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      Multiple surveys employing a new sample‐processing protocol reveal the genetic diversity of placozoans in Japan

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          Abstract

          Placozoans, flat free‐living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest‐branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S r RNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, “ethanol‐treated substrate sampling,” for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine‐jima, Chichi‐jima, and Haha‐jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine‐jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.

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          The Ctenophore Genome and the Evolutionary Origins of Neural Systems

          The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores, or comb jellies, have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here, we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well-recognized in ctenophores, many bilaterian neuron-specific genes and genes of “classical” neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.
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            A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

            Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals ("Porifera-sister" hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The "Ctenophora-sister" hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
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              Genomic data do not support comb jellies as the sister group to all other animals.

              Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
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                Author and article information

                Contributors
                hmiyazawa0209@shimoda.tsukuba.ac.jp , h.nakano@shimoda.tsukuba.ac.jp
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                29 January 2018
                March 2018
                : 8
                : 5 ( doiID: 10.1002/ece3.2018.8.issue-5 )
                : 2407-2417
                Affiliations
                [ 1 ] Shimoda Marine Research Center University of Tsukuba Shimoda Shizuoka Japan
                Author notes
                [*] [* ] Correspondence

                Hideyuki Miyazawa and Hiroaki Nakano, Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan.

                Emails: hmiyazawa0209@ 123456shimoda.tsukuba.ac.jp ; h.nakano@ 123456shimoda.tsukuba.ac.jp

                Author information
                http://orcid.org/0000-0003-2319-1893
                Article
                ECE33861
                10.1002/ece3.3861
                5838039
                29531663
                f430fcc5-d896-4b61-ac06-c1c3c5b21224
                © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 03 August 2017
                : 19 December 2017
                : 02 January 2018
                Page count
                Figures: 7, Tables: 1, Pages: 11, Words: 7337
                Funding
                Funded by: Japan Society for the Promotion of Science
                Award ID: 22870003
                Award ID: B24770069
                Award ID: A26711022
                Funded by: The Japan Society
                Award ID: 24‐715
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece33861
                March 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.3.2.2 mode:remove_FC converted:05.03.2018

                Evolutionary Biology
                distribution,genetic diversity,phylogeography,placozoa,sampling method
                Evolutionary Biology
                distribution, genetic diversity, phylogeography, placozoa, sampling method

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