The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.
The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy-identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution.
In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.), but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although it has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and, in three of these, the break is located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28S rRNA and will be consistently underestimated in the great majority of animal species with a break.
The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data, which can help to elucidate phylogenetic relationships and provide important comparative data, remain sparse for early branching bilaterians. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of ~110 Mbp in 18 chromosome like scaffolds, with repeat content, and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.
10In some eukaryotes, a 'hidden break' has been described in which the 28S ribosomal RNA molecule is 11 cleaved into two subparts. The break is common in protostome animals but has also been reported in 12 some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine 13 the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find an homologous 14 break is present across protostomes although has been lost in some taxa. We show that rare breaks in 15 vertebrates are not homologous to the protostome break. A break is found in just 3 out of 307 species of 16 non-animal eukaryotes studied but these are located in the same position as the protostome break 17 suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28s 18 rRNA and will be consistently underestimated in the great majority of animal species with a break. 193 Introduction. 20Ribosomes are made up of up to 80 ribosomal proteins and three (in prokaryotes) or four (in eukaryotes) 21 structural ribosomal RNAs named according to their sizes: in eukaryotes these are the 5S (~120 22 nucleotides), the 5.8S (~150 nucleotides), the 18S (~1800 nucleotides) and the 28S (~4000 to 5000 23 nucleotides). The 5.8S, 18S and 28S rRNAs are initially transcribed as a single RNA operon (the 5S is at a 24 separate locus in eukaryotes). The 18S and 5.8S are separated by the Internal Transcribed Spacer 1 (ITS1) 25 and 5.8S and 28S are separated by ITS2. The initial transcript is cleaved into three functional RNAs by 26 removing ITS1 and ITS2 (Fig. 1A). 28In some species this picture is complicated by observations of a 'hidden break' in the 28S ribosomal RNA. 29In organisms with a hidden break, the 28S rRNA molecule itself is cleaved into two approximately equal 30 sized molecules of ~2000 nucleotides each (Fig. 1A) (Winnebeck et al., 2010). These two RNAs (the 5' 31 28Sa and the 3' 28Sb) are nevertheless intimately linked by inter-molecular hydrogen bonding within the 32 large subunit of the ribosome, just as the 28S and 5.8S rRNAs as well as different regions of the intact 33 28S rRNA are in species without a break. 35The hidden break, first described in pupae of the silkmoth Hyalophora cecropia (Applebaum et al., 1966) 36 manifests itself experimentally when total RNA is extracted and separated according to size using gel 37 electrophoresis. If the RNA is first denatured by heating in order to separate hydrogen bonded stretches 38 of RNAs before electrophoresis, the hydrogen bonded 28Sa and 28Sb subunits separate. These two 39 molecules, being approximately the same size, then migrate on a gel at the same rate as each other and, 40 coincidentally, at the same rate as the almost identically sized 18S rRNA molecule. The effect is that, rather 41 than observing two distinct ribosomal RNA bands on the gel of ~2000 and ~4000 nucleotides, a single 42 (and more intense) band composed of three different molecules each approximately 2kb long (18S, 43 28Sa and 28Sb) is seen (McCarthy et ...
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.
19Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 20 species with high popularity and commercial value, such as porgies and seabreams. Although 21 the phylogeny of this family has been investigated multiple times, its position among other 22 teleost groups remains ambiguous. Most studies have used a single or few genes to decipher 23 the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to 24 resolve the position of the family using five recently available Sparidae gene-sets and 26 25 available fish proteomes from species with a sequenced genome, to ensure higher quality of 26 the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes 27 (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding 28 that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the 29 european seabass as closest taxa of sparids. By analytically comparing the methodologies 30 applied in both cases, we show that this discordance is not due to different orthology 31 assignment algorithms; on the contrary, we prove that it is caused by the increased taxon 32 sampling of the present study, outlining the great importance of this aspect in phylogenomic 33 analyses in general. 34 35 Keywords: Sparidae; fish phylogenomics; orthology assignment; jackknife phylogeny test; 36 taxon sampling; 37Teleostei represent the dominant group within ray-finned fish (Actinopterygii), with 39 more than 26,000 extant species. Their evolution has been extensively studied through past 40 decades, using a variety of data including fossil records, morphological characters and 41 molecular data, leading to a gradual resolution of teleost phylogeny (Betancur-R. et al., 2013(Betancur-R. et al., 42 & 2017. 43 With the continuous emergence of new whole-genome sequences, phylogenomic 44 techniques are applied to characterise the evolutionary relationships among species. Whole-45 genome information can help in resolving uncertain nodes, as well as provide stronger evidence 46 on already established relationships. Regarding fish phylogeny, several genome-wide 47 approaches have been implemented so far. One of the first efforts to study ray-finned fish 48 phylogenomics was conducted by (Li et al., 2007). Since then, several studies have been 49 published using not only gene markers, but also noncoding elements such as the work of 50 (Faircloth et al., 2013) who used UCE (ultra-conserved elements) to investigate the 51 diversification of basal clades in ray-finned fish. Most genome papers include a phylogenomic 52 analysis albeit with limited taxon sampling (e.g. Vij et al., 2016 and Xu et al., 2017), while the 53 use of whole-transcriptome data is being employed to uncover phylogenetic relationships of 54 specific taxonomic groups as well (Dai et al., 2018; Rodgers et al., 2018). With the emergence 55 of new genomes and the possibilities of modern sequencing technologies, bigger datasets are ...
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