Evolution: A sisterly dispute

  title={Evolution: A sisterly dispute},
  author={Maximilian J. Telford and Leonid L. Moroz and Kenneth M. Halanych},
Which phylum first branched off from the animal phylogenetic tree is a contested issue. A new analysis challenges the proposal that comb jellies are the sister group to all other animals, and emphasizes a 'sponges-first' view. Three evolutionary biologists weigh up the evidence. 

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

Improvement is shown in partitioned phylogenomic analyses when using site-heterogeneous models and amino acid recoding, including in resolving the debated phylogenetic placement of comb jellies.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

The last common animal ancestor may has been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

Analysis of newly assembled genome gene content and morphological datasets provide additional insights into the early evolution of animals and are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the niece of the other Bilateria, and tentatively support monophyletic Deuterostomia.

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

These analyses reveal a metazoan-typical genome architecture, with highly shared synteny across metazoa, and show that adaptation to the extreme temperatures and conditions found in freshwater largely involves gene duplication.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

It is demonstrated that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy.

Phylogenetics: Tertiary protein structures needed

  • D. Penny
  • Biology
    Nature Ecology &Evolution
  • 2017
We need to estimate protein tertiary structure, as well as using primary sequences, in order to further our understanding of protein evolution and evolutionary processes in general.

Zootaxa 20 years: Phylum Porifera.

This present article analyses taxonomic contributions to describing new taxa of Porifera over the past 20 years of Zootaxa, including their trends and highlights pertaining to sponge publications.

Highlight: Sponges Reveal Stepping Stones in Early Animal Evolution

  • D. Venton
  • Biology
    Genome biology and evolution
  • 2017
The results suggest that all cell types—except one—are expected to be multipotent in this species, and further confirmation that genes classically thought to be only involved in the germline, are quite active in all stages of life for some animals.

Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics

The most significant outcomes of current genomic and transcriptomic analyses of sponges are reviewed, and limitations and future directions of sponge transcriptomic and genomic studies are discussed.

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

This chapter provides a detailed step-by-step practical introduction to phylogenetic analyses using PhyloBayes, using as an example a previously published dataset addressing the phylogenetic position of Microsporidia within eukaryotes.



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

It is concluded that the alternative scenario of animal evolution according to which ctenophores evolved morphological complexity independently from cnidarians and bilaterians or, alternatively, sponges secondarily lost a nervous system, muscles, and other characters, is not supported by the available evidence.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

The phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans and provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses.

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

Investigating possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systemic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model finds a single, statistically robust placement of ctenophores as the authors' most distant animal relatives.

The phylogenetic position of ctenophores and the origin(s) of nervous systems

It is argued that characters like neuropeptide signaling, ciliary photoreceptors, gap junctions and presynaptic molecules are consistent with a shared ancestry of nervous systems, however, that phylogenetic-tree construction artifacts may have placed ctenophores too deep in the metazoan tree.

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

This study characterizes the genomes and transcriptomes of two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and another cnidarian parasite, Polypodium hydriforme, and suggests that the degeneration of the myxozoans body plan was accompanied by extreme reduction in genome size and gene content.

The genealogy of genealogy of neurons

  • L. Moroz
  • Biology
    Communicative & integrative biology
  • 2014
Two scenarios of neuronal evolution (monophyly and polyphyly) are discussed in the historical timeline starting from the 19th century and a possibility of the independent origin of neurons and synapses was introduced well before modern advances in genomic biology.

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

The genome of the ctenophore the warty comb jelly or sea walnut, Mnemiopsis leidyi, is sequenced and it is concluded that c tenophores alone, not sponges or the clade consisting of both ctenphores and cnidarians, are the most basal extant animals.

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

A software package, PhyloBayes 3, is proposed, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.