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Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses

https://doi.org/10.1101/603191
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1047openalex-snapshot
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inferredcites →https://doi.org/10.1002/j.1537-2197.1968.tb07397.xopenalex-snapshot
THE INDUCTION OF BIOCHEMICAL AND MORPHOLOGICAL MUTANTS IN THE MOSS PHYSCOMITRELLA PATENS
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Evolution by Gene Duplication
inferredcites →https://doi.org/10.1016/j.pbi.2012.03.010openalex-snapshot
Rarely successful polyploids and their legacy in plant genomes
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Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model
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Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?
inferredcites →https://doi.org/10.1016/j.ympev.2016.01.008openalex-snapshot
A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)
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Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae
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KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
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Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum
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Phyutility: a phyloinformatics tool for trees, alignments and molecular data
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Trimmomatic: a flexible trimmer for Illumina sequence data
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
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Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants
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A codon-based model of nucleotide substitution for protein-coding DNA sequences.
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Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms
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Circos: An information aesthetic for comparative genomics
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A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
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inferredcites →https://doi.org/10.1111/j.1475-4983.2011.01111.xopenalex-snapshot
Permian bryophytes of Western Gondwanaland from the Paraná Basin in Brazil
inferredcites →https://doi.org/10.1111/nph.13887openalex-snapshot
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inferredcites →https://doi.org/10.1111/nph.14812openalex-snapshot
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inferredcites →https://doi.org/10.1111/tpj.13801openalex-snapshot
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inferredcites →https://doi.org/10.1126/sciadv.1501084openalex-snapshot
Early genome duplications in conifers and other seed plants
inferredcites →https://doi.org/10.1126/sciadv.1603195openalex-snapshot
Revisiting ancestral polyploidy in plants
inferredcites →https://doi.org/10.1126/science.1150646openalex-snapshot
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
inferredcites →https://doi.org/10.1126/science.1163197openalex-snapshot
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
inferredcites →https://doi.org/10.1126/science.1207205openalex-snapshot
Recently Formed Polyploid Plants Diversify at Lower Rates
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Diversification of land plants: insights from a family-level phylogenetic analysis
inferredcites →https://doi.org/10.1186/1471-2148-7-130openalex-snapshot
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens
inferredcites →https://doi.org/10.1186/1756-0500-7-490openalex-snapshot
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis
inferredcites →https://doi.org/10.1186/gb-2012-13-1-r3openalex-snapshot
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inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1186/s13059-017-1241-zopenalex-snapshot
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
inferredcites →https://doi.org/10.1201/9781420005592.ch17openalex-snapshot
Dating the Diversification of the Pleurocarpous Mosses
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1639/0007-2745(2005)108[27:eoplog]2.0.co;2openalex-snapshot
Effect of Ploidy Level on Growth, Differentiation, and Morphology in Physcomitrella patens
inferredcites →https://doi.org/10.1639/0007-2745(2007)110[533:tapite]2.0.co;2openalex-snapshot
Taxonomy and phylogeny in the earliest diverging pleurocarps: square holes and bifurcating pegs
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Dynamic Display of Changing Posterior in Bayesian Survival Analysis: The Software
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The meaning of Darwin's “abominable mystery”
inferredcites →https://doi.org/10.3732/ajb.1000055openalex-snapshot
Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)
inferredcites →https://doi.org/10.3732/ajb.1000316openalex-snapshot
Bryophyte diversity and evolution: Windows into the early evolution of land plants
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Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
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Exploring the fossil history of pleurocarpous mosses: Tricostaceae fam. nov. from the Cretaceous of Vancouver Island, Canada
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How to Summarize Estimates of Ancestral Divergence Times

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106965openalex-snapshot
High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae
inferred← citeshttps://doi.org/10.1038/s41477-021-00888-zopenalex-snapshot
Charting the genomic landscape of seed-free plants
inferred← citeshttps://doi.org/10.11646/bde.43.1.12openalex-snapshot
Karyotypic diversity and cryptic speciation: Have we vastly underestimated moss species diversity?
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