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Bursts of novel composite gene families at major nodes in animal evolution

https://doi.org/10.1101/2023.07.10.548381

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis

inferredcites →https://doi.org/10.1007/s13238-011-1018-1openalex-snapshot

Structure and function of WD40 domain proteins

inferredcites →https://doi.org/10.1016/j.cub.2015.09.066openalex-snapshot

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

inferredcites →https://doi.org/10.1016/j.cub.2017.02.031openalex-snapshot

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

inferredcites →https://doi.org/10.1016/j.jmb.2007.06.022openalex-snapshot

Quantification of the Elevated Rate of Domain Rearrangements in Metazoa

inferredcites →https://doi.org/10.1016/j.sbi.2013.02.012openalex-snapshot

Dynamics and adaptive benefits of modular protein evolution

inferredcites →https://doi.org/10.1016/j.tibs.2008.05.008openalex-snapshot

Arrangements in the modular evolution of proteins

inferredcites →https://doi.org/10.1016/j.ydbio.2017.09.015openalex-snapshot

Furcation and fusion: The phylogenetics of evolutionary novelty

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

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Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules

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Exon shuffling and other ways of module exchange

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Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1

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The Capsaspora genome reveals a complex unicellular prehistory of animals

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/nrg1204openalex-snapshot

The origin of new genes: glimpses from the young and old

inferredcites →https://doi.org/10.1038/s41467-018-04136-5openalex-snapshot

Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty

inferredcites →https://doi.org/10.1038/s41467-021-22074-7openalex-snapshot

Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding

inferredcites →https://doi.org/10.1038/s41559-017-0331-3openalex-snapshot

Ctenophore relationships and their placement as the sister group to all other animals

inferredcites →https://doi.org/10.1038/s41559-019-1069-xopenalex-snapshot

Gene gain and loss across the metazoan tree of life

inferredcites →https://doi.org/10.1038/s41559-020-1129-2openalex-snapshot

Widespread patterns of gene loss in the evolution of the animal kingdom

inferredcites →https://doi.org/10.1038/s41559-020-1156-zopenalex-snapshot

Deeply conserved synteny resolves early events in vertebrate evolution

inferredcites →https://doi.org/10.1038/s41586-022-05110-4openalex-snapshot

Divergent genomic trajectories predate the origin of animals and fungi

inferredcites →https://doi.org/10.1038/s41586-023-05936-6openalex-snapshot

Ancient gene linkages support ctenophores as sister to other animals

inferredcites →https://doi.org/10.1038/s41598-018-28948-zopenalex-snapshot

GOATOOLS: A Python library for Gene Ontology analyses

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TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

inferredcites →https://doi.org/10.1073/pnas.0712259105openalex-snapshot

MicroRNAs and the advent of vertebrate morphological complexity

inferredcites →https://doi.org/10.1073/pnas.1210909110openalex-snapshot

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot

Genomic data do not support comb jellies as the sister group to all other animals

inferredcites →https://doi.org/10.1073/pnas.95.15.8744openalex-snapshot

Nitrilase and Fhit homologs are encoded as fusion proteins in Drosophila melanogaster and Caenorhabditis elegans

inferredcites →https://doi.org/10.1074/jbc.m002208200openalex-snapshot

Nuclear Import of Insulin-like Growth Factor-binding Protein-3 and -5 Is Mediated by the Importin β Subunit

inferredcites →https://doi.org/10.1074/mcp.m113.035600openalex-snapshot

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

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A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data

inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot

An Approximately Unbiased Test of Phylogenetic Tree Selection

inferredcites →https://doi.org/10.1080/10635150802434394openalex-snapshot

Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos

inferredcites →https://doi.org/10.1093/bioinformatics/bti204openalex-snapshot

Convergent evolution of domain architectures (is rare)

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/gbe/evu097openalex-snapshot

Repeated Evolution of Chimeric Fusion Genes in the β-Globin Gene Family of Laurasiatherian Mammals

inferredcites →https://doi.org/10.1093/gbe/evu213openalex-snapshot

Complex Patterns of Gene Fission in the Eukaryotic Folate Biosynthesis Pathway

inferredcites →https://doi.org/10.1093/gbe/evy096openalex-snapshot

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss

inferredcites →https://doi.org/10.1093/gbe/evz163openalex-snapshot

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msab170openalex-snapshot

Rooting the Animal Tree of Life

inferredcites →https://doi.org/10.1093/molbev/msi151openalex-snapshot

Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms

inferredcites →https://doi.org/10.1093/molbev/msr184openalex-snapshot

Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster

inferredcites →https://doi.org/10.1093/molbev/mst017openalex-snapshot

Evolution of Ancient Functions in the Vertebrate Insulin-Like Growth Factor System Uncovered by Study of Duplicated Salmonid Fish Genomes

inferredcites →https://doi.org/10.1093/molbev/mst228openalex-snapshot

A Pluralistic Account of Homology: Adapting the Models to the Data

inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

inferredcites →https://doi.org/10.1093/molbev/msx283openalex-snapshot

CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection

inferredcites →https://doi.org/10.1093/molbev/msz067openalex-snapshot

Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics

inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot

MAFFT version 5: improvement in accuracy of multiple sequence alignment

inferredcites →https://doi.org/10.1093/nar/gkr1060openalex-snapshot

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

inferredcites →https://doi.org/10.1093/nar/gku1158openalex-snapshot

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot

The Pfam protein families database in 2019

inferredcites →https://doi.org/10.1093/sysbio/syw021openalex-snapshot

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

inferredcites →https://doi.org/10.1098/rstb.2016.0455openalex-snapshot

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

inferredcites →https://doi.org/10.1101/gr.087072.108openalex-snapshot

Domain shuffling and the evolution of vertebrates

inferredcites →https://doi.org/10.1101/gr.gr-1405ropenalex-snapshot

Fusion of the Human Gene for the Polyubiquitination Coeffector UEV1 with Kua, a Newly Identified Gene

inferredcites →https://doi.org/10.1111/2041-210x.13750openalex-snapshot

RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes

inferredcites →https://doi.org/10.1111/bij.12746openalex-snapshot

Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

inferredcites →https://doi.org/10.1126/science.1123061openalex-snapshot

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

inferredcites →https://doi.org/10.1126/science.7682012openalex-snapshot

Natural Selection and the Origin of jingwei , a Chimeric Processed Functional Gene in Drosophila

inferredcites →https://doi.org/10.1126/science.aam5979openalex-snapshot

Contingency and determinism in evolution: Replaying life’s tape

inferredcites →https://doi.org/10.1126/science.abc6405openalex-snapshot

Recurrent evolution of vertebrate transcription factors by transposase capture

inferredcites →https://doi.org/10.1186/gb-2001-2-1-reviews0001openalex-snapshot

The nitrilase superfamily: classification, structure and function.

inferredcites →https://doi.org/10.1186/s12862-020-1591-0openalex-snapshot

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life

inferredcites →https://doi.org/10.1186/s12915-018-0499-2openalex-snapshot

A phylogenomic framework and timescale for comparative studies of tunicates

inferredcites →https://doi.org/10.1186/s13059-017-1287-yopenalex-snapshot

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

inferredcites →https://doi.org/10.1186/s13059-018-1559-1openalex-snapshot

Chromosome evolution at the origin of the ancestral vertebrate genome

inferredcites →https://doi.org/10.1186/s13059-018-1592-0openalex-snapshot

A new look at an old question: when did the second whole genome duplication occur in vertebrate evolution?

inferredcites →https://doi.org/10.1186/s13059-019-1925-7openalex-snapshot

Gene content evolution in the arthropods

inferredcites →https://doi.org/10.1210/en.2007-0959openalex-snapshot

A Functional Nuclear Localization Signal in Insulin-Like Growth Factor Binding Protein-6 Mediates Its Nuclear Import

inferredcites →https://doi.org/10.1210/en.2011-0047openalex-snapshot

Evolution of the Insulin-Like Growth Factor Binding Protein (IGFBP) Family

inferredcites →https://doi.org/10.1210/en.2013-1201openalex-snapshot

Structural and Functional Analysis of the Amphioxus IGFBP Gene Uncovers Ancient Origin of IGF-Independent Functions

inferredcites →https://doi.org/10.1242/dev.00848openalex-snapshot

The immunoglobulin superfamily inDrosophila melanogasterandCaenorhabditis elegansand the evolution of complexity

inferredcites →https://doi.org/10.1371/journal.pcbi.1002701openalex-snapshot

This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes

inferredcites →https://doi.org/10.1371/journal.pgen.1008314openalex-snapshot

Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba

inferredcites →https://doi.org/10.7554/elife.26036openalex-snapshot

Dynamics of genomic innovation in the unicellular ancestry of animals

inferredcites →https://doi.org/10.7554/elife.34226openalex-snapshot

Gene family innovation, conservation and loss on the animal stem lineage

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.cell.2024.10.049openalex-snapshot

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

inferred← citeshttps://doi.org/10.1038/s41559-025-02728-1openalex-snapshot

An episodic burst of massive genomic rearrangements and the origin of non-marine annelids

inferred← citeshttps://doi.org/10.1101/2024.02.19.579948openalex-snapshot

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

inferred← citeshttps://doi.org/10.1186/s12864-025-11338-xopenalex-snapshot

Gene novelty and gene family expansion in the early evolution of Lepidoptera

inferred← citeshttps://doi.org/10.21203/rs.3.rs-4346819/v1openalex-snapshot

A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

inferred← citeshttps://doi.org/10.70675/9088c249zeb37z4826zbcc2ze3898a07d32fopenalex-snapshot

Metabolism of the extracellular matrix in brown algae : from gene identification to biochemical characterization

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