Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

/pdf/broad-phylogenomic-sampling-improves-resolution-of-the-2luslhzjqq.pdf

Broad phylogenomic sampling improves resolution of the animal tree of life

The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenet- ics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, stepping- stone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed. (Bayes factor; harmonic mean; phylogenetics, marginal likelihood; model selection; path sampling; thermodynamic integration; steppingstone sampling.)

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

In most environments, bacteria reside primarily in biofilms, which are social consortia of cells that are embedded in an extracellular matrix and undergo developmental programmes resulting in a predictable biofilm 'life cycle'. Recent research on many different bacterial species has now shown that the final stage in this life cycle includes the production and release of differentiated dispersal cells. The formation of these cells and their eventual dispersal is initiated through diverse and remarkably sophisticated mechanisms, suggesting that there are strong evolutionary pressures for dispersal from an otherwise largely sessile biofilm. The evolutionary aspect of biofilm dispersal is now being explored through the integration of molecular microbiology with eukaryotic ecological and evolutionary theory, which provides a broad conceptual framework for the diversity of specific mechanisms underlying biofilm dispersal. Here, we review recent progress in this emerging field and suggest that the merging of detailed molecular mechanisms with ecological theory will significantly advance our understanding of biofilm biology and ecology.

Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal.

The Cambrian appearance of fossils representing diverse phyla has long inspired hypotheses about possible genetic or environmental catalysts of early animal evolution. Only recently, however, have data begun to emerge that can resolve the sequence of genetic and morphological innovations, environmental events, and ecological interactions that collectively shaped Cambrian evolution. Assembly of the modern genetic tool kit for development and the initial divergence of major animal clades occurred during the Proterozoic Eon. Crown group morphologies diversified in the Cambrian through changes in the genetic regulatory networks that organize animal ontogeny. Cambrian radiation may have been triggered by environmental perturbation near the Proterozoic-Cambrian boundary and subsequently amplified by ecological interactions within reorganized ecosystems.

/pdf/early-animal-evolution-emerging-views-from-comparative-4wfpul73pd.pdf

Early Animal Evolution: Emerging Views from Comparative Biology and Geology

The Annelida, which includes the polychaetes and the clitellates, has long held the taxonomic rank of phylum. The unsegmented, mud-dwelling echiuran spoon worms and the gutless, deep-sea pogonophoran tube worms (including vestimentiferans) share several embryological and morphological features with annelids, but each group also has been considered as a separate metazoan phylum based on the unique characters each group displays. Phylogenetic analyses of DNA sequences from the nuclear gene elongation factor-1α place echiurans and pogonophorans within the Annelida. This result, indicating the derived loss of segmentation in echiurans, has profound implications for our understanding of the evolution of metazoan body plans and challenges the traditional view of the phylum-level diversity and evolutionary relationships of protostome worms.

https://www.pnas.org/content/pnas/94/15/8006.full.pdf

Molecular evidence that echiurans and pogonophorans are derived annelids

Annelida comprises an ancient and ecologically important animal phylum with over 16,500 described species and members are the dominant macrofauna of the deep sea. Traditionally, two major groups are distinguished: Clitellata (including earthworms, leeches) and "Polychaeta" (mostly marine worms). Recent analyses of molecular data suggest that Annelida may include other taxa once considered separate phyla (i.e., Echiura, and Sipuncula) and that Clitellata are derived annelids, thus rendering "Polychaeta" paraphyletic; however, this contradicts classification schemes of annelids developed from recent analyses of morphological characters. Given that deep-level evolutionary relationships of Annelida are poorly understood, we have analyzed comprehensive datasets based on nuclear and mitochondrial genes, and have applied rigorous testing of alternative hypotheses so that we can move towards the robust reconstruction of annelid history needed to interpret animal body plan evolution. Sipuncula, Echiura, Siboglinidae, and Clitellata are all nested within polychaete annelids according to phylogenetic analyses of three nuclear genes (18S rRNA, 28S rRNA, EF1α; 4552 nucleotide positions analyzed) for 81 taxa, and 11 nuclear and mitochondrial genes for 10 taxa (additional: 12S rRNA, 16S rRNA, ATP8, COX1-3, CYTB, NAD6; 11,454 nucleotide positions analyzed). For the first time, these findings are substantiated using approximately unbiased tests and non-scaled bootstrap probability tests that compare alternative hypotheses. For echiurans, the polychaete group Capitellidae is corroborated as the sister taxon; while the exact placement of Sipuncula within Annelida is still uncertain, our analyses suggest an affiliation with terebellimorphs. Siboglinids are in a clade with other sabellimorphs, and clitellates fall within a polychaete clade with aeolosomatids as their possible sister group. None of our analyses support the major polychaete clades reflected in the current classification scheme of annelids, and hypothesis testing significantly rejects monophyly of Scolecida, Palpata, Canalipalpata, and Aciculata. Using multiple genes and explicit hypothesis testing, we show that Echiura, Siboglinidae, and Clitellata are derived annelids with polychaete sister taxa, and that Sipuncula should be included within annelids. The traditional composition of Annelida greatly underestimates the morphological diversity of this group, and inclusion of Sipuncula and Echiura implies that patterns of segmentation within annelids have been evolutionarily labile. Relationships within Annelida based on our analyses of multiple genes challenge the current classification scheme, and some alternative hypotheses are provided.

/pdf/annelid-phylogeny-and-the-status-of-sipuncula-and-echiura-2g3ibbuodk.pdf

Annelid phylogeny and the status of Sipuncula and Echiura

Biogeography seeks to distinguish patterns in the distribution of species and to determine causal processes. Hydrothermal vent habitats have several properties that invite biogeographic studies: constrained to active deep-sea ocean ridges, known in most oceans and anticipated in the rest, patchy in distribution, extreme conditions and a limited group of inhabitants. Biologists have studied 30 vent sites mostly in the Pacific and Atlantic. Currently, 443 invertebrate species are known to generic level although many more are under study. Additionally, 32 octopus and fish species are observed in and around vents. The faunas of other sulphide-rich deep-water habitats such as margin cold seeps and organic masses (wood, carcasses) do not show great affinity at the species level to the vent fauna but the higher taxonomic affiliations suggest close evolutionary ties for many groups. Many studies address the formation of regional faunas using the first- known sites on the Galapagos Rift and northern East Pacific Rise as the major sites of comparison. Physical disjunction of ridge crests is a likely factor in promoting the extensive provinciality that currently exists. Nonetheless, faunas on two sides of the Pacific and in the Atlantic have closer relations to each other than to the nearby “normal” deep-sea fauna. At the individual ridge scale, extensive gene flow among separated populations occurs in many species and serves to maintain the regional species pool. However, major discontinuities between major ridges reduce or eliminate gene flow; vicariant processes appear to be important. The role of differing rates of spreading in different provinces and the concomitant effects on vent habitats and faunas need further investigation. Over 75% of vent species occur at only one site and none occur at all sites. Examination of the reproductive characters of some widespread species reveals no special dispersal strategy nor does reproductive strategy predict the extent of distribution. Vestimentiferan tubeworm species are highly endemic and found only at Pacific vents; their limited spread may be a result of recent entry into the habitat. Alvinellid polychaete cladogenetic pattern does not match geographic regions, indicating independent penetration by numerous lineages. Endemicity among vent gastropods is high with over 60% of genera limited to this habitat; many affiliations with other sulphide-rich habitats can be identified. Among the vent gastropods there are some lineages that may have entered the vent habitat in the Mesozoic. Hydrothermal vents provide a good testing ground for processes that control patterns in diversity. Ecological and historical controls at both local and regional scales can be discerned with further study.

A Biogeographical Perspective of the Deep-Sea Hydrothermal Vent Fauna

Traditionally, the Annelida has been classified as a group comprising the Polychaeta and the Clitellata. Recent phylogenetic analyses have led to profound changes in the view that the Annelida, as ...

Molecular phylogeny of the Annelida

The echinoderm symbionts Myzostomida are marine worms that show an enigmatic lophotrochozoan body plan. Historically, their phylogenetic origins were obscured due to disagreement about which morphological features are evolutionarily conserved, but now most morphological evidence points to annelid origins. In contrast, recent phylogenetic analyses using different molecular markers produced variable results regarding the position of myzostomids, but all suggested these worms are not derived annelids. To reexamine this issue, we analyzed data from nuclear genes (18S rDNA, 28S rDNA, Myosin II, and Elongation Factor-1α), and a nearly complete myzostomid mitochondrial genome. Here, we show that the molecular data are in agreement with the morphological evidence that myzostomids are part of the annelid radiation. This result is robustly supported by mitochondrial (gene order and sequence data) and nuclear data, as well as by recent ultrastructural investigations. Using Bayes factor comparison, alternative hypotheses are shown to lack support. Thus, myzostomids probably evolved from a segmented ancestor and gained a derived anatomy during their long evolutionary history as echinoderm symbionts. © The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.

Damhnait McHugh

Papers

Molecular evidence that echiurans and pogonophorans are derived annelids

Annelid phylogeny and the status of Sipuncula and Echiura

A Biogeographical Perspective of the Deep-Sea Hydrothermal Vent Fauna

Molecular phylogeny of the Annelida

Mitochondrial Genome and Nuclear Sequence Data Support Myzostomida As Part of the Annelid Radiation