TreeBASE Search-Matrices for study 1794

@ARTICLE{TreeBASE2Ref17692, author = {Torsten H. Struck and Nancy Schult and Tiffany Kusen and Emily Hickman and Christoph Bleidorn and Damhnait McHugh and Kenneth M. Halanych}, title = {Annelid Phylogeny and the Status of Sipuncula and Echiura}, year = {2007}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {BMC Evolutionary Biology}, volume = {}, number = {}, pages = {}, abstract = {Background: 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. Results: Sipuncula, Echiura, Siboglinidae, and Clitellata are all nested within polychaete annelids according to phylogenetic analyses of three nuclear genes (18S rRNA, 28S rRNA, EF1a; 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). This study substantially furthers previous findings by using approximately unbiased tests and non-scaled bootstrap probability tests to compare significance of differences between 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 hint at 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. Conclusions: 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.} }

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Matrices for Study 1794

Citation title: "Annelid Phylogeny and the Status of Sipuncula and Echiura".

This study was previously identified under the legacy study ID S1766 (Status: Published).

Matrices

ID	Matrix Title	Data type	NTAX	NCHAR	Taxa
M57816	Fig. 5 Neofusicoccum ITS TEF1 TUB2 RPB2 alignment	Nucleic Acid	208	1840	View Taxa
M57817	Fig. 6 Neofusicoccum parvum ITS TEF1 TUB2 RPB2 alignment	Nucleic Acid	75	1805	View Taxa
M57819	Fig. 8 Phaeobotryon ITS LSU TEF1 alignment	Nucleic Acid	54	1726	View Taxa
M57815	Fig. 4 Lasiodiplodia ITS TEF1 TUB2 RPB2 alignment	Nucleic Acid	148	1612	View Taxa
M57821	Fig. 10 Saccharata ITS TEF1 RPB2 alignment	Nucleic Acid	41	1529	View Taxa
M57813	Fig. 2. Diplodia ITS TEF1 TUB2 alignment	Nucleic Acid	180	1291	View Taxa
M57814	Fig. 3 Dothiorella ITS TEF1 TUB2 alignment	Nucleic Acid	123	1272	View Taxa
M57820	Fig. 9 Pseudofusicoccum TEF1 TUB2 ITS alignment	Nucleic Acid	30	1256	View Taxa
M57812	Fig. 1. Botryosphaeria ITS TEF1 TUB2 alignment	Nucleic Acid	51	1206	View Taxa
M57818	Fig. 7 Neoscytalidium ITS TEF1 TUB2 alignment	Nucleic Acid	66	1133	View Taxa
M57893	Fig. S10B Saccharata RPB2 alignment	Nucleic Acid	32	627	View Taxa
M57887	Fig. S8B Phaeobotryon LSU alignment	Nucleic Acid	44	556	View Taxa
M57892	Fig. S10A Saccharata ITS alignment	Nucleic Acid	41	550	View Taxa
M57874	Fig. S5B Neofusicoccum RPB2 alignment	Nucleic Acid	176	539	View Taxa
M57879	Fig. S6B Neofusicoccum parvum complex RPB2 alignment	Nucleic Acid	61	535	View Taxa
M57825	Fig. S2A Diplodia ITS alignment	Nucleic Acid	179	522	View Taxa
M57868	Fig. S4B Lasiodiplodia RPB2 alignment	Nucleic Acid	112	520	View Taxa
M57872	Fig. S5A Neofusicoccum ITS alignment	Nucleic Acid	208	510	View Taxa
M57886	Fig. S8A Phaeobotryon ITS alignment	Nucleic Acid	54	500	View Taxa
M57883	Fig. S7A Neoscytalidium ITS alignment	Nucleic Acid	66	499	View Taxa
M57889	Fig. S9A Pseudofusicoccum ITS alignment	Nucleic Acid	30	493	View Taxa
M57877	Fig. S6A Neofusicoccum parvum complex ITS alignment	Nucleic Acid	75	481	View Taxa
M57863	Fig. S3A Dothiorella ITS alignment	Nucleic Acid	123	479	View Taxa
M57822	Fig. S1A Botryosphaeria ITS alignment	Nucleic Acid	51	461	View Taxa
M57891	Fig. S9C Pseudofusicoccum TUB2 alignment	Nucleic Acid	23	427	View Taxa
M57865	Fig. S3C Dothiorella TUB2 alignment	Nucleic Acid	109	415	View Taxa
M57871	Fig. S4D Lasiodiplodia TUB2 alignment	Nucleic Acid	130	402	View Taxa
M57881	Fig. S6D Neofusicoccum parvum complex TUB2 alignment	Nucleic Acid	72	394	View Taxa
M57862	Fig. S2C Diplodia TUB2 alignment	Nucleic Acid	167	389	View Taxa
M57824	Fig. S1C Botryosphaeria TUB2 alignment	Nucleic Acid	44	387	View Taxa
M57876	Fig. S5D Neofusicoccum TUB2 alignment	Nucleic Acid	203	381	View Taxa
M57866	Fig. S4A Lasiodiplodia ITS alignment	Nucleic Acid	147	368	View Taxa
M57885	Fig. S7C Neoscytalidium TUB2 alignment	Nucleic Acid	65	358	View Taxa
M57888	Fig. S8C Phaeobotryon TEF1 alignment	Nucleic Acid	45	339	View Taxa
M57896	Fig. S10C Saccharata TEF1 alignment	Nucleic Acid	39	302	View Taxa
M57890	Fig. S9B Pseudofusicoccum TEF1 alignment	Nucleic Acid	30	295	View Taxa
M57880	Fig. S6C Neofusicoccum parvum complex TEF1 alignment	Nucleic Acid	71	281	View Taxa
M57826	Fig. S2B Diplodia TEF1 alignment	Nucleic Acid	174	276	View Taxa
M57875	Fig. S5C Neofusicoccum TEF1 alignment	Nucleic Acid	200	275	View Taxa
M57864	Fig. S3B Dothiorella TEF1 alignment	Nucleic Acid	121	269	View Taxa
M57823	Fig. S1B Botryosphaeria TEF1 alignment	Nucleic Acid	50	263	View Taxa
M57869	Fig. S4C Lasiodiplodia TEF1 alignment	Nucleic Acid	146	258	View Taxa
M57884	Fig. S7B Neoscytalidium TEF1 alignment	Nucleic Acid	65	187	View Taxa