The Vestigial Olfactory Receptor Subgenome of Odontocete Whales: Phylogenetic Congruence between Gene-Tree Reconciliation and Supermatrix Methods
Tóm tắt
Từ khóa
Tài liệu tham khảo
Allard, 1992, DNA systematics and evolution of the artiodactyl family Bovidae, Proc. Natl. Acad. Sci. USA, 89, 3972, 10.1073/pnas.89.9.3972
Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Barnes, 2002, Delphinoids, evolution of the modern families, Encyclopedia of marine mammals, 314
Bininda-Emonds, 2004, The evolution of supertrees, Trends Ecol. Evol., 19, 315, 10.1016/j.tree.2004.03.015
Bininda-Emonds, 2004, Trees versus characters and the supertree/supermatrix “paradox.”, Syst. Biol., 53, 356, 10.1080/10635150490440396
Bininda-Emonds, 2007, Fast genes and slow clades: Comparative rates of molecular evolution in mammals, Evol. Bioinformatics, 3, 59, 10.1177/117693430700300008
Brown, 1982, Mitochondrial DNA sequences of primates: Tempo and mode of evolution, J. Mol. Evol., 18, 225, 10.1007/BF01734101
Bull, 1993, Partitioning and combining data in phylogenetic analysis, Syst. Biol., 42, 384, 10.1093/sysbio/42.3.384
Caballero, 2008, Molecular systematics of South American dolphins Sotalia: Sister taxa determination and phylogenetic relationships, with insights into a multi-locus phylogeny of the Delphinidae, Mol. Phylogenet. Evol., 46, 252, 10.1016/j.ympev.2007.10.015
Carlini, 2000, Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda), Mol. Biol. Evol., 17, 1353, 10.1093/oxfordjournals.molbev.a026419
Cave, 1988, Note on olfactory activity in mysticetes, J. Zool. Lond., 214, 307, 10.1111/j.1469-7998.1988.tb04724.x
Cotton, 2002, Going nuclear: Gene family evolution and vertebrate phylogeny reconciled, Proc. R Soc. B, 269, 1555, 10.1098/rspb.2002.2074
Cotton, 2003, Gene tree parsimony vs. uninode coding in phylogenetic reconstruction, Mol. Phylogenet. Evol., 29, 298, 10.1016/S1055-7903(03)00109-X
de Jong, 1981, Causes of more frequent deletions than insertions in mutations and protein evolution, Nature, 290, 157, 10.1038/290157a0
Deméré, 2008, Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales, Syst. Biol., 57, 15, 10.1080/10635150701884632
de Muizon, 1988, Les relations phylogénétiques des Delphinida (Cetacea, Mammalia), Ann. Paléontol., 74, 159
de Queiroz, 2007, The supermatrix approach to systematics, Trends Ecol. Evol., 22, 34, 10.1016/j.tree.2006.10.002
Dohl, 1974, A porpoise hybrid: Tursiops X Steno, J. Mammal., 11, 207
Durand, 2006, A hybrid micro-macroevolutionary approach to gene tree reconstruction, J. Comput. Biol., 13, 320, 10.1089/cmb.2006.13.320
Felsenstein, 1985, Confidence limits on phylogenies: An approach using the bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x
Freitag, 1998, Olfactory receptors in aquatic and terrestrial vertebrates, J. Comp. Physiol. A, 183, 635, 10.1007/s003590050287
Gatesy, 1996, Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls, Mol. Biol. Evol., 13, 954, 10.1093/oxfordjournals.molbev.a025663
Geisler, 2003, Morphological evidence for the phylogeny of Cetacea, J. Mammal. Evol., 10, 23, 10.1023/A:1025552007291
Gilad, 2003, Human specific loss of olfactory receptor genes, Proc. Natl. Acad. Sci. USA, 100, 3324, 10.1073/pnas.0535697100
Gilad, 2004, Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates, PLoS Biol., 2, 120, 10.1371/journal.pbio.0020005
Glusman, 2000, The olfactory receptor gene superfamily: Data mining, classification, and nomenclature, Mammal. Genome, 11, 1016, 10.1007/s003350010196
Gojobori, 1982, Patterns of nucleotide substitution in pseudogenes and functional genes, J. Mol. Evol., 18, 360, 10.1007/BF01733904
Goodman, 1979, Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences, Syst. Zool., 28, 132, 10.2307/2412519
Guindon, 2003, A simple and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520
Harlin-Cognato, 2006, Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: Character synergy improves phylogenetic resolution, BMC Evol. Biol., 6, 87, 10.1186/1471-2148-6-87
Hoch, 2000, Olfaction in whales: Evidence from a young odontocete of the Late Oligocene North Sea, Historical Biol., 14, 67, 10.1080/10292380009380556
Huelsenbeck, 1996, Combining data in phylogenetic analysis, Trends Ecol. Evol., 11, 152, 10.1016/0169-5347(96)10006-9
Kasuya, 1973, Systematic consideration of recent toothed whales based on morphology of tympano-periotic bone, Sci. Rep. Whales Res. Inst., 25, 1
Kellogg, 1928, The history of whales—Their adaptation to life in the water, Q. Rev. Biol., 3, 29, 10.1086/394293
Kishida, 2007, The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: Evidence for reduction of the functional proportions in cetaceans, Biol. Lett., 3, 428, 10.1098/rsbl.2007.0191
Kraus, 1991, Cladogenesis among the pecoran ruminants: Evidence from mitochondrial DNA sequences, Syst. Zool., 40, 117, 10.2307/2992252
Kubatko, 2007, Inconsistency of phylogenetic estimates from concatenated data under coalescence, Syst. Biol., 56, 17, 10.1080/10635150601146041
LeDuc, 1999, Phylogenetic relationships among delphinid cetaceans based on full cytochrome b sequences, Mar. Mammal Sci., 15, 619, 10.1111/j.1748-7692.1999.tb00833.x
Machado, 2003, The causes of phylogenetic conflict in a classic Drosophila species group, Proc. R. Soc. Lond. B, 270, 1193, 10.1098/rspb.2003.2333
Martin, 2002, Perils of paralogy: Using HSP70 genes for inferring organismal phylogenies, Syst. Biol., 51, 570, 10.1080/10635150290069995
Martin, 1993, Body size, metabolic rate, generation time, and the molecular clock, Proc. Natl. Acad. Sci. USA, 90, 4087, 10.1073/pnas.90.9.4087
Mathews, 2000, Basal angiosperm phylogeny inferred from duplicate phytochromes A and C, Int. J. Plant Sci., 161, 541, 10.1086/317582
Matthee, 2001, Mining the mammalian genome for artiodactyl systematics, Syst. Biol., 50, 367, 10.1080/10635150119683
Matthee, 2001, Molecular insights into the evolution of the family Bovidae: A nuclear DNA perspective, Mol. Biol. Evol., 18, 1220, 10.1093/oxfordjournals.molbev.a003908
May-Collado, 2006, Cytochrome b and Bayesian inference of whale phylogeny, Mol. Phylogenet. Evol., 38, 344, 10.1016/j.ympev.2005.09.019
Milinkovitch, 1998, Cetaceans are highly derived artiodactyls, The emergence of whales, 113, 10.1007/978-1-4899-0159-0_4
Milinkovitch, 1994, Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes, Mol. Biol. Evol., 11, 939
Miyamoto, 1995, Testing species phylogenies and phylogenetic methods with congruence, Syst. Biol., 44, 64, 10.1093/sysbio/44.1.64
Mombaerts, 2004, Genes and ligands for odorant, vomeronasal and taste receptors, Nat. Rev. Neurosci., 5, 263, 10.1038/nrn1365
Montgelard, 1997, Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences, Mol. Biol. Evol., 14, 550, 10.1093/oxfordjournals.molbev.a025792
Müller, 2005, SeqState—Primer design and sequence statistics for phylogenetic DNA data sets, Appl. Bioinformatics, 4, 65
Niimura, 2003, Evolution of olfactory receptor genes in the human genome, Proc. Natl. Acad. Sci. USA, 100, 12235, 10.1073/pnas.1635157100
Niimura, 2005, Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods, Proc. Natl. Acad. Sci. USA, 102, 6039, 10.1073/pnas.0501922102
Nikaido, 2007, Toothed whale monophyly reassessed by SINE insertion analysis: The absence of lineage sorting effects suggests a small population of a common ancestral species, Mol. Phylogenet. Evol., 43, 216, 10.1016/j.ympev.2006.08.005
Nylander, 2004, MrModelTest v2. Program distributed by the author
Oelschläger, 1992, Development of the olfactory and terminalis systems in whales and dolphins, Chemical signals in vertebrates VI, 141, 10.1007/978-1-4757-9655-1_23
Ophir, 1997, Patterns and rates of indel evolution in processed pseudogenes from humans and murids, Gene, 205, 191, 10.1016/S0378-1119(97)00398-3
Page, 1998, GeneTree: Comparing gene and species phylogenies using reconciled trees, Bioinformatics, 14, 819, 10.1093/bioinformatics/14.9.819
Page, 2000, Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny, Mol. Phylogenet. Evol., 14, 89, 10.1006/mpev.1999.0676
Page, 1997, From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem, Mol. Phylogenet. Evol., 7, 231, 10.1006/mpev.1996.0390
Posada, 2004, Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests, Syst. Biol., 53, 793, 10.1080/10635150490522304
Posada, 1998, ModelTest: Testing the model of DNA substitution, Bioinformatics, 9, 817, 10.1093/bioinformatics/14.9.817
Queralt, 1995, Evolution of protamine P1 genes in mammals, J. Mol. Evol., 40, 601, 10.1007/BF00160507
Rambaut A Drummond A. J. Tracer v1.4 2007 Available from http://beast.bio.ed.ac.uk/Trace
Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180
Ronquist F. Huelsenbeck J. P. van der Mark P. MrBayes 3.1 manual. Draft 26 May 2005 2005 Distributed by the authors, http://mrbayes.csit.fsu.edu/manual.php
Rouquier, 2000, The olfactory receptor gene repertoire in primates and mouse: Evidence for reduction of the functional fraction in primates, Proc. Natl. Acad. Sci. USA, 97, 2870, 10.1073/pnas.040580197
Simmons, 2000, Phylogeny reconstruction using duplicate genes, Mol. Biol. Evol., 17, 469, 10.1093/oxfordjournals.molbev.a026327
Simmons, 2002, Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes, Mol. Phylogenet. Evol., 23, 481, 10.1016/S1055-7903(02)00033-7
Simmons, 2000, Gaps as characters in sequence-based phylogenetic analyses, Syst. Biol., 49, 369, 10.1093/sysbio/49.2.369
Slowinski, 1997, Inferring species trees from gene trees: A phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins, Mol. Phylogenet. Evol., 8, 349, 10.1006/mpev.1997.0434
Slowinski, 1999, How should species phylogenies be inferred from sequence data?, Syst. Biol., 48, 814, 10.1080/106351599260030
Springer, 2001, Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction, Mol. Biol. Evol., 18, 132, 10.1093/oxfordjournals.molbev.a003787
Steppan, 2005, Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes, Mol. Phylogenet. Evol., 37, 370, 10.1016/j.ympev.2005.04.016
Swofford, 2002, PAUP*: Phylogenetic analysis using parsimony (*and other methods)
Thompson, 1994, CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position–specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673
Whinnett, 2003, Isolation of novel olfactory receptor genes in marmosets (Callithrix): Insights into pseudogene formation and evidence for functional degeneracy in non-human primates, Gene, 304, 87, 10.1016/S0378-1119(02)01182-4