Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate

[1]  M. Suchard,et al.  Posterior summarisation in Bayesian phylogenetics using Tracer , 2022 .

[2]  M. Mutanen,et al.  Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression , 2018, Molecular ecology.

[3]  Haojie Tong,et al.  Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient , 2018, BMC Genomics.

[4]  O. Flores-Villela,et al.  Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes , 2018 .

[5]  E. Brzuszkiewicz,et al.  Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile , 2018, BMC Genomics.

[6]  Sebastián Duchêne,et al.  The impacts of drift and selection on genomic evolution in insects , 2017, PeerJ.

[7]  O. Thalmann,et al.  Prediction of harmful variants on mitochondrial genes: Test of habitat‐dependent and demographic effects in a euryhaline fish , 2017, Ecology and evolution.

[8]  Luan Thanh Nguyen,et al.  Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species , 2017, ZooKeys.

[9]  P. Sunnucks,et al.  Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation , 2017, Front. Genet..

[10]  P. Sunnucks,et al.  Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish , 2017, Heredity.

[11]  R. Murphy,et al.  The complete mitochondrial genome of the black-tailed brush lizard Urosaurus nigricaudus (Reptilia, Squamata, Phrynosomatidae) , 2016, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.

[12]  Jiajie Zhang,et al.  Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo , 2016, bioRxiv.

[13]  R. Bouckaert,et al.  bModelTest: Bayesian phylogenetic site model averaging and model comparison , 2016, bioRxiv.

[14]  T. Wai,et al.  Mitochondrial Dynamics and Metabolic Regulation , 2016, Trends in Endocrinology & Metabolism.

[15]  A. Bouskila,et al.  Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons , 2015, Genome biology and evolution.

[16]  R. Murphy,et al.  Concordant species delimitation from multiple independent evidence: A case study with the Pachytriton brevipes complex (Caudata: Salamandridae). , 2015, Molecular phylogenetics and evolution.

[17]  Greer A. Scott E. K. Andrés Benjamin T. Adrian Dolby,et al.  Assessing the Geological and Climatic Forcing of Biodiversity and Evolution Surrounding the Gulf of California , 2015 .

[18]  L. Joseph,et al.  Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance , 2015, Molecular ecology.

[19]  T. Mielke,et al.  Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes , 2015, Genome biology and evolution.

[20]  B. Murrell,et al.  RDP4: Detection and analysis of recombination patterns in virus genomes , 2015, Virus evolution.

[21]  G. Hill Mitonuclear Ecology. , 2015, Molecular biology and evolution.

[22]  Daniel C. Jeffares,et al.  A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. , 2015, Methods in molecular biology.

[23]  D. Mishmar,et al.  Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations , 2014, Front. Genet..

[24]  William C. Copeland,et al.  Mitochondrial Disease , 2014, Journal of child neurology.

[25]  P. Boursot,et al.  The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression , 2014, Genome biology and evolution.

[26]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[27]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[28]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[29]  Angel Amores,et al.  Stacks: an analysis tool set for population genomics , 2013, Molecular ecology.

[30]  Jinzhong Fu,et al.  Genetic evidence for male-biased dispersal in the Qinghai toad-headed agamid Phrynocephalus vlangalii and its potential link to individual social interactions , 2013, Ecology and evolution.

[31]  E. Nevo,et al.  Cytochrome b gene selection of subterranean rodent Gansu zokor Eospalax cansus (Rodentia, Spalacidae) , 2013 .

[32]  S. Antonarakis,et al.  Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes. , 2013, Molecular biology and evolution.

[33]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[34]  M. Culver,et al.  Localized extinction of an arboreal desert lizard caused by habitat fragmentation , 2013 .

[35]  Vladimir N. Minin,et al.  A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection , 2012, Bioinform..

[36]  H. Hoekstra,et al.  Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species , 2012, PloS one.

[37]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[38]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[39]  H. Akashi,et al.  Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex. , 2012, Molecular biology and evolution.

[40]  Thibaut Jombart,et al.  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data , 2011, Bioinform..

[41]  Yaping Zhang,et al.  Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation. , 2011, Mitochondrion.

[42]  William N. Venables,et al.  Modern Applied Statistics with S , 2010 .

[43]  Emmanuel Paradis,et al.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[44]  Green,et al.  toward a phylogeny of the kukri snakes, genus oligodon , 2010 .

[45]  M. On Toward a Phylogeny of the Kukri Snakes, Genus Oligodon , 2010 .

[46]  J. Graves,et al.  Sex Chromosome Evolution in Lizards: Independent Origins and Rapid Transitions , 2010, Cytogenetic and Genome Research.

[47]  G. Kenagy,et al.  Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in populations of deer mice (Peromyscus maniculatus) , 2009, Molecular ecology.

[48]  E. Wapstra,et al.  Female aggression predicts mode of paternity acquisition in a social lizard , 2009, Proceedings of the Royal Society B: Biological Sciences.

[49]  N. Dingemanse,et al.  Genetic modulation of energy metabolism in birds through mitochondrial function , 2009, Proceedings of the Royal Society B: Biological Sciences.

[50]  J. Plotkin,et al.  The Population Genetics of dN/dS , 2008, PLoS genetics.

[51]  J. Elson,et al.  Purifying selection of mtDNA and its implications for understanding evolution and mitochondrial disease , 2008, Nature Reviews Genetics.

[52]  Thibaut Jombart,et al.  adegenet: a R package for the multivariate analysis of genetic markers , 2008, Bioinform..

[53]  R. Murphy,et al.  Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard , 2008 .

[54]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[55]  Leila A. Mamirova,et al.  Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals , 2007, Proceedings of the National Academy of Sciences.

[56]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[57]  Chris D. Jiggins,et al.  Speciation by hybridization in Heliconius butterflies , 2006, Nature.

[58]  R. Murphy,et al.  Deep genealogical history without population differentiation: discordance between mtDNA and allozyme divergence in the zebra-tailed lizard (Callisaurus draconoides). , 2005, Molecular phylogenetics and evolution.

[59]  W. Wong,et al.  Bayes empirical bayes inference of amino acid sites under positive selection. , 2005, Molecular biology and evolution.

[60]  D. J. Funk,et al.  REPRODUCTIVE ISOLATION CAUSED BY NATURAL SELECTION AGAINST IMMIGRANTS FROM DIVERGENT HABITATS , 2005 .

[61]  Paul D. N. Hebert,et al.  Identifying spiders through DNA barcodes , 2005 .

[62]  J. Goudet HIERFSTAT , a package for R to compute and test hierarchical F -statistics , 2005 .

[63]  D. Rand,et al.  Cytonuclear coevolution: the genomics of cooperation. , 2004, Trends in ecology & evolution.

[64]  P. Hebert,et al.  Identification of Birds through DNA Barcodes , 2004, PLoS biology.

[65]  Michael C Whitlock,et al.  The incomplete natural history of mitochondria , 2004, Molecular ecology.

[66]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[67]  Y. Kumazawa,et al.  Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. , 2004, DNA research : an international journal for rapid publication of reports on genes and genomes.

[68]  L. Grismer Amphibians and Reptiles of Baja California, Including Its Pacific Islands and the Islands in the Sea of Cortés , 2002 .

[69]  D. Presgraves,et al.  PATTERNS OF POSTZYGOTIC ISOLATION IN LEPIDOPTERA , 2002, Evolution; international journal of organic evolution.

[70]  N. Barton,et al.  Genetic hitchhiking. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[71]  M. Saraste Oxidative phosphorylation at the fin de siècle. , 1999, Science.

[72]  R. Murphy,et al.  THE PENINSULAR ARCHIPELAGO OF BAJA CALIFORNIA : A THOUSAND KILOMETERS OF TREE LIZARD GENETICS , 1999 .

[73]  H. A. Orr,et al.  HALDANE'S RULE , 1997 .

[74]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[75]  R. Murphy,et al.  Phylogeny of the side-blotched lizards (Phrynosomatidae:Uta) based on mtDNA sequences: support for midpeninsular seaway in Baja California. , 1997, Molecular phylogenetics and evolution.

[76]  M. Olsson,et al.  Determinants of breeding dispersal in the sand lizard,Lacerta agilis, (Reptilia, Squamata) , 1997 .

[77]  S. Palumbi Genetic Divergence, Reproductive Isolation, and Marine Speciation , 1994 .

[78]  M. Slatkin,et al.  Estimation of levels of gene flow from DNA sequence data. , 1992, Genetics.

[79]  T. Ohta THE NEARLY NEUTRAL THEORY OF MOLECULAR EVOLUTION , 1992 .

[80]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[81]  M. Shaw,et al.  Minute Y chromosome in the lizard genus Uta (family Iguanidae). , 1969, Cytogenetics.