Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants
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Gregory W. Stull | Drew A. Larson | Joseph F. Walker | Karolis Ramanauskas | Holly Robertson | Alexa S. Tyszka | Eric C. Bretz | Miles D. Woodcock-Girard
[1] Stephen A. Smith,et al. Compositional shifts associated with major evolutionary transitions in plants , 2023, bioRxiv.
[2] R. Bock,et al. Control of plastid inheritance by environmental and genetic factors , 2023, Nature Plants.
[3] T. Lenton,et al. The origin and early evolution of plants. , 2022, Trends in plant science.
[4] C. Davis,et al. PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data , 2022, Applications in plant sciences.
[5] M. F. Camus,et al. Inheritance through the cytoplasm , 2022, Heredity.
[6] Sunil Kumar Sahu,et al. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants , 2022, Frontiers in Plant Science.
[7] Xiangdong Yang,et al. Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus , 2021, Diversity.
[8] Li-an Xu,et al. Parent–offspring variation transmission in full-sib families revealed predominantly paternal inheritance of chloroplast DNA in Pinus massoniana (Pinaceae) , 2021, Tree Genetics & Genomes.
[9] J. Doyle. Defining coalescent genes: Theory meets practice in organelle phylogenomics. , 2021, Systematic biology.
[10] Gregory W. Stull,et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms , 2021, Nature Plants.
[11] Matthew G. Johnson,et al. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life , 2021, bioRxiv.
[12] Xianchun Zhang,et al. NOVOWrap: An automated solution for plastid genome assembly and structure standardization , 2020, Molecular ecology resources.
[13] C. Cox,et al. The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models , 2020, Frontiers in Plant Science.
[14] Diego F. Morales-Briones,et al. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l , 2020, Systematic biology.
[15] Gregory W. Stull,et al. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. , 2020, American journal of botany.
[16] C. Cox,et al. The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models , 2020, PeerJ.
[17] Antonis Rokas,et al. Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices , 2020, bioRxiv.
[18] Don C. Jones,et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement , 2020, Nature Genetics.
[19] Gregory W. Stull,et al. Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae , 2020, Systematic biology.
[20] S. Ho,et al. Phylogenetic signal is associated with the degree of variation in root-to-tip distances , 2020, bioRxiv.
[21] Diego F. Morales-Briones,et al. Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l , 2020 .
[22] Stephen A. Smith,et al. PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS. , 2019, Systematic biology.
[23] C. dePamphilis,et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes , 2019, bioRxiv.
[24] Xun Xu,et al. One thousand plant transcriptomes and the phylogenomics of green plants , 2019, Nature.
[25] Robert K. Jansen,et al. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. , 2019, Molecular phylogenetics and evolution.
[26] T. Yi,et al. Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat , 2019, Genome biology and evolution.
[27] G. Petersen,et al. Mitochondrial genome evolution in parasitic plants , 2019, BMC Evolutionary Biology.
[28] Ming-Hui Chen,et al. Assessing Combinability of Phylogenomic Data using Bayes Factors , 2018, bioRxiv.
[29] Gregory W. Stull,et al. Characterizing gene tree conflict in plastome-inferred phylogenies , 2019, bioRxiv.
[30] Seung In Park,et al. Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles , 2018, Genome biology and evolution.
[31] Jeremy M. Brown,et al. Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological? , 2018, Systematic biology.
[32] A. Schneider,et al. Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae , 2018, Genome biology and evolution.
[33] Jin-Hua Ran,et al. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms , 2018, Proceedings of the Royal Society B: Biological Sciences.
[34] Bruno Contreras-Moreira,et al. Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. , 2018, The New phytologist.
[35] Stephen A Smith,et al. So many genes, so little time: A practical approach to divergence-time estimation in the genomic era , 2018, PloS one.
[36] Mark N. Puttick,et al. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte , 2018, Current Biology.
[37] Stephen A. Smith,et al. Constructing a broadly inclusive seed plant phylogeny. , 2018, American journal of botany.
[38] Pamela S Soltis,et al. Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. , 2018, American journal of botany.
[39] A. von Haeseler,et al. Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model , 2017, bioRxiv.
[40] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[41] A. von Haeseler,et al. UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.
[42] Y. van de Peer,et al. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants , 2017, Molecular biology and evolution.
[43] Joseph W. Brown,et al. Phyx: phylogenetic tools for unix , 2017, Bioinform..
[44] Karen B Barnard-Kubow,et al. Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility. , 2017, The New phytologist.
[45] N. Street,et al. Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae) , 2016, bioRxiv.
[46] Charles S. P. Foster,et al. Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale , 2016, Systematic biology.
[47] Ben Nichols,et al. Distributed under Creative Commons Cc-by 4.0 Vsearch: a Versatile Open Source Tool for Metagenomics , 2022 .
[48] M. Christenhusz,et al. The number of known plants species in the world and its annual increase , 2016 .
[49] Olga Chernomor,et al. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices , 2016, Systematic biology.
[50] Jeffrey P. Mower,et al. Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution. , 2016, Molecular biology and evolution.
[51] G. Petersen,et al. Massive gene loss in mistletoe (Viscum, Viscaceae) mitochondria , 2015, Scientific Reports.
[52] Jeffrey P. Mower,et al. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. , 2015, The New phytologist.
[53] Peter Crane,et al. Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms Systematic Biology Advance Access Published May 4, 2015 , 2022 .
[54] Stephen A. Smith,et al. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants , 2015, BMC Evolutionary Biology.
[55] P. Keeling,et al. Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes , 2015, Proceedings of the National Academy of Sciences.
[56] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[57] Mark Fishbein,et al. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics , 2014, Applications in plant sciences.
[58] M. Zanis,et al. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae). , 2014, American journal of botany.
[59] T. Embley,et al. Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions , 2014, Systematic biology.
[60] Pamela S Soltis,et al. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes , 2014, BMC Evolutionary Biology.
[61] Andrew J. Alverson,et al. Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella , 2013, Science.
[62] Antonis Rokas,et al. Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.
[63] Susana M. Coelho,et al. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida , 2013, Proceedings of the National Academy of Sciences.
[64] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[65] T. Vandergon,et al. Loss of the Acetyl-CoA Carboxylase (accD) Gene in Poales , 2013, Plant Molecular Biology Reporter.
[66] Brian C. O'Meara,et al. treePL: divergence time estimation using penalized likelihood for large phylogenies , 2012, Bioinform..
[67] R. Lanfear,et al. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. , 2012, Molecular biology and evolution.
[68] Shane S. Sturrock,et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..
[69] Saravanaraj N. Ayyampalayam,et al. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). , 2012, American journal of botany.
[70] Jeffrey P. Mower,et al. Plant Mitochondrial Genome Diversity: The Genomics Revolution , 2012 .
[71] D. E. Soltis,et al. Angiosperm phylogeny: 17 genes, 640 taxa. , 2011, American journal of botany.
[72] Felix Grewe,et al. Mitochondrial Genome Evolution in the Plant Lineage , 2011 .
[73] Y. Qiu,et al. Angiosperm phylogeny inferred from sequences of four mitochondrial genes , 2010 .
[74] Jeet Sukumaran,et al. DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..
[75] Andrew J. Alverson,et al. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). , 2010, Molecular biology and evolution.
[76] Douglas L. Theobald,et al. A formal test of the theory of universal common ancestry , 2010, Nature.
[77] J. G. Burleigh,et al. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots , 2010, Proceedings of the National Academy of Sciences.
[78] Bartek Wilczynski,et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..
[79] Tae-Kun Seo. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. , 2008, Molecular biology and evolution.
[80] David Q. Matus,et al. Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.
[81] Linda A. Raubeson,et al. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates , 2008, BMC Evolutionary Biology.
[82] Pamela S Soltis,et al. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms , 2007, Proceedings of the National Academy of Sciences.
[83] D. Lavrov. Key transitions in animal evolution: a mitochondrial DNA perspective. , 2007, Integrative and comparative biology.
[84] Y. Qiu,et al. A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes , 2007, International Journal of Plant Sciences.
[85] Gábor Csárdi,et al. The igraph software package for complex network research , 2006 .
[86] M. Neiman,et al. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. , 2005, The New phytologist.
[87] R. Baker,et al. Hidden likelihood support in genomic data: can forty-five wrongs make a right? , 2005, Systematic biology.
[88] Peter G Foster,et al. Modeling compositional heterogeneity. , 2004, Systematic biology.
[89] A. Rokas,et al. Animal mitochondrial DNA recombination revisited , 2003 .
[90] M. Donoghue,et al. The root of the angiosperms revisited , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[91] H. Philippe,et al. Heterotachy, an important process of protein evolution. , 2002, Molecular biology and evolution.
[92] M. Sanderson. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.
[93] Laurence D. Hurst,et al. The evolution of isochores , 2001, Nature Reviews Genetics.
[94] J. Palmer,et al. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. , 2000, Molecular biology and evolution.
[95] James Lyons-Weiler,et al. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[96] W. Kress,et al. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences , 2000 .
[97] Yangrae Cho,et al. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[98] J. Palmer,et al. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[99] C. dePamphilis,et al. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[100] Mark W. Chase,et al. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes , 1999, Nature.
[101] M. Donoghue,et al. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. , 1999, Science.
[102] W. John Kress,et al. Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences , 1997 .
[103] H. Mogensen,et al. INVITED SPECIAL PAPER: The hows and whys of cytoplasmic inheritance in seed plants , 1996 .
[104] D. Mccauley. Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[105] M T Clegg,et al. Chloroplast gene sequences and the study of plant evolution. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[106] James F. Smith. Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .
[107] J. Doyle,et al. Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy , 1992 .
[108] M. Asmussen,et al. Comparative effects of pollen and seed migration on the cytonuclear structure of plant populations. II. Paternal cytoplasmic inheritance. , 1992, Genetics.
[109] Edward M. Reingold,et al. Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..
[110] M. Asmussen,et al. Comparative effects of pollen and seed migration on the cytonuclear structure of plant populations. I. Maternal cytoplasmic inheritance. , 1991, Genetics.
[111] L. Rieseberg,et al. Phylogenetic consequences of cytoplasmic gene flow in plants. , 1991 .
[112] J. Palmer,et al. Chloroplast DNA Variation and Plant Phylogeny , 1988 .
[113] Wen-Hsiung Li,et al. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[114] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[115] J. Farris. Estimating Phylogenetic Trees from Distance Matrices , 1972, The American Naturalist.