Phylogenomics: The beginning of incongruence?

JEFFROY, O, BRINKMANN, H, DELSUC, F, PHILIPPE, H·2006·Trends in Genetics
DOI 10.1016/j.tig.2006.02.003

Cited by (700)

Items 301–400 of 700

  1. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
    Maria del Carmen Montero‐Calasanz, Jan P. Meier‐Kolthoff, Dao‐Feng Zhang, Adnan Yaramis, Manfred Rohde, Tanja Woyke, Nikos C. Kyrpides, Peter Schümann, Wen‐Jun Li, Markus Göker · 2017 · Frontiers in Microbiology
  2. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
    John Gatesy, Daniel B. Sloan, Jessica M. Warren, Richard H. Baker, Mark P. Simmons, Mark S. Springer · 2018 · Molecular Phylogenetics and Evolution
  3. Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity
    Fernando D. K. Tria, Julia Brueckner, Josip Skejo, Joana C. Xavier, Nils Kapust, Michael R. Knopp, Jessica L. E. Wimmer, Falk S. P. Nagies, Verena Zimorski, Sven B. Gould et al. · 2021 · Genome Biology and Evolution
  4. Species Tree Estimation Using ASTRAL: Practical Considerations
    Siavash Mirarab · 2019 · arXiv (Cornell University)
  5. Genotyping to distinguish microbial pathogenicity in periodontitis
    Masae Kuboniwa, Hiroaki Inaba, Atsuo Amano · 2010 · Periodontology 2000
  6. A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genusPungitius
    Baocheng Guo, Bohao Fang, Takahito Shikano, Paolo Momigliano, Cui Wang, Alexandra Kravchenko, Juha Merilä · 2019 · Molecular Ecology
  7. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within “Nassophorea–Synhymenia–Phyllopharyngea” Assemblage
    Bo Pan, Xiao Chen, Lina Hou, Qianqian Zhang, Zhishuai Qu, Alan Warren, Miao Miao · 2019 · Frontiers in Microbiology
  8. Fast and accurate distance‐based phylogenetic placement using divide and conquer
    Metin Balaban, Yueyu Jiang, Daniel Roush, Qiyun Zhu, Siavash Mirarab · 2021 · Molecular Ecology Resources
  9. Conflicting gene trees and phylogenomics
    Xinhui Zou, Song Ge · 2008 · Institute of Botany, CAS Institutional Repository
  10. Phylogenetic analysis of Microlicieae (Melastomataceae), with emphasis on the re-circumscription of the large genusMicrolicia
    Ana Flávia Alves Versiane, Rosana Romero, Marcelo Reginato, Cassiano Aimberê Dorneles Welker, Fabián Armando Michelangeli, Renato Goldenberg · 2021 · Botanical Journal of the Linnean Society
  11. Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin
    Vicky Merhej, Didier Raoult · 2012 · Frontiers in Cellular and Infection Microbiology
  12. Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
    Jéssica P. Gillung, Shaun L. Winterton, Keith M. Bayless, Ziad Khouri, Marek L. Borowiec, David K. Yeates, Lynn S. Kimsey, Bernhard Y. Misof, Seunggwan Shin, Xin Yu Zhou et al. · 2018 · Molecular Phylogenetics and Evolution
  13. Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)
    Felipe V. Freitas, Michael G. Branstetter, Terry Griswold, Eduardo A. B. Almeida · 2020 · Molecular Biology and Evolution
  14. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota
    Lucía Muggia, Claudio Gennaro Ametrano, Katja Sterflinger, Donatella Tesei · 2020 · Life
  15. Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)
    Kin Onn Chan, Carl R. Hutter, Perry L. Wood, L. Lee Grismer, Rafe M. Brown · 2020 · Proceedings of the Royal Society B Biological Sciences
  16. The complete mitochondrial genomes of deep-sea squid (Bathyteuthis abyssicola), bob-tail squid (Semirossia patagonica) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharanis), and their application to the phylogenetic analysis of Decapodiformes
    Yuumi Kawashima, Hidenori Nishihara, Tetsuya Akasaki, Masato Nikaido, Kotaro Tsuchiya, Susumu Segawa, Norihiro Okada · 2013 · Molecular Phylogenetics and Evolution
  17. Bioinformatics Approach in Plant Genomic Research
    Quang Ong, Phuc Nguyen, Nguyễn Phương Thảo, Ly Le · 2016 · Current Genomics
  18. Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North AmericanNyssa(Nyssaceae)
    Wenbin Zhou, Qiu‐Yun Xiang, Jun Wen · 2020 · Journal of Systematics and Evolution
  19. Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
    Fengming Han, Yong Li Peng, Lijia Xu, Pei‐Gen Xiao · 2014 · BMC Genomics
  20. Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes
    Ren Ren, Yazhou Sun, Yue Zhao, D. Geiser, Hong Ma, Xiao-Fan Zhou · 2016 · Genome Biology and Evolution
  21. Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles
    Kai Wang, Wei Hong, Hengwu Jiao, Huabin Zhao · 2017 · Scientific Reports
  22. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing
    Lisa N. Barrow, Hannah F. Ralicki, Sandra A. Emme, Emily Moriarty Lemmon · 2014 · Molecular Phylogenetics and Evolution
  23. Identifying and addressing methodological incongruence in phylogenomics: A review
    James F. Fleming, Alberto Valero‐Gracia, Torsten H. Struck · 2023 · Evolutionary Applications
  24. Phylogenomic Analysis Resolves the Formerly Intractable Adaptive Diversification of the Endemic Clade of East Asian Cyprinidae (Cypriniformes)
    Wenjing Tao, Ming Zou, Xuzhen Wang, Xiaoni Gan, Richard L. Mayden, Shunping He · 2010 · PLoS ONE
  25. A new basal porpoise,Pterophocaena nishinoi(Cetacea, Odontoceti, Delphinoidea), from the upper Miocene of Japan and its phylogenetic relationships
    Mizuki Murakami, Chieko Shimada, Yoshinori Hikida, Hiromichi Hirano · 2012 · Journal of Vertebrate Paleontology
  26. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon
    Nicolas Magain, Jolanta Miądlikowska, Olaf Mueller, Michael T. Gajdeczka, Camille Truong, Asaf A. Salamov, Inna L Dubchak, Igor V. Grigoriev, Bernard Goffinet, Emmanuël Sérusiaux et al. · 2017 · Molecular Phylogenetics and Evolution
  27. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata
    Nicolás Mongiardino Koch, Jacques A. Gauthier · 2018 · PLoS ONE
  28. Phylogeny of gracillariid leaf‐mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data
    Xuankun Li, Ryan A. St Laurent, Chandra Earl, Camiel Doorenweerd, Erik J. van NIEUKERKEN, Donald Ray Davis, Chris A. Johns, Atsushi Kawakita, Shigeki Kobayashi, Andreas Zwick et al. · 2021 · Cladistics
  29. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
    Gergely J. Szöllősi, Vincent Daubin · 2012 · Methods in molecular biology
  30. Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation
    Lihua Yang, AJ Harris, Fang Wen, Zheng Li, Chao Feng, Hanghui Kong, Ming Kang · 2023 · Systematic Biology
  31. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
    Alex Dornburg, Jeffrey P. Townsend, Zheng Wang · 2017 · Advances in genetics
  32. Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses
    Jessica A. Rick, Chad D. Brock, Alexander L. Lewanski, Jimena Golcher‐Benavides, Catherine E. Wagner · 2023 · Systematic Biology
  33. Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)
    Verônica A. Thode, Lúcia G. Lohmann, Isabel Sanmartín · 2020 · Journal of Systematics and Evolution
  34. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox
    Rémi Allio, Marie‐Ka Tilak, Céline Scornavacca, Nico L. Avenant, Andrew C. Kitchener, Erwan Corre, Benoît Nabholz, Frédéric Delsuc · 2021 · eLife
  35. Revisiting Papillomavirus Taxonomy: A Proposal for Updating the Current Classification in Line with Evolutionary Evidence
    Koenraad Van Doorslaer · 2022 · Viruses
  36. Evidence for Homologous Recombination in Intracellular Chemosynthetic Clam Symbionts
    Frank J. Stewart, C. Robert Young, Colleen M. Cavanaugh · 2009 · Molecular Biology and Evolution
  37. Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)
    Andrew J. Mason, Felipe G. Grazziotin, Hussam Zaher, Alan R. Lemmon, Emily Moriarty Lemmon, Christopher L. Parkinson · 2019 · Journal of Biogeography
  38. Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)
    Min Zhao, Sarah M. Kurtis, Noor D. White, Andre E. Moncrieff, Rafael N. Leite, Robb Thomas Brumfield, Edward Louis Braun, Rebecca T. Kimball · 2022 · Systematic Biology
  39. Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)
    Lily C. Hughes, Chloe M. Nash, William T. White, Mark W. Westneat · 2022 · Systematic Biology
  40. Deep Questions in the Tree of Life
    Keeling, Patrick J. · 2007 · Science
  41. Histories of molecules: Reconciling the past
    Maureen A. O’Malley · 2015 · Studies in History and Philosophy of Science Part A
  42. Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress, Promise, and Future Prospects
    Pamela S. Soltis, Michael J. Moore, Gordon Burleigh, Pamela S. Soltis · 2009 · Critical Reviews in Plant Sciences
  43. A synopsis of rodent molecular phylogenetics, systematics and biogeography
    Pierre‐Henri Fabre, Lionel Hautier, Emmanuel Douzery · 2015 · Cambridge University Press eBooks
  44. Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis)
    Peter J. Unmack, Jonathan Sandoval‐Castillo, Michael P. Hammer, Mark Adams, Tarmo A. Raadik, Luciano Bellagamba Beheregaray · 2017 · Molecular Phylogenetics and Evolution
  45. The impact of HGT on phylogenomic reconstruction methods
    Pascal Lapierre, Erica Lasek‐Nesselquist, Johann Peter Gogarten · 2012 · Briefings in Bioinformatics
  46. Repeated Evolution of Identical Domain Architecture in Metazoan Netrin Domain-Containing Proteins
    Lucas Leclère, Fabian Rentzsch · 2012 · Genome Biology and Evolution
  47. Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles
    Bin Lu, Weizhao Yang, Qiang Dai, Jinzhong Fu · 2013 · PLoS ONE
  48. Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
    Josefin Stiller, Guojie Zhang · 2019 · Diversity
  49. Higher‐level molecular phylogeny of jumping plant lice (Hemiptera: Sternorrhyncha: Psylloidea)
    Geonho Cho, Igor Malenovský, Seunghwan Lee · 2019 · Systematic Entomology
  50. Maintaining replication origins in the face of genomic change
    Sara C. Di Rienzi, Kimberly C. Lindstrom, Tobias P. Mann, William Stafford Noble, M. K. Raghuraman, Bonita J. Brewer · 2012 · Genome Research
  51. Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups
    Chenhong Li, K. A. M. Rosana, Michael Garcia, Gavin J. P. Naylor · 2012 · Molecular Phylogenetics and Evolution
  52. Overly simplistic substitution models obscure green plant phylogeny
    Endymion D. Cooper · 2014 · Trends in Plant Science
  53. Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes)
    Ralf Britz, Kevin W. Conway, Lukas Rüber · 2014 · Zoological Journal of the Linnean Society
  54. Phylogenetic analysis of RAD ‐seq data: examining the influence of gene genealogy conflict on analysis of concatenated data
    David M. Rivers, Clive Terence Darwell, David M. Althoff · 2016 · Cladistics
  55. An In Silico Comparison of Protocols for Dated Phylogenomics
    Rupert A. Collins, Tomas Hrbek · 2018 · Systematic Biology
  56. Conidae phylogenomics and evolution
    Samuel Abalde, M. Jimenez-Tenorio, Juan E. Uribe, Rafael Zardoya · 2019 · Zoologica Scripta
  57. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)
    Kévin Debray, Jordan Marie‐Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot · 2019 · BMC Evolutionary Biology
  58. The complex evolutionary history of sulfoxide synthase in ovothiol biosynthesis
    Marco Gerdol, Marco Sollitto, Alberto Pallavicini, Immacolata Castellano · 2019 · Proceedings of the Royal Society B Biological Sciences
  59. Complete genomes derived by directly sequencing freshwater bloom populations emphasize the significance of the genus level ADA clade within the Nostocales
    Theo W. Dreher, Edward W. Davis, Ryan Mueller · 2021 · Harmful Algae
  60. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection
    Hans‐Jürgen Bandelt, Arne Dür · 2006 · Molecular Phylogenetics and Evolution
  61. Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum
    Vadim V. Goremykin, Roberto Viola, Frank H. Hellwig · 2009 · Journal of Molecular Evolution
  62. An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework
    Jean‐Philippe Doyon, Sylvie Hamel, Cédric Chauve · 2011 · IEEE Transactions on Computational Biology and Bioinformatics
  63. Plastome Rearrangements in the “Adenocalymma-Neojobertia” Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications
    Luiz Henrique M. Fonseca, Lúcia G. Lohmann · 2017 · Frontiers in Plant Science
  64. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies
    Cynthia Steiner, Anna Mitelberg, Rosanna Tursi, Oliver A. Ryder · 2012 · Molecular Phylogenetics and Evolution
  65. Phylogenomic approaches to deciphering the tree of life
    Jun Wen, Jianquan Liu, Song Ge, Qiu‐Yun Xiang, Elizabeth A. Zimmer · 2015 · Journal of Systematics and Evolution
  66. Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)
    Noor D. White, Michael J. Braun · 2019 · Molecular Phylogenetics and Evolution
  67. Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past
    Robert J. M. Eveleigh, Conor Joseph Meehan, John M. Archibald, Robert Gerald Beiko · 2013 · Genome Biology and Evolution
  68. Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes
    M. Vincent Hirt, Gloria Arratia F., Wei‐Jen Chen, Richard L. Mayden, Kevin L. Tang, Robert M. Wood, Andrew M. Simons · 2017 · Biological Journal of the Linnean Society
  69. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)
    Claudio Gennaro Ametrano, Felix Grewe, Pedro Willem Crous, Stephen B. Goodwin, Chen Bao Liang, Laura Selbmann, Helge Thorsten Lumbsch, Steven Don Leavitt, Lucía Muggia · 2019 · IMA Fungus
  70. Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data
    Stefanie A. Hartmann, Conrad Helm, Birgit Nickel, Matthias Meyer, Torsten H. Struck, Ralph Tiedemann, Joachim Selbig, Christoph Bleidorn · 2012 · PLoS ONE
  71. Evolutionary history of chloridoid grasses estimated from 122 nuclear loci
    Amanda E. Fisher, Kristen M. Hasenstab, Hester L. Bell, Ellen Blaine, Amanda L. Ingram, J. Travis Columbus · 2016 · Molecular Phylogenetics and Evolution
  72. A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans
    James F. Fleming, Roberto Feuda, Nicholas William Roberts, Davide Pisani · 2020 · Genome Biology and Evolution
  73. Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)
    Dennis V. Lavrov, Maria Cristina Díaz, Manuel Maldonado, Christine C. Morrow, Thierry Pérez, Shirley A. Pomponi, ROBERT W. THACKER · 2023 · PLoS ONE
  74. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction
    Erfan Sayyari, Siavash Mirarab · 2016 · BMC Genomics
  75. Retrieving a mitogenomic mammal tree using composite taxa
    Véronique Campbell, François‐Joseph Lapointe · 2010 · Molecular Phylogenetics and Evolution
  76. HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences
    Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, Max Essex, Simon D. W. Frost, Astrid Gall, Simani Gaseitsiwe, M. Kate Grabowski, Ronald Henry Gray et al. · 2017 · AIDS Research and Human Retroviruses
  77. Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes
    Qijing Xia, Hongbin Zhang, Dong Lv, Yousry Aly El-Kassaby, Wei Li · 2023 · BMC Genomics
  78. The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models
    Filipe Sousa, Peter Civáň, Peter Gordon Foster, Cymon J. Cox · 2020 · Frontiers in Plant Science
  79. Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
    Mezzalina Vankan, Simon Y. W. Ho, David Alejandro Duchêne · 2021 · Systematic Biology
  80. Phylogenomics
    José Salvatore Leister Patané, Joaquim Martins, João Carlos Setúbal · 2017 · Methods in molecular biology
  81. Multiple outgroups can cause random rooting in phylogenomics
    Rob DeSalle, Apurva Narechania, Michael Tessler · 2023 · Molecular Phylogenetics and Evolution
  82. Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
    Jaqueline Hess, Nick Goldman · 2011 · PLoS ONE
  83. Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)
    Zheng Bin Randolph Quek, Danwei Huang · 2019 · Molecular Phylogenetics and Evolution
  84. Evolution of the GST Omega Gene Family in 12 Drosophila Species
    Kathryn B. Walters, Paaqua A. Grant, Diana L. E. Johnson · 2009 · Journal of Heredity
  85. Application of phylogenomic tools to unravel anthozoan evolution
    Zheng Bin Randolph Quek, Danwei Huang · 2021 · Coral Reefs
  86. Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus–host interaction proteins
    Xiao-Yong Zhan, Gao‐Feng Zha, Yulong He · 2023 · Frontiers in Cellular and Infection Microbiology
  87. Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae)
    Lihua Yang, Xi‐Zuo Shi, Fang Wen, Ming Kang · 2023 · Annals of Botany
  88. The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes
    Adam Dawid Urantówka, Aleksandra Kroczak, Paweł Mackiewicz · 2017 · BMC Evolutionary Biology
  89. Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets
    László G. Nagy, Gergely J. Szöllősi · 2017 · Advances in genetics
  90. Sources of Error and Incongruence in Phylogenomic Analyses
    Christoph Bleidorn · 2017 · Springer eBooks
  91. Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)
    Yi‐Kai Tea, Xin Xu, Joseph D. DiBattista, Nathan C. Lo, Peter F. Cowman, Simon Y. W. Ho · 2021 · Systematic Biology
  92. Different Phylogenomic Approaches to Resolve the Evolutionary Relationships among Model Fish Species
    Enrico Negrisolo, Heiner Kuhl, Claudio Forcato, Nicola Vitulo, Richard Reinhardt, Tomaso Patarnello, Luca Bargelloni · 2010 · Molecular Biology and Evolution
  93. Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing
    Augusto Giaretta, Bruce Murphy, Olivier Maurin, Fiorella Fernanda Mazine, Paulo Takeo Sano, Eve Lucas · 2022 · Frontiers in Plant Science
  94. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex
    Michael San Jose, Camiel Doorenweerd, Scott M. Geib, Norman B. Barr, Julian R. Dupuis, Luc Leblanc, Angela N Kauwe, Kimberley Y. Morris, Daniel Rubinoff · 2023 · Molecular Phylogenetics and Evolution
  95. Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?
    Emmanuelle Jousselin, Armelle Cœur d’Acier, Anne‐Laure Clamens, Maxime Galan, Corinne Cruaud, Valérie Barbe, Alejandro Manzano-Marı́n · 2024 · Zoological Journal of the Linnean Society
  96. Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)
    Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José Einicker Lamas, Christine L. Lambkin, Neal Luit Evenhuis, James A. Nicholls, DIANA M. HARTLEY et al. · 2020 · Cladistics
  97. Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes
    Samuel Blanquart, Olivier Gascuel · 2011 · BMC Evolutionary Biology
  98. Application of multigene phylogenetics and site‐stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)
    Gina V. Filloramo, Gary W. Saunders · 2016 · Journal of Phycology
  99. GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level
    Laura G. Macías, Eladio Barrio, Christina Toft · 2020 · G3 Genes Genomes Genetics
  100. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order
    Simone M. Gable, Jasmine Mendez, Nicholas Bushroe, Adam Wilson, Michael I. Byars, Marc Tollis · 2023 · Genes