TreeBASE Search-Matrices for study 28360

@ARTICLE{TreeBASE2Ref32216, author = {Charles R Lindsey and Raphael F Rosenzweig and Matthew D Herron}, title = {Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae}, year = {2021}, keywords = {phylotranscriptomics; volvocine algae; green algae; multicellularity}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Biology}, volume = {}, number = {}, pages = {}, abstract = {Background The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. Results We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Conclusions Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.} }

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Matrices for Study 28360

Citation title: "Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae".

Study name: "Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae".

This study is part of submission 28360 (Status: Published).

Matrices

ID	Matrix Title	Description	Data type	NTAX	NCHAR	Taxa
M59777	Volvocine Algae gene002242	Amino acid alignment for single-gene phylogeny.	Amino Acid	59	349	View Taxa
M59779	Volvocine Algae gene002369	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	168	View Taxa
M59783	Volvocine Algae gene002356	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	355	View Taxa
M59809	Volvocine Algae gene003266	Amino acid alignment for single-gene phylogeny.	Amino Acid	55	164	View Taxa
M59781	Volvocine Algae gene002373	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	182	View Taxa
M59791	Volvocine Algae gene004274	Amino acid alignment for single-gene phylogeny.	Amino Acid	68	125	View Taxa
M59803	Volvocine Algae gene002814	Amino acid alignment for single-gene phylogeny.	Amino Acid	65	311	View Taxa
M59786	Volvocine Algae gene002371	Amino acid alignment for single-gene phylogeny.	Amino Acid	66	299	View Taxa
M59805	Volvocine Algae gene002538	Amino acid alignment for single-gene phylogeny.	Amino Acid	48	198	View Taxa
M59797	Volvocine Algae gene002888	Amino acid alignment for single-gene phylogeny.	Amino Acid	56	288	View Taxa
M59787	Volvocine Algae gene002273	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	166	View Taxa
M59794	Volvocine Algae gene003755	Amino acid alignment for single-gene phylogeny.	Amino Acid	66	1042	View Taxa
M59789	Volvocine Algae gene002763	Amino acid alignment for single-gene phylogeny.	Amino Acid	61	366	View Taxa
M59801	Volvocine Algae gene002581	Amino acid alignment for single-gene phylogeny.	Amino Acid	64	568	View Taxa
M59776	Volvocine Algae gene001976	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	501	View Taxa
M59807	Volvocine Algae gene002962	Amino acid alignment for single-gene phylogeny.	Amino Acid	65	219	View Taxa
M59810	Volvocine Algae gene003211	Amino acid alignment for single-gene phylogeny.	Amino Acid	64	211	View Taxa
M59784	Volvocine Algae gene002252	Amino acid alignment for single-gene phylogeny.	Amino Acid	68	487	View Taxa
M59813	Volvocine Algae gene002447	Amino acid alignment for single-gene phylogeny.	Amino Acid	66	260	View Taxa
M59800	Volvocine Algae gene003157	Amino acid alignment for single-gene phylogeny.	Amino Acid	68	328	View Taxa
M59778	Volvocine Algae gene002177	Amino acid alignment for single-gene phylogeny.	Amino Acid	60	230	View Taxa
M59782	Volvocine Algae gene002345	Amino acid alignment for single-gene phylogeny.	Amino Acid	66	408	View Taxa
M59793	Volvocine Algae gene002396	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	179	View Taxa
M59785	Volvocine Algae gene002313	Amino acid alignment for single-gene phylogeny.	Amino Acid	62	234	View Taxa
M59773	Volvocine Algae gene001811	Amino acid alignment for single-gene phylogeny.	Amino Acid	62	426	View Taxa
M59815	Volvocine Algae IQtree concatenated AA alignment	Amino acid alignment for multi-gene phylogeny.	Amino Acid	68	12650	View Taxa
M59804	Volvocine Algae gene002762	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	222	View Taxa
M59806	Volvocine Algae gene003786	Amino acid alignment for single-gene phylogeny.	Amino Acid	65	446	View Taxa
M59799	Volvocine Algae gene002537	Amino acid alignment for single-gene phylogeny.	Amino Acid	58	171	View Taxa
M59808	Volvocine Algae gene003057	Amino acid alignment for single-gene phylogeny.	Amino Acid	62	294	View Taxa
M59775	Volvocine Algae gene001650	Amino acid alignment for single-gene phylogeny.	Amino Acid	63	500	View Taxa
M59812	Volvocine Algae gene003095	Amino acid alignment for single-gene phylogeny.	Amino Acid	68	123	View Taxa
M59790	Volvocine Algae gene002681	Amino acid alignment for single-gene phylogeny.	Amino Acid	63	511	View Taxa
M59792	Volvocine Algae gene002544	Amino acid alignment for single-gene phylogeny.	Amino Acid	64	435	View Taxa
M59811	Volvocine Algae gene003199	Amino acid alignment for single-gene phylogeny.	Amino Acid	67	377	View Taxa
M59795	Volvocine Algae gene002624	Amino acid alignment for single-gene phylogeny.	Amino Acid	65	207	View Taxa
M59798	Volvocine Algae gene003203	Amino acid alignment for single-gene phylogeny.	Amino Acid	63	196	View Taxa
M59780	Volvocine Algae gene002381	Amino acid alignment for single-gene phylogeny.	Amino Acid	68	222	View Taxa
M59788	Volvocine Algae gene002810	Amino acid alignment for single-gene phylogeny.	Amino Acid	63	229	View Taxa
M59796	Volvocine Algae gene002986	Amino acid alignment for single-gene phylogeny.	Amino Acid	66	358	View Taxa
M59802	Volvocine Algae gene002640	Amino acid alignment for single-gene phylogeny.	Amino Acid	65	295	View Taxa