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A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

https://doi.org/10.1101/2020.02.13.947796

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

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Biotic Interactions in Recent and Fossil Benthic Communities

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Sediment-Mediated Biological Disturbance and the Evolution of Marine Benthos

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Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

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Comparative morphology and phylogenetic significance of Gregory’s diverticulum in sand dollars (Echinoidea: Clypeasteroida)

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The phylogenomic revolution and its conceptual innovations: a text mining approach

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Phylogeny of Sea Urchins

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Sea Urchins as Drivers of Shallow Benthic Marine Community Structure

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Phylogeny and classification of echinoids

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Sea Urchins: Biology and Ecology

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Early Triassic recovery of echinoderms

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Morphological Phylogenetics in the Genomic Age

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The first mitochondrial genome of the model echinoid Lytechinus variegatus and insights into Odontophoran phylogenetics

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The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida)

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BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

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Biases of tree-independent-character-subsampling methods

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Molecular phylogeny of extant Holothuroidea (Echinodermata)

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The Ecological Implications of Body Size

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inferredcites →https://doi.org/10.1017/s0016756800106600openalex-snapshot

Morphological Studies on the Echinoidea Holectypoida and their Allies

inferredcites →https://doi.org/10.1017/s0016756800201842openalex-snapshot

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inferredcites →https://doi.org/10.1017/s0022336000061321openalex-snapshot

Evolutionary Trends and Their Functional Significance in the Post-Paleozoic Echinoids

inferredcites →https://doi.org/10.1017/s0025315400029118openalex-snapshot

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inferredcites →https://doi.org/10.1017/s0094837300006527openalex-snapshot

Constructional morphology of sand dollars

inferredcites →https://doi.org/10.1017/s0094837300009714openalex-snapshot

Paedomorphosis, Aristotle's lantern, and the origin of the sand dollars (Echinodermata: Clypeasteroida)

inferredcites →https://doi.org/10.1017/s0094837300009982openalex-snapshot

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inferredcites →https://doi.org/10.1017/s0094837300013300openalex-snapshot

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inferredcites →https://doi.org/10.1017/s1089332600000322openalex-snapshot

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inferredcites →https://doi.org/10.1017/s1089332600001893openalex-snapshot

Models and Methods for Analyzing Phenotypic Evolution in Lineages and Clades

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inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

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inferredcites →https://doi.org/10.1038/s42003-019-0417-3openalex-snapshot

Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity

inferredcites →https://doi.org/10.1038/srep15541openalex-snapshot

Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid

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Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

inferredcites →https://doi.org/10.1073/pnas.071524598openalex-snapshot

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inferredcites →https://doi.org/10.1073/pnas.1302642110openalex-snapshot

Clades reach highest morphological disparity early in their evolution

inferredcites →https://doi.org/10.1073/pnas.1319091111openalex-snapshot

The fossilized birth–death process for coherent calibration of divergence-time estimates

inferredcites →https://doi.org/10.1073/pnas.1418153112openalex-snapshot

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inferredcites →https://doi.org/10.1073/pnas.1503453112openalex-snapshot

Error, signal, and the placement of Ctenophora sister to all other animals

inferredcites →https://doi.org/10.1073/pnas.1610603114openalex-snapshot

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

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Pulsed evolution shaped modern vertebrate body sizes

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British Jurassic Regular Echinoids Part 1, Introduction, Cidaroida, Echinothurioida, Aspidodiadematoida and Pedinoida

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The Adaptive Landscape in Evolutionary Biology

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phangorn: phylogenetic analysis in R

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ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

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Echinobase: an expanding resource for echinoderm genomic information

inferredcites →https://doi.org/10.1093/molbev/msh194openalex-snapshot

Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior

inferredcites →https://doi.org/10.1093/molbev/msl039openalex-snapshot

Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata)

inferredcites →https://doi.org/10.1093/molbev/msq097openalex-snapshot

Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships

inferredcites →https://doi.org/10.1093/molbev/msu235openalex-snapshot

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

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

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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

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Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

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Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

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Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates

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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

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Demographic history ofDiadema antillarum, a keystone herbivore on Caribbean reefs

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Global regime shift dynamics of catastrophic sea urchin overgrazing

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Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals

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SURFACE : detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion

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Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution

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Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models

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Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

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STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION

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phytools: an R package for phylogenetic comparative biology (and other things)

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Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes

inferredcites →https://doi.org/10.1111/jeb.13050openalex-snapshot

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions

inferredcites →https://doi.org/10.1111/pala.12329openalex-snapshot

Cope's rule and the adaptive landscape of dinosaur body size evolution

inferredcites →https://doi.org/10.1111/pala.12392openalex-snapshot

The youngest ophiocistioid: a first Palaeozoic‐type echinoderm group representative from the Mesozoic

inferredcites →https://doi.org/10.1111/pala.12443openalex-snapshot

The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

inferredcites →https://doi.org/10.1117/12.930832openalex-snapshot

Macro- and microstructural diversity of sea urchin teeth revealed by large-scale mircro-computed tomography survey

inferredcites →https://doi.org/10.1126/science.1084786openalex-snapshot

Tempo and Mode of Evolutionary Radiation in Iguanian Lizards

inferredcites →https://doi.org/10.1126/science.1232392openalex-snapshot

Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations

inferredcites →https://doi.org/10.1126/science.265.5178.1547openalex-snapshot

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inferredcites →https://doi.org/10.1130/g38909.1openalex-snapshot

Paleozoic echinoderm hangovers: Waking up in the Triassic

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Agalma: an automated phylogenomics workflow

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SIMMAP: Stochastic character mapping of discrete traits on phylogenies

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TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

inferredcites →https://doi.org/10.1186/s12915-018-0486-7openalex-snapshot

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

inferredcites →https://doi.org/10.1201/9781003078951-23openalex-snapshot

Progenetic miniaturization in the sand dollar Sinaechinocyamus: implications for clypeasteroid phylogeny

inferredcites →https://doi.org/10.1371/journal.pone.0066245openalex-snapshot

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

inferredcites →https://doi.org/10.1371/journal.pone.0119627openalex-snapshot

Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa

inferredcites →https://doi.org/10.1371/journal.pone.0194575openalex-snapshot

Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna

inferredcites →https://doi.org/10.1371/journal.pone.0197433openalex-snapshot

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

inferredcites →https://doi.org/10.1371/journal.pone.0202729openalex-snapshot

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

inferredcites →https://doi.org/10.1520/stp32150sopenalex-snapshot

A Simple Method for Estimating In Situ Stresses at Great Depths

inferredcites →https://doi.org/10.1554/0014-3820(2003)057[0717:tfpsic]2.0.co;2openalex-snapshot

TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE

inferredcites →https://doi.org/10.1643/ch-14-015openalex-snapshot

Forked Tongues Revisited: Molecular Apomorphies Support Morphological Hypotheses of Squamate Evolution

inferredcites →https://doi.org/10.1666/0094-8373(2000)026<0056:cefisg>2.0.co;2openalex-snapshot

Contrasting evolutionary flexibility in sister groups: disparity and diversity in Mesozoic atelostomate echinoids

inferredcites →https://doi.org/10.1666/0094-8373(2001)027<0392:ptcooc>2.0.co;2openalex-snapshot

Probing the cassiduloid origins of clypeasteroid echinoids using stratigraphically restricted parsimony analysis

inferredcites →https://doi.org/10.1666/06073.1openalex-snapshot

Intrinsic versus extrinsic biases in the fossil record: contrasting the fossil record of echinoids in the Triassic and early Jurassic using sampling data, phylogenetic analysis, and molecular clocks

inferredcites →https://doi.org/10.1666/07074.1openalex-snapshot

Body size, energetics, and the Ordovician restructuring of marine ecosystems

inferredcites →https://doi.org/10.2307/1483846openalex-snapshot

Treatise on Invertebrate Paleontology

inferredcites →https://doi.org/10.2307/1541476openalex-snapshot

FEEDING STRUCTURES, BEHAVIOR, AND MICROHABITAT OF ECHINOCYAMUS PUSILLUS (ECHINOIDEA: CLYPEASTEROIDA)

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.5281/zenodo.13473681openalex-snapshot

Living Cassiduloids (Echinodermata, Echinoidea) - A Key And Annotated List

inferredcites →https://doi.org/10.5281/zenodo.16046014openalex-snapshot

Implications of lantern morphology for the phylogeny of post-Palaeozoic echinoids

inferredcites →https://doi.org/10.5281/zenodo.593947openalex-snapshot

alien_index 2.0

inferredcites →https://doi.org/10.5962/bhl.title.4630openalex-snapshot

Phylogeny of the Echini, with a revision of Palaeozoic species

inferredcites →https://doi.org/10.7208/chicago/9780226012285.001.0001openalex-snapshot

Animal Body Size

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ece3.6892openalex-snapshot

Endless forms most stupid, icky, and small: The preponderance of noncharismatic invertebrates as integral to a biologically sound view of life

inferred← citeshttps://doi.org/10.32942/osf.io/vqejtopenalex-snapshot

Molecular Paleobiology of the Echinoderm Skeleton

inferred← citeshttps://doi.org/10.3389/fimmu.2021.744783openalex-snapshot

Sequence Diversity, Locus Structure, and Evolutionary History of the SpTransformer Genes in the Sea Urchin Genome

inferred← citeshttps://doi.org/10.3389/fmars.2021.737886openalex-snapshot

Interspecific Analysis of Sea Urchin Adhesive Composition Emphasizes Variability of Glycans Conjugated With Putative Adhesive Proteins

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