Dense sampling of bird diversity increases power of comparative genomics

Timothy B Sackton | Bette A. Loiselle | A. T. Vasconcelos | Rebecca B. Dikow | Matthew J. Fuxjager | Araxi O. Urrutia | Libby C. Megna | Adam M. Fudickar | Scott A. Taylor | D. Haussler | M. Diekhans | A. Clark | Huanming Yang | Jian Wang | T. Sicheritz-Pontén | J. Cracraft | M. Braun | Qiye Li | M. Cox | B. Paten | E. Jarvis | B. Faircloth | L. Eckhart | H. Mouritsen | Miriam Liedvogel | D. Burt | A. Vignal | C. Mello | O. Ryder | N. Gemmell | A. Franke | G. Graves | K. Jønsson | J. Fjeldså | C. Rahbek | J. Mudge | J. Fitzpatrick | J. Rozas | Bent Petersen | I. Jamieson | I. Lovette | T. Székely | A. Margaryan | Guojie Zhang | M. Bertelsen | B. Shapiro | J. McGuire | F. Sheldon | S. Edwards | S. Hackett | T. Ryder | M. Bunce | J. Armstrong | S. Mirarab | C. Witt | G. Borgia | P. Ryan | M. Carling | R. T. Brumfield | L. Christidis | E. Braun | R. D. da Fonseca | M. Hauber | L. Keller | Matthew I. M. Louder | F. Lei | R. van der Sluis | P. Njoroge | Josefin Stiller | Qi Zhou | M. Sinding | R. Bowman | B. Schlinger | E. Ketterson | A. Urrutia | Jason T. Howard | Morgan E. Wirthlin | M. G. Campana | A. Fidler | C. Visser | A. Vasconcelos | Nancy Chen | C. Balakrishnan | P. Battley | P. Houde | Alexander Suh | F. Prosdocimi | P. Frandsen | J. DaCosta | M. Gilbert | Peter A. Hosner | Alison Cloutier | J. Dumbacher | R. Fleischer | H. C. Lim | L. Dalén | Yang Liu | B. Milá | B. Loiselle | Guillermo Friis | J. Blake | A. Aleixo | L. Day | J. González‐Solís | B. Hansson | O. Krone | G. Song | Zongji Wang | D. T. Tietze | T. Parchman | Kim M Rutherford | A. Corvelo | J. Weir | S. Claramunt | V. Friesen | B. Robertson | M. Hoeppner | M. Riutort | Guanliang Meng | George Pacheco | A. H. Reeve | Mikkel-Holger S. Sinding | Kira E. Delmore | Anna Tigano | S. Cowen | J. Fuchs | N. C. B. Lima | Maude W. Baldwin | Biao Wang | Shaohong Feng | H. van der Zwan | Qi Fang | Duo Xie | Yuan Deng | Hanna Sigeman | M. Stervander | Suvi Ponnikas | S. Andreu-Sánchez | Chunxue Guo | Lara C. Puetz | G. Camenisch | N. Dussex | Guangji Chen | Wanjun Chen | Carole Parent | Emily Cavill | Â. M. Ribeiro | Dustin J Foote | Subir B Shakya | André E. R. Soares | Joan Ferrer-Obiol | N. Thiele | Á. M. Parody-Merino | M. Baldwin | Glaucia Del-Rio | Guojie Zhang | K. Delmore | N. C. Lima | D. Tietze | M. Liedvogel | Subir B. Shakya | P. Hosner | A. Cloutier | Lara C Puetz | Dustin J. Foote | E. Cavill | Â. Ribeiro | Matthew D. Carling | Jeffrey M. DaCosta | Emily L. Cavill | Ângela M. Ribeiro | A. Clark | Scott A. Taylor | Martin Stervander | Thomas Sicheritz-Pontén | A. Clark | J. Howard | Lara Puetz | S. Andreu‐Sánchez

[1]  Voichita D. Marinescu,et al.  Progressive Cactus is a multiple-genome aligner for the thousand-genome era , 2020, Nature.

[2]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[3]  C. Lalueza-Fox,et al.  Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet , 2019, Current Biology.

[4]  V. Fellman,et al.  A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase , 2019, bioRxiv.

[5]  David Haussler,et al.  Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era , 2019, bioRxiv.

[6]  Berend Snel,et al.  Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences , 2019, PLoS Comput. Biol..

[7]  Qiye Li,et al.  Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits , 2019, Science.

[8]  Yiyuan Li,et al.  MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization , 2019, Nucleic acids research.

[9]  Joel Armstrong,et al.  Whole-Genome Alignment and Comparative Annotation. , 2019, Annual review of animal biosciences.

[10]  Martin Kuhlwilm,et al.  The Genomic Footprints of the Fall and Recovery of the Crested Ibis , 2019, Current Biology.

[11]  David Haussler,et al.  The UCSC Genome Browser database: 2019 update , 2018, Nucleic Acids Res..

[12]  J. Armstrong Enabling comparative genomics at the scale of hundreds of species , 2019 .

[13]  Leucopsar rothschildi: BirdLife International , 2018, IUCN Red List of Threatened Species.

[14]  Juan Carlos Castilla-Rubio,et al.  Earth BioGenome Project: Sequencing life for the future of life , 2018, Proceedings of the National Academy of Sciences.

[15]  Xun Xu,et al.  10KP: A phylodiverse genome sequencing plan , 2018, GigaScience.

[16]  Sheng Chen,et al.  Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data , 2018, GigaScience.

[17]  Michael Q. Zhang,et al.  NONCODEV5: a comprehensive annotation database for long non-coding RNAs , 2017, Nucleic Acids Res..

[18]  Ning Wang,et al.  The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies. , 2017, Molecular phylogenetics and evolution.

[19]  L. Keller,et al.  The Global Ant Genomics Alliance (GAGA) , 2017 .

[20]  Patrick Mardulyn,et al.  NOVOPlasty: de novo assembly of organelle genomes from whole genome data. , 2016, Nucleic acids research.

[21]  SH Song,et al.  The BIG Data Center: from deposition to integration to translation , 2016, Nucleic Acids Res..

[22]  Brant C. Faircloth,et al.  PHYLUCE is a software package for the analysis of conserved genomic loci , 2015, bioRxiv.

[23]  J. Townsend,et al.  A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2015, Nature.

[24]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[25]  Guojie Zhang,et al.  Genomics: Bird sequencing project takes off , 2015, Nature.

[26]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[27]  Alexey M. Kozlov,et al.  ExaML version 3: a tool for phylogenomic analyses on supercomputers , 2015, Bioinform..

[28]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[29]  Md. Shamsuzzoha Bayzid,et al.  Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.

[30]  E. Jarvis,et al.  Evidence for a single loss of mineralized teeth in the common avian ancestor , 2014, Science.

[31]  Andreas R. Pfenning,et al.  Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.

[32]  L. Eckhart,et al.  Trichohyalin-like proteins have evolutionarily conserved roles in the morphogenesis of skin appendages. , 2014, The Journal of investigative dermatology.

[33]  Daniel R. Zerbino,et al.  WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis , 2013, Bioinform..

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

[35]  Susan J. Brown,et al.  The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. , 2013, The Journal of heredity.

[36]  M. Albà,et al.  Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. , 2013, Molecular biology and evolution.

[37]  A. Azem,et al.  Methylation-controlled J-protein MCJ acts in the import of proteins into human mitochondria. , 2013, Human molecular genetics.

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

[39]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[40]  Travis C Glenn,et al.  Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.

[41]  Liam J. Revell,et al.  phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .

[42]  F. Peñagaricano,et al.  Differential expression of heat shock protein genes and their splice variants in bovine preimplantation embryos. , 2011, Journal of dairy science.

[43]  Colin N. Dewey Positional orthology: putting genomic evolutionary relationships into context , 2011, Briefings Bioinform..

[44]  Alex A. Pollen,et al.  Human-specific loss of regulatory DNA and the evolution of human-specific traits , 2011, Nature.

[45]  Adam C. Siepel,et al.  PHAST and RPHAST: phylogenetic analysis with space/time models , 2011, Briefings Bioinform..

[46]  J. Plotkin,et al.  Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.

[47]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[48]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[49]  Joshua M. Stuart,et al.  Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.

[50]  M. Braun,et al.  Duplication of accelerated evolution and growth hormone gene in passerine birds. , 2008, Molecular biology and evolution.

[51]  J. Mank,et al.  Fast-X on the Z: rapid evolution of sex-linked genes in birds. , 2007, Genome research.

[52]  N. Fletcher,et al.  Songbirds tune their vocal tract to the fundamental frequency of their song. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Laurent Excoffier,et al.  Conserved noncoding sequences are selectively constrained and not mutation cold spots , 2006, Nature Genetics.

[54]  D. Burt,et al.  Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. , 2005, Genome research.

[55]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[56]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[57]  S. Batzoglou,et al.  Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. , 2003, Genome research.

[58]  E C Dickinson,et al.  THE HOWARD AND MOORE COMPLETE CHECKLIST OF THE BIRDS OF THE WORLD. 4 th EDITION VOLUME 2 (2014) , 2003 .

[59]  W. Fitch Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

[60]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[61]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[62]  F. Wright The 'effective number of codons' used in a gene. , 1990, Gene.

[63]  Nicholas H. Barton,et al.  The Relative Rates of Evolution of Sex Chromosomes and Autosomes , 1987, The American Naturalist.

[64]  R. Clarke,et al.  Theory and Applications of Correspondence Analysis , 1985 .

[65]  W. Fitch Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.