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Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates., (© 2017 The Authors.)

Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.

Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Pulmonates, with over 30,000 described species, represent the largest radiation of non-marine animals outside of Arthropoda. The pulmonate lung was a key evolutionary innovation enabling diversification of terrestrial and freshwater snails and slugs. However, recent studies drew conflicting conclusions about pulmonate monophyly, and support for a sister group is lacking, hindering our understanding of this major animal radiation. Analyses of mitochondrial protein-coding genes recovered a paraphyletic Pulmonata grading into a monophyletic Opisthobranchia, a traditional group of sea slugs long considered sister to pulmonates. Conversely, analyses of datsets dominated by nuclear rDNA indicated Opisthobranchia is paraphyletic with respect to Pulmonata. No study resolved the placement of two key taxa: Sacoglossa, an opisthobranch group including photosynthetic sea slugs, and Siphonarioidea, intertidal limpet-like snails traditionally in Pulmonata. To examine evolutionary relationships at the base of the pulmonate radiation, we performed a phylogenomic analysis of 102 nuclear protein-coding gene regions for 19 gastropods. Opisthobranchia was recovered as paraphyletic with respect to Panpulmonata, a clade in which Sacoglossa was sister to Pulmonata, with Siphonarioidea as the basal pulmonate lineage. Siphonarioideans share a similar gill structure with shelled sacoglossans but lack the contractile pneumostome of pulmonates, suggesting descent from an evolutionary intermediate that facilitated the pulmonate radiation into non-marine habitats., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Phylogenetic relationships among and within the more than 70 recognized families of Annelida are poorly understood. In some cases, such as the monotypic Poeobiidae, derived morphology hinders the ability to find convincing synapomorphies that help elucidate evolutionary origins. In such cases, molecular data can be useful. Poeobiidae consists of the holopelagic polychaete Poeobius meseres, which is typically found in midwater depths off California. Morphologists have speculated that it is close to or within Flabelligeridae, but definitive evidence was lacking. Herein we use maximum likelihood phylogenetic reconstruction methods to examine the nuclear 18S rDNA (SSU) gene and the mitochondrial cytochrome b gene. Our results strongly support the hypothesis that P. meseres is a highly derived flabelligerid annelid closely related to Therochaeta. Thus, Poeobiidae is a junior synonym for Flabelligeridae. This result raises interesting questions about the evolution of the holopelagic P. meseres from a benthic ancestral flabelligerid.

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635–560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low‐oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia‐inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low‐oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957–1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole‐genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre‐Tonian emergence of metazoans under low‐oxygen conditions, and an increase in oxygen response elements during animal evolution. [ABSTRACT FROM AUTHOR]

Cnidarians are commonly recognized as sea jellies, corals, or complex colonies such as the Portuguese man-of-war. While some cnidarians possess rigid internal calcareous skeletons (e.g., corals), many are soft-bodied. Intriguingly, genes coding for the chitin-biosynthetic enzyme, chitin synthase (CHS), were recently identified in the model anemone Nematostella vectensis, a species lacking hard structures. Here we report the prevalence and diversity of CHS across Cnidaria and show that cnidarian chitin synthase genes display diverse protein domain organizations. We found that CHS is expressed in cnidarian species and/or developmental stages with no reported chitinous or rigid morphological structures. Chitin affinity histochemistry indicates that chitin is present in soft tissues of some scyphozoan and hydrozoan medusae. To further elucidate the biology of chitin in cnidarian soft tissues, we focused on CHS expression in N. vectensis. Spatial expression data show that three CHS orthologs are differentially expressed in Nematostella embryos and larvae during development, suggesting that chitin has an integral role in the biology of this species. Understanding how a non-bilaterian lineage such as Cnidaria employs chitin may provide new insight into hitherto unknown functions of polysaccharides in animals, as well as their role in the evolution of biological novelty. [ABSTRACT FROM AUTHOR]

Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e. NLR's NACHT domain), whereas impact on other domains (e.g. rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e. Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt's flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species. [ABSTRACT FROM AUTHOR]

Background: Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods: To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results: Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions. [ABSTRACT FROM AUTHOR]

Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of the Capitella telata and Helobdella robusta genomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leech H. robusta contains many more copies (12) of the sodium–potassium pump alpha‐subunit (Na+/K+‐ATPase) gene than does the marine polychaete C. telata (2). The sodium–potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na+/K+‐ATPase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na+/K+‐ATPase duplications coincided with the marine‐to‐freshwater transition in Clitellata, we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na+/K+‐ATPase gene transcripts in order to infer the timing of gene duplication events using tree‐based methods. The inferred timing of Na+/K+‐ATPase duplication events is consistent with the timing of the initial marine‐to‐freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats. [ABSTRACT FROM AUTHOR]

Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role,with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that "Hrs" reported from Cnidaria and Arthropodawere not consistentwith that of othermetazoan Hrs. Contrary to previous suggestions that Hr geneswere absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions. [ABSTRACT FROM AUTHOR]

Background: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. Methods: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. Results and discussion: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. Conclusions: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships. [ABSTRACT FROM AUTHOR]

Nemerteans are one of fewanimal groups that have evolved the ability toutilize toxins for both defense and subduing prey, but little is known about specific nemertean toxins. In particular, no study has identified specific toxin genes even though peptide toxins are known from some nemertean species. Information about toxin genes is needed to better understand evolution of toxins across animals and possibly provide novel targets for pharmaceutical and industrial applications. We sequenced and annotated transcriptomes of twofree-living and one commensal nemertean and annotated an additional six publicly available nemertean transcriptomes to identify putative toxin genes. Approximately 63-74% of predicted open reading frames in each transcriptome were annotated with gene names, and all species had similar percentages of transcripts annotated with each higher-level GO term. Every nemertean analyzed possessed genes with high sequence similarities to known animal toxins including those from stonefish, cephalopods, and sea anemones. One toxin-like gene found in all nemerteans analyzed had high sequence similarity to Plancitoxin-1, a DNase II hepatotoxin thatmay function well at low pH,which suggests that the acidic bodywalls of somenemerteans couldwork to enhance the efficacy of protein toxins. The highest number of toxin-like genes found in any one species was seven and the lowest was three. The diversity of toxin-like nemertean genes found here is greater than previously documented, and these animals are likely an ideal system for exploring toxin evolution and industrial applications of toxins. [ABSTRACT FROM AUTHOR]

We investigated the recent evolutionary history of demersal sea stars in the genus Odontaster throughout the Western Antarctic waters and on the South American shelf. The mitochondrial 16S ribosomal and cytochrome c oxidase subunit I (COI) genes were sequenced from adult and larval specimens. TCS parsimony network analysis and Bayesian inference were used to examine evolutionary history. Hierarchical AMOVA and mitochondrial DNA diversity statistics were also computed. Additionally, morphological characters were used. In assessing O. validus, we discovered morphological and range descriptions of Odontaster species to be inaccurate and include other Odontaster species in the Southern Ocean. We found O. meridionalis on both sides of the Antarctic circumpolar current (ACC) and Antarctic polar front (APF), whereas O. validus and O. penicillatus do not appear to have permeated these oceanographic features. Additionally, we discovered previously unrecognized species of Odontaster. Subsequent examination revealed diagnostic morphological differences in the number of spinelets on the abactinal and actinal plates. Mitochondrial characterization of Odontaster species suggests their recent history has been influenced by the APF and ACC in different ways. With the exception of O. meridionalis, Odontaster species are restricted to either side of the Drake Passage. O. validus shows genetic connectivity throughout sampled Antarctic waters. [ABSTRACT FROM AUTHOR]

Struck, T. H. & Halanych, K. M. (2010). Origins of holopelagic Typhloscolecidae and Lopadorhynchidae within Phyllodocidae (Phyllodocida, Annelida).- Zoologica Scripta, 39, 269-275. Several distinct lineages of annelids have evolved holopelagic life styles. Unfortunately, our knowledge of the biology and evolution of most of these groups is limited. Typhloscolecidae and Lopadorhynchidae are two such examples of recognized families of holopelagic annelids about which little is known. Both groups have a limited number of known species (13 and 15, respectively) and are rarely discussed in the literature other than to note occurrence. Placing these groups in a phylogenetic context has been difficult due to their seemingly unique morphology, and, to the best of our knowledge, lack of molecular data. Nonetheless, previous authors have suspected that they are members of Phyllodocida and perhaps within Phyllodocidae. To test such hypotheses, we have employed nuclear 18S and 28S ribosomal data in both a Bayesian inference and a maximum-likelihood framework. The resultant topology indicates that typhloscolecids and lopadorhynchs are sister taxa nested within Phyllodocidae near another holopelagic taxon, alciopids. Whereas posterior probabilities strongly support this placement, an AU hypothesis testing approach and bootstrap values are more equivocal but both still strongly suggest Phyllodocidae affiliations. Recognition of Typhloscolecidae and Lopadorhynchidae as annelid families is called into question. [ABSTRACT FROM AUTHOR]

Molecular tools have profoundly rearranged our understanding of metazoan phylogeny. Initially based on the nuclear small ribosomal subunit (SSU or 18S) gene, recent hypotheses have been corroborated by several sources of data (including the nuclear large ribosomal subunit, Hox genes, mitochondrial gene order, concatenated mitochondrial genes, and the myosin II heavy chain gene). Herein, the evidence supporting our current understanding is discussed on a clade by clade basis. Bilaterian animals consist of three clades: Deuterostomia, Lophotrochozoa, and Ecdysozoa. Each clade is supported by molecular and morphological data. Deuterostomia is smaller than traditionally recognized, consisting of hemichordates, echinoderms, chordates, and Xenoturbella (an enigmatic worm-like animal). Lophotrochozoa groups animals with a lophophore feeding apparatus (Brachiopoda, Bryozoa, and Phoronida) and trochophore larvae (e.g., annelids and mollusk), as well as several other recognized phyla (e.g., platyhelminthes, sipunculans, nemerteans). Ecdysozoa comprises molting animals (e.g., arthropods, nematodes, tardigrades, priapulids), grouping together two major model organisms (Drosophila and Caenorhabditis)inthe same lineage. Platy-helminthes do not appear to be monophyletic, with Acoelomorpha holding a basal position in Bilateria. Before the emergence of bilateral animals, sponges, ctenophorans, cnidarians, and placozoans split from the main animal lineage, but order of divergence is less than certain. Many questions persist concerning relationships within Ecdysozoa and Lophotrochozoa, poriferan monophyly, and the placement of many less-studied taxa (e.g., kinorhynchs, gastrotrichs, gnathostomulids, and entoprocts). [ABSTRACT FROM AUTHOR]

Abstract: Ctenophores are one of the most basally branching lineages of metazoans with the largest mitochondrial organelles in the animal kingdom. We sequenced the mitochondrial (mtDNA) genome from the Pacific cidipid ctenophore, Pleurobrachia bachei. The circular mitochondrial genome is 11,016nts, with only 12 genes, and one of the smallest metazoan mtDNA genomes recorded. The protein coding genes are intronless cox1–3, cob, nad1, 3, 4, 4L and 5. The nad2 and 6 genes are represented as short fragments whereas the atp6 gene was found in the nuclear genome. Only the large ribosomal RNA subunit and two tRNAs were present with possibly the small subunit unidentifiable due to extensive fragmentation. The observed unique features of this mitochondrial genome suggest that nuclear and mitochondrial genomes have evolved at very different rates. This reduced mtDNA genome sharply contrasts with the very large sizes of mtDNA found in other basal metazoans including Porifera (sponges), and Placozoa (Trichoplax). [Copyright &y& Elsevier]

Abstract: Hemichordates have occupied a central role in hypotheses of deuterostome and early chordate evolution. However, surprisingly little is understood about evolution within hemichordates, including hemichordate ancestral characters that may relate to other deuterostome taxa. Previous phylogenetic studies suggested that enteropneust worms are either monophyletic (based on 28S rDNA) or paraphyletic (based on 18S rDNA). Here, we expand the number of hemichordate taxa used in phylogenetic analyses for 18S rDNA data and employ more quickly evolving mitochondrial gene sequences. Novel data from an undescribed deep-sea enteropneust species similar to Torquarator bullocki and a Gulf Stream tornaria larva suggest that these taxa are closely allied to or possibly within Ptychoderidae. Saxipendium coronatum, another deep-sea species commonly called the spaghetti worm, is shown to be a member of Harrimaniidae. Recognition of these deep-sea lineages as distinct families calls into question features used in hemichordate taxonomy. In the new analyses, enteropneusts fall into two distinct monophyletic clades, with the colonial pterobranchs sister to Harrimaniidae, similar to earlier published 18S results. These results indicate that colonial pterobranchs may have evolved from a solitary acorn worm-like hemichordate ancestor. If true, pterobranchs would be unlikely to represent the deuterostome ancestral form as has been suggested by many traditional theories of deuterostome evolution. [Copyright &y& Elsevier]