New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

Rouse, Greg W.; Wilson, Nerida G.; Carvajal, Jose I.; Vrijenhoek, Robert C.

doi:10.1038/nature16545

Cited by 128 publications

(154 citation statements)

References 34 publications

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“…The recent description of new Xenoturbella species that can be larger than 20 cm (Figure 1a) is broadening the biodiversity of the clade and extends their biogeographical distribution [17 ]. The discovery also shows that Xenoturbella is cosmopolitan rather than a unique outlier found in Scandinavian fjords.…”

Section: Evolution and Variation Within Xenacoelomorphamentioning

confidence: 68%

Xenacoelomorpha's significance for understanding bilaterian evolution

Hejnol

Pang

2016

Current Opinion in Genetics & Development

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The Xenacoelomorpha, with its phylogenetic position as sister group of the Nephrozoa (Protostomia+Deuterostomia), plays a key-role in understanding the evolution of bilaterian cell types and organ systems. Current studies of the morphological and developmental diversity of this group allow us to trace the evolution of different organ systems within the group and to reconstruct characters of the most recent common ancestor of Xenacoelomorpha. The disparity of the clade shows that there cannot be a single xenacoelomorph 'model' species and strategic sampling is essential for understanding the evolution of major traits. With this strategy, fundamental insights into the evolution of molecular mechanisms and their role in shaping animal organ systems can be expected in the near future.

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Section: Evolution and Variation Within Xenacoelomorphamentioning

confidence: 68%

Xenacoelomorpha's significance for understanding bilaterian evolution

Hejnol

Pang

2016

Current Opinion in Genetics & Development

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Section: Limiting Systematic Errormentioning

confidence: 99%

“…Even the best-fitting evolutionary model currently available is unable to accurately position acoels in the absence of Xenoturbella and nematodermatids. Two recent phylogenomic studies which focused on these organisms (Cannon et al 2016;Rouse et al 2016) illustrate that a larger number of genes (212 and 1178 in these studies vs 68 and 197 in older studies) exacerbates systematic error: when outgroups and fast-evolving acoelomorphs are included, Xenacoelomorpha (Xenoturbella + Acoelomorpha) emerge far from Ambulacraria, as sister of all other bilaterians, but when excluded, Xenoturbella is robustly sister of Ambulacraria in both studies (unpublished results), two obviously incompatible results.While very useful, the strategy of enriching the taxon sampling is limited in two different ways. The first one is inescapable: the history of speciation and extinction that has generated the Tree of Life has led to many taxon-poor clades (e.g., coelacanth or Amborella), and ancient DNA techniques are of very little help in filling in the gaps because they are restricted to recently extinct taxa.…”

mentioning

confidence: 99%

Pitfalls in supermatrix phylogenomics

Piégay

Vienne

Ranwez

et al. 2017

EJT

100

122

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Abstract. In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted "the end of incongruence", it soon appeared that analysing large amounts of sequence data without an adequate model of sequence evolution amplifies systematic error and leads to phylogenetic artefacts. With the increasing flood of (sometimes low-quality) genomic data resulting from the rise of high-throughput sequencing, a new type of error has emerged. Termed here "data errors", it lumps together several kinds of issues affecting the construction of phylogenomic supermatrices (e.g., sequencing and annotation errors, contaminant sequences). While easy to deal with at a single-gene scale, such errors become very difficult to avoid at the genomic scale, both because hand curating thousands of sequences is prohibitively time-consuming and because the suitable automated bioinformatics tools are still in their infancy. In this paper, we first review the pitfalls affecting the construction of supermatrices European Journal of Taxonomy 283: 1-25 (2017) 2 and the strategies to limit their adverse effects on phylogenomic inference. Then, after discussing the relative non-issue of missing data in supermatrices, we briefly present the approaches commonly used to reduce systematic error.Keywords. Phylogenomics, supermatrix, systematic error, data quality, incongruence. From phylogenetics to phylogenomicsThe last two decades have seen significant changes taking place in the practice of phylogenetic inference from molecular data. These changes have mostly been triggered by the ever-increasing size of the datasets being assembled and analysed in the form of supermatrices of concatenated genes (Driskell et al. 2004). The evolution of the size and shape of these datasets, thanks to new technological advances in DNA amplification and sequencing, has been associated with different phases in the field of phylogenetic inference ( Fig. 1). In the early days of molecular phylogenetics based on PCR amplification and manual Sanger sequencing of a handful of genes for a limited number of taxa, the field laid somewhat in the "uncertainty zone" dominated by stochastic error, even if some naïve over-interpretations did occur. Then, the development of automated Sanger sequencing typically led to a few standard genes (e.g., SSU rRNA, elongation factors, RNA polymerases) being sequenced for a large number of taxa, projecting the field into the "irresolution zone" with only limited information available to resolve a large number of nodes. Yet, at that time the focus was not on resolving large-scale phylogenetic relationships, rather than on identifying species or strains by molecular means, which eventually gave rise to the field of DNA barcoding (Hebert et al. 2003). The first genome sequences from model organisms reverted the situation, with few taxa being sequenced for their entire set of genes causing a sort of "inconsis...

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“…Within the past decade, newly described species include a yeti crab (Kiwa spp.) that lives 2,600 m deep near hydrothermal vents in the Antarctic Ocean and farms chemosynthetic bacteria on its claws (Thurber et al, 2011;Thatje et al, 2015), and four species of deep-sea worm that live near vents in the Pacific Ocean (Rouse et al, 2016). Goffredi et al (2017) found a high diversity of fauna inhabiting vents in the southern Gulf of California, reporting that only three of 116 macrofaunal species that they observed or collected were found on all four of the vent fields they studied.…”

Section: Seafloor Massive Sulfides At Hydrothermal Ventsmentioning

confidence: 99%

An Overview of Seabed Mining Including the Current State of Development, Environmental Impacts, and Knowledge Gaps

et al. 2018

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Rising demand for minerals and metals, including for use in the technology sector, has led to a resurgence of interest in exploration of mineral resources located on the seabed. Such resources, whether seafloor massive (polymetallic) sulfides around hydrothermal vents, cobalt-rich crusts (CRCs) on the flanks of seamounts or fields of manganese (polymetallic) nodules on the abyssal plains, cannot be considered in isolation of the distinctive, in some cases unique, assemblages of marine species associated with the same habitats and structures. In addition to mineral deposits, there is interest in extracting methane from gas hydrates on continental slopes and rises. Many of the regions identified for future seabed mining are already recognized as vulnerable marine ecosystems (VMEs). Since its inception in 1982, the International Seabed Authority (ISA), charged with regulating human activities on the deep-sea floor beyond the continental shelf, has issued 27 contracts for mineral exploration, encompassing a combined area of more than 1.4 million km 2 , and continues to develop rules for commercial mining. At the same time, some seabed mining operations are already taking place within continental shelf areas of nation states, generally at relatively shallow depths, and with others at advanced stages of planning. The first commercial enterprise, expected to target mineral-rich sulfides in deeper waters, at depths between 1,500 and 2,000 m on the continental shelf of Papua New Guinea, is scheduled to begin early in 2019. In this review, we explore three broad aspects relating to the exploration and exploitation of seabed mineral resources: (1) the current state of development of such activities in areas both within and beyond national jurisdictions, (2) possible environmental impacts both close to and more distant from mining activities and (3) the uncertainties and gaps in scientific knowledge and understanding which render baseline and impact assessments particularly difficult for the deep sea. We also consider whether there are alternative approaches to the management of existing mineral reserves and resources, which may reduce incentives for seabed mining.

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New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

Cited by 128 publications

References 34 publications

Xenacoelomorpha's significance for understanding bilaterian evolution

Xenacoelomorpha's significance for understanding bilaterian evolution

Pitfalls in supermatrix phylogenomics

An Overview of Seabed Mining Including the Current State of Development, Environmental Impacts, and Knowledge Gaps

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