiple males. Understanding sperm performance is therefore crucial to fully understand the evolution of male reproductive strategies. In this study, we examined the repeatability of sperm morphology and motility measures over three breeding seasons, and we studied relationships between sperm morphology and function. We conducted this study in wild-derived captive house sparrows (Passer domesticus) and Spanish sparrows (P. hispaniolensis). Results for the two species were similar. As predicted from results in other passerine species, total sperm length was highly repeatable across ejaculates, and repeatability for the length of other components was moderate. The repeatability of sperm swimming speed across ejaculates was lower, but statistically significant, suggesting that sperm velocity may be a relatively dynamic trait. Surprisingly, swimming speed did not correlate with the relative length of the midpiece, and it correlated negatively with the relative length of the flagellum and with total sperm length. This pattern is the opposite of what theory predicts and differs from what has been found in house sparrows before. Also contrary to previous work, we found no evidence that total sperm length correlates with sperm longevity. These results therefore highlight the need for a better understanding of relationships between sperm morphology and function in passerine birds.
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Affiliation(s)
- Emily R A Cramer
- Natural History Museum, University of Oslo, Blindern, 0318, Oslo, Norway
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A re-evaluation of phylogenetic relationships within reed warblers (Aves: Acrocephalidae) based on eight molecular loci and ISSR profiles. Mol Phylogenet Evol 2014; 78:304-13. [PMID: 24910156 DOI: 10.1016/j.ympev.2014.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/24/2022]
Abstract
Acrocephalidae is the most monomorphic family among passerines and has seen a long history of different classifications and successive revisions. In this study, we evaluated the phylogenetic relationships among 35 species of Acrocephalidae based on DNA sequences from five nuclear loci (MB, ODC, LDH, FIB5 and RAG-1), three mitochondrial genes (CYB, ND2 and COI) and genomic fingerprinting with ISSR-PCR. We could improve the resolution of phylogenetic relationships among many species, but despite the use of 6280 nucleotides, some deep-level relationships remain enigmatic. Lack of nodal support at some branches may be the result of rapid radiation. The last common ancestor of this family dated for the Middle Miocene (14 MYA). In agreement with previous studies, we recovered the major clades of Acrocephalus, Iduna (except I. aedon), Hippolais, Nesillas and Calamonastides. We accept the current taxonomic position of Calamonastides gracilirostris as a monotypic genus and the inclusion of Iduna natalensis and I. similis within Iduna but phylogenetic analyses based on mitochondrial and nuclear genes as well as ISSR profiles did not support the position of I. aedon in Iduna. Therefore, we resurrect the former genus Phragamaticola for this species in order to avoid paraphyletic clades.
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Testing a post-copulatory pre-zygotic reproductive barrier in a passerine species pair. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-014-1724-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Cibois A, Thibault JC, Bonillo C, Filardi CE, Watling D, Pasquet E. Phylogeny and biogeography of the fruit doves (Aves: Columbidae). Mol Phylogenet Evol 2014; 70:442-53. [DOI: 10.1016/j.ympev.2013.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 11/24/2022]
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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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Triant DA, Hayes LD. Molecular approaches in behavioural research: a cautionary note regarding mitochondrial transfers to the nucleus (numts). Anim Behav 2011. [DOI: 10.1016/j.anbehav.2011.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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TIBBETTS EA, SAFRAN RJ. Co-evolution of plumage characteristics and winter sociality in New and Old World sparrows. J Evol Biol 2009; 22:2376-86. [DOI: 10.1111/j.1420-9101.2009.01861.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Tsurim I, Abramsky Z, Kotler BP. Differences in Patch Use Behavior Between an Urban and Rural Species: Effects of Distance from Shelter and Wing Molt-Gaps. Isr J Ecol Evol 2009. [DOI: 10.1560/ijee.55.4.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It has been suggested that urban bird populations and communities are controlled by bottom-up mechanisms because predation costs are lower in urban than in non-urban habitats. We hypothesized that urban birds are less sensitive to variations in the cost of predation than non-urban birds. We predicted that the house sparrow, a widespread urban species, is less sensitive to variations in predation risk, while foraging, than its rural (less urban) congener, the Spanish sparrow. We quantified foraging behavior of these species, as affected by the proximity to shelter, in large outdoor aviaries. We then clipped feathers from the birds' wings to manipulate escape ability and increase predation risk. We predicted that birds experience increasing predation risk with increasing distance from shelter, and that reduced wing surface increases the birds' sensitivity to risk of predation with respect to distance from shelter. Both species displayed increasing giving-up densities in seed trays with increasing distance from shelter, indicating that foraging costs increase with distance from shelter. As predicted, the two species differed in their response to proximity of shelter: we concluded that house sparrows experienced a less pronounced increase in perceived predation cost with increasing distance from shelter than did Spanish sparrows. Contrary to our prediction, wing surface reduction had no effect on seed tray utilization. Therefore, it appears that, when feeding in patches at distances from shelter, as used in the present study, the cost of predation affects foraging and micro-habitat use in Spanish sparrows more than in house sparrows.
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Affiliation(s)
- Ido Tsurim
- Department of Life Sciences, Ben-Gurion University of the Negev
| | - Zvika Abramsky
- Department of Life Sciences, Ben-Gurion University of the Negev
| | - Burt P. Kotler
- The Jacob Blaustein Institute for Desert Research, Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev
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IZUMI H, HASEGAWA O, HIGASHI S. Isolation of polymorphic microsatellite markers in the tree sparrow (Passer montanus). Mol Ecol Resour 2009; 9:245-7. [DOI: 10.1111/j.1755-0998.2008.02427.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Qu Y, Ericson PGP, Lei F, Gebauer A, Kaiser M, Helbig AJ. Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau. Mol Phylogenet Evol 2006; 40:218-26. [PMID: 16624593 DOI: 10.1016/j.ympev.2006.02.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 02/24/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
The snow finch complex (Montifringilla, Pyrgilauda, and Onychostruthus) has its center of distribution on the Tibetan plateau, with six out of seven species in the genera occurring there. Phylogenetic relationships among these six species of three genera have been studied based on DNA sequence data obtained from the mitochondrial cytochrome b gene and the nuclear myoglobin gene. The results support monophyly of the snow finch complex group and three major evolutionary lineages are recognized. The first clade consists of ruficollis, blanfordi, and davidiana. These three taxa are sometimes placed in their own genus, Pyrgilauda, and the DNA data supports this. The three taxa nivalis, henrici, and adamsi have traditionally been placed in the genus Montifringilla, and they group together strongly in the present analysis. The results further suggest that nivalis and adamsi are more closely related to each other than are nivalis and henrici, despite that the latter two are often regarded as conspecific. The third distinct lineage within the snow finch complex consists of taczanowskii, which has been placed its own genus, Onychostruthus. This taxon has a basal position in the phylogenetic tree and is sister to all other snow finches. We estimated that taczanowskii split from the other taxa between 2 and 2.5 mya, i.e., about the time for the most recent uplift of the Tibetan plateau, "the Tibet movement", 3.6-1.7 mya. Cladogenesis within the Montifringilla and Pyrgilauda clades seems to be contemporary with the second phase of "Tibet movement" at 2.5 mya and the third phase at 1.7 mya and "Kunhuang movement" in 1.5-0.6 mya. The dramatic climatic and ecological changes following from the uplift of the Tibetan plateau, together with the cyclic contraction and expansion of suitable habitats during the Pleistocene, are probably the most important factors for the cladogenesis in snow finch complex.
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Affiliation(s)
- Yanhua Qu
- Institute of Zoology, Chinese Academy of Sciences, 19 Zhongguancun Road, Haidian District, Beijing 100080, China
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Sol D, Lefebvre L, Rodríguez-Teijeiro JD. Brain size, innovative propensity and migratory behaviour in temperate Palaearctic birds. Proc Biol Sci 2005; 272:1433-41. [PMID: 16011917 PMCID: PMC1559823 DOI: 10.1098/rspb.2005.3099] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Accepted: 03/18/2005] [Indexed: 11/12/2022] Open
Abstract
The evolution of migration in birds remains an outstanding, unresolved question in evolutionary ecology. A particularly intriguing question is why individuals in some species have been selected to migrate, whereas in other species they have been selected to be sedentary. In this paper, we suggest that this diverging selection might partially result from differences among species in the behavioural flexibility of their responses to seasonal changes in the environment. This hypothesis is supported in a comparative analysis of Palaearctic passerines. First, resident species tend to rely more on innovative feeding behaviours in winter, when food is harder to find, than in other seasons. Second, species with larger brains, relative to their body size, and a higher propensity for innovative behaviours tend to be resident, while less flexible species tend to be migratory. Residence also appears to be less likely in species that occur in more northerly regions, exploit temporally available food sources, inhabit non-buffered habitats and have smaller bodies. Yet, the role of behavioural flexibility as a response to seasonal environments is largely independent of these other factors. Therefore, species with greater foraging flexibility seem to be able to cope with seasonal environments better, while less flexible species are forced to become migratory.
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Affiliation(s)
- Daniel Sol
- Department of Biology, McGill University, 1205, Avenue Docteur Penfield, Montréal, Québec H3A 1B1 Canada.
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Olsson U, Alstrom P, Sundberg P. Non-monophyly of the avian genus Seicercus (Aves: Sylviidae) revealed by mitochondrial DNA. ZOOL SCR 2004. [DOI: 10.1111/j.0300-3256.2004.00166.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pereira SL, Baker AJ. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evol Biol 2004; 4:17. [PMID: 15219233 PMCID: PMC449702 DOI: 10.1186/1471-2148-4-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 06/25/2004] [Indexed: 01/28/2023] Open
Abstract
Background Mitochondrial DNA has been detected in the nuclear genome of eukaryotes as pseudogenes, or Numts. Human and plant genomes harbor a large number of Numts, some of which have high similarity to mitochondrial fragments and thus may have been inadvertently included in population genetic and phylogenetic studies using mitochondrial DNA. Birds have smaller genomes relative to mammals, and the genome-wide frequency and distribution of Numts is still unknown. The release of a preliminary version of the chicken (Gallus gallus) genome by the Genome Sequencing Center at Washington University, St. Louis provided an opportunity to search this first avian genome for the frequency and characteristics of Numts relative to those in human and plants. Results We detected at least 13 Numts in the chicken nuclear genome. Identities between Numts and mitochondrial sequences varied from 58.6 to 88.8%. Fragments ranged from 131 to 1,733 nucleotides, collectively representing only 0.00078% of the nuclear genome. Because fewer Numts were detected in the chicken nuclear genome, they do not represent all regions of the mitochondrial genome and are not widespread in all chromosomes. Nuclear integrations in chicken seem to occur by a DNA intermediate and in regions of low gene density, especially in macrochromosomes. Conclusion The number of Numts in chicken is low compared to those in human and plant genomes, and is within the range found for most sequenced eukaryotic genomes. For chicken, PCR amplifications of fragments of about 1.5 kilobases are highly likely to represent true mitochondrial amplification. Sequencing of these fragments should expose the presence of unusual features typical of pseudogenes, unless the nuclear integration is very recent and has not yet been mutated. Metabolic selection for compact genomes with reduced repetitive DNA and gene-poor regions where Numts occur may explain their low incidence in birds.
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Affiliation(s)
- Sérgio L Pereira
- Centre for Biodiversity and Conservation Biology – Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6 Canada
| | - Allan J Baker
- Department of Zoology, University of Toronto, Toronto ON, M5S 1A1, Canada
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Abbott CL, Double MC. Phylogeography of shy and white-capped albatrosses inferred from mitochondrial DNA sequences: implications for population history and taxonomy. Mol Ecol 2003; 12:2747-58. [PMID: 12969477 DOI: 10.1046/j.1365-294x.2003.01944.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The evolutionary relationship between shy (Thalassarche cauta) and white-capped (T. steadi) albatrosses was examined using mitochondrial control region sequences. Results were interpreted in the context of a recent and contentious taxonomic revision that recommended full species status for shy and white-capped albatrosses. Low sequence divergence between shy and white-capped albatrosses (1.8%) and between their close relatives, Salvin's and Chatham albatrosses (2.9%), was observed. Much higher sequence divergence was found between the shy/white-capped pair and the Salvin's/Chatham pair (7.0%). Phylogenetic analyses confirmed the separation of the shy/white-capped pair from the Salvin's/Chatham pair but did not provide species-level resolution. Phylogeographic analyses, including a nested clade analysis, FST estimates and an analysis of molecular variance, indicated unambiguous genetic structuring between shy and white-capped albatrosses, thus confirming the demographic isolation of the species, but showed little to no structuring within each species. The geographical distribution of mtDNA haplotypes and other evidence suggest that shy albatrosses arose through range expansion by white-capped albatrosses.
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Affiliation(s)
- Cathryn L Abbott
- School of Botany and Zoology, The Australian National University, Canberra ACT 0200, Australia.
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