2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomology
2013
Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs
Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli K, Leonard JA, Meyer M, Krause J, Pääbo S, Green RE, Wayne RK. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 2013, 342: 871-874. PMID: 24233726, DOI: 10.1126/science.1243650.Peer-Reviewed Original ResearchConceptsModern dogsMitochondrial genomeOnset of domesticationPrehistoric canidsAncient canidsComplete mitochondrial genomeModern canidsNew WorldDomestic dogsEast AsiaEuropean originDomestication processMolecular datingGenetic dataEuropeGenomeTemporal originCanidsDatingEurasiaCulminationSiberiaAsiaOriginDomesticationPhylogenetic and phylogenomic overview of the Polyporales
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013, 105: 1350-1373. PMID: 23935031, DOI: 10.3852/13-003.Peer-Reviewed Original ResearchConceptsSingle-copy genePhylogenetic informativeness analysesResidual polyporoid cladeBayesian phylogenetic analysisPolyporales speciesMajor lineagesPhylogenomic datasetsAvailable genomesCorresponding cladesPhlebioid cladePolyporoid cladeNew genomesGenome dataPhylogenetic analysisSuprageneric taxonomyCertain taxaPhylogenetic systematicsGenomic datasetsIdentical topologiesPolyporalesGenomeCladeSupport valuesGenesLineagesEvaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
2011
Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes
Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes. PLOS ONE 2011, 6: e27239. PMID: 22076140, PMCID: PMC3208591, DOI: 10.1371/journal.pone.0027239.Peer-Reviewed Original ResearchConceptsEvolutionary breakpoint regionsTandem repeatsEvolutionary regionBreakpoint regionSpecific tandem repeatMore base pairsGreat apesGenome architectureMammalian genomesGenome organizationSynteny blocksChromatin conformationEvolutionary biologistsGenomic architectureAncestral reconstructionGenome instabilityMacaque genomeChromosomal reorganizationTransposable elementsGenomic regionsHuman genomeGenomic areasAlu elementsGenomeBase pairsPhyDesign: an online application for profiling phylogenetic informativeness
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessPhylogenetic studiesPhylogenetic informativeness analysesBroad taxonomic samplingMolecular phylogenetic studiesTree of lifeOrthologous genesPhylogenetic samplingTaxonomic samplingPhylogenetic questionsPhylogenetic purposesEfficiency of sequencingSequence alignmentMarker selectionUltrametric treeDiverse suiteUtility of locusLociTreesUser-friendly toolGenomeGenesSequencingSpeciesDiversityTasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data. PLOS ONE 2011, 6: e19039. PMID: 21533038, PMCID: PMC3080880, DOI: 10.1371/journal.pone.0019039.Peer-Reviewed Original ResearchConceptsFungal lineagesSoil fungal diversityNovel fungal lineagesTree estimationITS dataNuclear ribosomal ITS regionEnvironmental samplesRibosomal ITS regionFungal diversityPublic sequence databasesComplex communitiesDivergent taxaBasal classPhylogenetic testsNovel lineageITS phylogenyPhylogenetic analysisEctomycorrhizal isolatesITS sequencesITS regionEnvironmental samplingSequence databasesSATéFocal questionLineages
2010
Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
Townsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology 2010, 59: 446-457. PMID: 20547780, DOI: 10.1093/sysbio/syq025.Peer-Reviewed Original ResearchConceptsPhylogenetic experimental designOptimal rateAsymptotic impactAnalytical predictionsAddition of charactersOptimal selectionObvious applicationApproximate ideaEstimation of ratesCurrent phylogenetic studiesOptimal efficiencyTheoryDeep internodesTaxon additionRate of evolutionExperimental designNew taxonPhylogenetic informativenessPhylogenetic relationships
2009
The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 2009, 58: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.Peer-Reviewed Original ResearchConceptsCharacter state reconstructionCommon ancestorAncestral character state reconstructionPhylogenetic informativeness analysesSexual reproductive structuresAscus dehiscenceMaximum likelihood phylogenyPhylogenetic informativenessEcological traitsFungal systematicsAncestral reconstructionNutritional modesRibosomal genesLargest phylumMorphological traitsRelated speciesReproductive structuresProtein geneAscomycota TreePezizomycotinaMultiple originsState reconstructionSporocarpsGene assessmentGenes
2008
The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
Townsend JP, López-Giráldez F, Friedman R. The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree. Journal Of Molecular Evolution 2008, 67: 437-447. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.Peer-Reviewed Original ResearchConceptsAmino acid sequencePhylogenetic informativenessAcid sequenceVertebrate treeDNA sequencesMolecular evolutionary patternsEarly placental mammalsGenes c-mycDivergence timesMolecular evolutionPhylogenetic conflictEarly vertebratesEvolutionary patternsPlacental mammalsNucleotide sequenceMuroid rodentsFunctional constraintsGenesC-MycSupport valuesSequenceNucleotidesNumber of charactersHigh informativenessTreesRPS4Ygene family evolution in primates
Andrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Ygene family evolution in primates. BMC Ecology And Evolution 2008, 8: 142. PMID: 18477388, PMCID: PMC2397393, DOI: 10.1186/1471-2148-8-142.Peer-Reviewed Original ResearchConceptsRPS4Y genesPositive selectionTestis-specific expression patternRibosomal protein genesRibosomal protein S4Non-synonymous substitutionsAmino acid replacementsMaximum likelihood analysisDuplication eventsFamily evolutionFunctional paralogsEvolutionary historyGene familyFunctional genesSex chromosomesProtein S4Protein functionPrimate phylogenyProtein domainsHuman lineageNew World monkeysProtein geneGene dosageAcid replacementsY chromosome
2006
Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia
MARMI J, LÓPEZ‐GIRÁLDEZ F, MACDONALD DW, CALAFELL F, ZHOLNEROVSKAYA E, DOMINGO‐ROURA X. Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia. Molecular Ecology 2006, 15: 1007-1020. PMID: 16599963, DOI: 10.1111/j.1365-294x.2006.02747.x.Peer-Reviewed Original ResearchConceptsPhylogeographic groupsAsian badgersMitochondrial DNAMitochondrial DNA control regionStrong phylogeographic structureDNA control regionWidespread geographic rangeMedian-joining networkTamura-Nei modelEurasian badgerPhylogeographic structureGenetic structuringBiogeographic processesMolecular varianceGroups of populationsLarge geographic variabilityEvolutionary significanceMantel testEnd of PlioceneMolecular dataControl regionGenetic variationGeographic rangeMorphological charactersRate heterogeneity
2005
Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores
DOMINGO-ROURA X, LÓPEZ-GIRÁLDEZ F, SAEKI M, MARMI J. Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores. Genetics Research 2005, 85: 223-233. PMID: 16174341, DOI: 10.1017/s0016672305007512.Peer-Reviewed Original ResearchConceptsPhylogenetic inferenceRepetitive motifsFlanking regionsBasal positionNon-coding lociAncestral DNA sequencesShort repetitive motifsHigh mutation rateRepeat additionDNA sequencesCarnivore phylogenyComplex microsatelliteMutational changesCarnivore speciesMutation rateMonotypic familyAilurus fulgensRed pandaMutational hotspotsTree topologyLociRepeat expansionComparative evolutionMeles melesDeletion