Testing for polytomies in phylogenetic species trees using quartet frequencies

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the ASTRAL package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest

A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella

BackgroundXenoturbella is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure.ResultsHere we describe a new Xenoturbella species from the western Pacific Ocean, and report a new xenoturbellid structure - the frontal pore. Non-destructive microCT was used to investigate the internal morphology of this soft-bodied animal. This revealed the presence of a frontal pore that is continuous with the ventral glandular network and which exhibits similarities with the frontal organ in acoelomorphs.ConclusionsOur results suggest that large size, oval mouth, frontal pore and ventral glandular network may be ancestral features for Xenoturbella. Further studies will clarify the evolutionary relationship of the frontal pore and ventral glandular network of xenoturbellids and the acoelomorph frontal organ. One of the habitats of the newly identified species is easily accessible from a marine station and so this species promises to be valuable for research on bilaterian and deuterostome evolution

Zoology: War of the Worms

The phylogenetic affinities of Xenacoelomorpha - the phylum comprising Xenoturbella bocki and acoelomorph worms - are debated. Two recent studies conclude they represent the earliest branching bilaterally symmetrical animals, but additional tests may be needed to confirm this notion

Ichnological evidence for meiofaunal bilaterians from the terminal Ediacaran and earliest Cambrian of Brazil

The evolutionary events during the Ediacaran–Cambrian transition (~541 Myr ago) are unparalleled in Earth history. The fossil record suggests that most extant animal phyla appeared in a geologically brief interval, with the oldest unequivocal bilaterian body fossils found in the Early Cambrian. Molecular clocks and biomarkers provide independent estimates for the timing of animal origins, and both suggest a cryptic Neoproterozoic history for Metazoa that extends considerably beyond the Cambrian fossil record. We report an assemblage of ichnofossils from Ediacaran–Cambrian siltstones in Brazil, alongside U–Pb radioisotopic dates that constrain the age of the oldest specimens to 555–542 Myr. X-ray microtomography reveals three-dimensionally preserved traces ranging from 50 to 600 μm in diameter, indicative of small-bodied, meiofaunal tracemakers. Burrow morphologies suggest they were created by a nematoid-like organism that used undulating locomotion to move through the sediment. This assemblage demonstrates animal–sediment interactions in the latest Ediacaran period, and provides the oldest known fossil evidence for meiofaunal bilaterians. Our discovery highlights meiofaunal ichnofossils as a hitherto unexplored window for tracking animal evolution in deep time, and reveals that both meiofaunal and macrofaunal bilaterians began to explore infaunal niches during the late Ediacaran

Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans

The phylum Rotifera consists of minuscule, nonsegmented animals with a unique body plan and an unresolved phylogenetic position. The presence of pharyngeal articulated jaws supports an inclusion in Gnathifera nested in the Spiralia. Comparison of Hox genes, involved in animal body plan patterning, can be used to infer phylogenetic relationships. Here, we report the expression of five Hox genes during embryogenesis of the rotifer Brachionus manjavacas and show how these genes define different functional components of the nervous system and not the usual bilaterian staggered expression along the anteroposterior axis. Sequence analysis revealed that the lox5-parapeptide, a key signature in lophotrochozoan and platyhelminthean Hox6/lox5 genes, is absent and replaced by different signatures in Rotifera and Chaetognatha, and that the MedPost gene, until now unique to Chaetognatha, is also present in rotifers. Collectively, our results support an inclusion of chaetognaths in gnathiferans and Gnathifera as sister group to the remaining spiralians

Cytoskeletal elements in an acoelomorph worm, Praesagittifera naikaiensis

Acoel flatworms can move in a variety of ways such as muscular and ciliary movements via cytoskeletal elements and their neural regulations. However, those locomotive mechanisms have not yet been fully elucidated. In this study, we examined the distribution of cytoskeletal elements including filamentous actin (F-actin) and tubulin, and the neuroanatomical organization in an acoelomorph worm, Praesagittifera naikaiensis (P. naikaiensis). Video microscopy revealed the elongation/contraction and the bending/rotation processes, and the ciliary gliding movement of P. naikaiensis. Histochemical and morphological analysis demonstrated that F-actin networks of inner longitudinal and outer circular muscle fibers were positioned along the entire surface of the body, and that the average distance between the circular muscle fibers in the contracted organism was decreased in the anterior region compared with that in the elongated organism. Electron microscopy showed dense bodies on the muscle cells of P. naikaiensis, which indicates that those muscle cells have the appearance of vertebrate smooth muscle cells. Immunohistochemical analysis revealed that -tubulin-positive signals on the ciliary microtubules had close contact with the F-actin network, and that neurite bundles labelled with anti dSap47 antibody as a neuronal marker run along the anterior-posterior body axis. These results indicate that the well-organized cytoskeletal elements and their neural control systems are preserved in P. naikaiensis, and that their mechanisms involved in those regulation systems are similar to those vertebrate systems. Further studies are needed to clarify the physiological mechanisms underlying the muscular and ciliary movements in P. naikaiensis

Zoology: Worming into the Origin of Bilaterians

Xenacoelomorphs, a group of worms with simple body organization, have been proposed to represent the first offshoot of bilaterians. A new study shows that they might instead belong to the deuterostomes, just as echinoderms and vertebrates

Unravelling body plan and axial evolution in the Bilateria with molecular phylogenetic markers

SETTING THE PROBLEM The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin’s theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for 150 years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from four-legged terrestrial ancestors. Key morphological transitions pose a basic difficulty: reconstruction of ancestral traits of derived clades is problematic because of a lack of transitional forms in the fossil record and obscure homologies between ‘ancestral’ and derived groups. Lack of transitional forms, in other words gaps in the fossil record, brought into question one of the basic tenets of Darwin’s theory, namely gradualism, as Darwin himself acknowledged. Since Darwin, however, and especially in the past 50 years, numerous examples that may reflect transitional stages between major groups of organisms have accumulated

SALMFamide2 and serotonin immunoreactivity in the nervous system of some acoels (Xenacoelomorpha)

Acoel worms are simple, often microscopic animals with direct development, a multiciliated epidermis, a statocyst, and a digestive parenchyma instead of a gut epithelium. Morphological characters of acoels have been notoriously difficult to interpret due to their relative scarcity. The nervous system is one of the most accessible and widely used comparative features in acoels, which have a so-called commissural brain without capsule and several major longitudinal neurite bundles. Here, we use the selective binding properties of a neuropeptide antibody raised in echinoderms (SALMFamide2, or S2), and a commercial antibody against serotonin (5-HT) to provide additional characters of the acoel nervous system. We have prepared whole-mount immunofluorescent stainings of three acoel species: Symsagittifera psammophila (Convolutidae), Aphanostoma pisae, and the model acoel Isodiametra pulchra (both Isodiametridae). The commissural brain of all three acoels is delimited anteriorly by the ventral anterior commissure, and posteriorly by the dorsal posterior commissure. The dorsal anterior commissure is situated between the ventral anterior commissure and the dorsal posterior commissure, while the statocyst lies between dorsal anterior and dorsal posterior commissure. S2 and serotonin do not co-localise, and they follow similar patterns to each other within an animal. In particular, S2, but not 5-HT, stains a prominent commissure posterior to the main (dorsal) posterior commissure. We have for the first time observed a closed posterior loop of the main neurite bundles in S. psammophila for both the amidergic and the serotonergic nervous system. In I. pulchra, the lateral neurite bundles also form a posterior loop in our serotonergic nervous system stainings