TreeBASE Search-Analyses for study 21486

@ARTICLE{TreeBASE2Ref27571, author = {Nathaniel Evans}, title = {Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa}, year = {2018}, keywords = {Evolution, Taxonomy, Phylogeny, Portunidae, Portunoidea, Symbiosis, Decapoda, Brachyura, Systematics, Swimming crab}, doi = {10.7717/peerj.4260}, url = {http://peerj.com/articles/4260/}, pmid = {}, journal = {PeerJ}, volume = {6:e4260}, number = {}, pages = {56}, abstract = {Portunoidea is a diverse lineage of ecologically and economically important marine crabs comprising 8 families and 14 subfamilies. Closely related portunid subfamilies Caphyrinae and Thalamitinae constitute some of this group?s greatest morphological and taxonomic diversity, and are the only known lineages to include symbiotic taxa. Emergence of symbiosis in decapods remains poorly studied and portunoid crabs provide an interesting, but often overlooked example. Yet the paucity of molecular phylogenetic data available for Portunoidea makes it challenging to investigate the evolution and systematics of the group. Phylogenetic analyses, though limited, suggest that many putative portunoid taxa are para- or polyphyletic. Here I augment existing molecular data?significantly increasing taxon sampling of Caphyrinae, Thalamitinae, and several disparate portunoid lineages?to investigate the phylogenetic origin of symbiosis within Portunoidea and reevaluate higher- and lower-level portunoid classifications. Phylogenetic analyses were carried out on sequences of H3, 28S rRNA, 16S rRNA, and CO1 for up to 168 portunoid taxa; this included, for the first time, molecular data from the genera Atoportunus, Brusinia, Caphyra, Coelocarcinus, Gonioinfradens, Raymanninus, and Thalamonyx. Results support the placement of all symbiotic taxa (Caphyra, Lissocarcinus, and two Thalamita) in a single clade derived within the thalamitine genus Thalamita. Caphyrina Paulson, 1875, nom. trans. is recognized here as a subtribe within the subfamily Thalamitinae. Results also support the following taxonomic actions: Cronius is reclassified as a thalamitine genus; Thalamonyx is reestablished as a valid genus; Goniosupradens is raised to the generic rank; and three new genera (Zygita gen. nov., Thranita gen. nov., and Trierarchus gen. nov.) are described to accommodate some Thalamita s.l. taxa rendered paraphyletic by Caphyrina. A new diagnosis of Thalamitinae is provided. Results also support a more conservative classification of Portunoidea comprising three instead of eight extant families: Geryonidae (Geryonidae + Ovalipidae; new diagnosis provided), Carcinidae (Carcinidae + Pirimelidae + Polybiidae + Thiidae + Coelocarcinus; new diagnosis provided) and Portunidae. Finally, 16s rRNA data suggests that family Brusiniidae might not be a portunoid lineage.} }

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Analyses for Study 21486

Citation title: "Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa".

Study name: "Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa".

This study is part of submission 21486 (Status: Published).

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begin sets; charset H3_pos3 = 1 - 327\3; charset H3_pos1 = 2 - 327\3; charset H3_pos2 = 3 - 327\3; charpartition byPartitionFinderSet = Part1:H3_pos3, Part2:H3_pos1, Part3:H3_pos2; [model1] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [model2] datatype = nucleotide ratematrix = (0 1 0 0 1 0) statefrequencies = estimate ratehetmodel = none numratecats = 1 invariantsites = estimate [model3] datatype = nucleotide ratematrix = 1rate statefrequencies = equal ratehetmodel = none numratecats = 1 invariantsites = estimate

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Analysis 2

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begin sets; charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charpartition byPartitionFinderSet = Part1:16SrRNA tRNALeu, Part2:ND1; end; [model1] datatype = nucleotide ratematrix = (0 1 2 3 1 4) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = (0 1 0 0 1 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate

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Analysis 3

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begin sets; charset CO1_pos1 = 1-657\3; charset CO1_pos2 = 2-657\3; charset CO1_pos3 = 3-657\3; charpartition byPartitionFinderSet = Part1:CO1_pos1, Part2:CO1_pos2, Part3:CO1_pos3; end; [model1] datatype = nucleotide ratematrix = 6rate statefrequencies = equal ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = 1rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model3] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none

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Analysis 4

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Analysis 5

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begin sets; charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; charpartition byPartitionFinderSet = Part1:16SrRNA tRNALeu, Part2:ND1, Part3:CO1_pos1, Part4:CO1_pos2, Part5:CO1_pos3, Part6:28SrRNA, Part7:H3_pos3, Part8:H3_pos1 H3_pos2; end; [model1] datatype = nucleotide ratematrix = (0 1 2 2 3 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = (0 1 0 0 1 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model3] datatype = nucleotide ratematrix = 6rate statefrequencies = equal ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model4] datatype = nucleotide ratematrix = 1rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model5] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model6] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model7] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [model8] datatype = nucleotide ratematrix = (0 1 0 0 2 0) statefrequencies = equal ratehetmodel = none numratecats = 1 invariantsites = estimate

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Analysis 6

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begin sets; charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; charpartition byPartitionFinderSet = Part1:16SrRNA tRNALeu, Part2:ND1, Part3:CO1_pos1, Part4:CO1_pos2, Part5:CO1_pos3, Part6:28SrRNA, Part7:H3_pos3, Part8:H3_pos1 H3_pos2; end; [model1] datatype = nucleotide ratematrix = (0 1 2 2 3 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model3] datatype = nucleotide ratematrix = 6rate statefrequencies = equal ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model4] datatype = nucleotide ratematrix = 1rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model5] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model6] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model7] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [model8] datatype = nucleotide ratematrix = (0 1 0 0 2 0) statefrequencies = equal ratehetmodel = none numratecats = 1 invariantsites = estimate

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Analysis 7

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begin sets; charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; charpartition byPartitionFinderSet = Part1:16SrRNA tRNALeu, Part2:ND1, Part3:CO1_pos1 H3_pos1, Part4:CO1_pos2 H3_pos2, Part5:CO1_pos3, Part6:28SrRNA, Part7:H3_pos3; end; [model1] datatype = nucleotide ratematrix = (0 1 2 2 3 0) statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model2] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model3] datatype = nucleotide ratematrix = 6rate statefrequencies = equal ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model4] datatype = nucleotide ratematrix = 1rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model5] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model6] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [model7] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate

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Analysis 8

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Analysis 9

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charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; partition favored = 8: 16SrRNA tRNALeu, ND1, CO1_pos1 H3_pos1, CO1_pos2, CO1_pos3, 28SrRNA, H3_pos3, H3_pos2; lset applyto=(1,2,5,6) nst=6 rates=invgamma; lset applyto=(3) nst=6 rates=invgamma; prset applyto=(3) statefreqpr=fixed(equal); lset applyto=(4) nst=1 rates=invgamma; lset applyto=(7) nst=6 rates=gamma; lset applyto=(8) nst=1 rates=propinv; prset applyto=(8) statefreqpr=fixed(equal);

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Analysis 10

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charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; partition favored = 8: 16SrRNA tRNALeu, ND1, CO1_pos1 H3_pos1, CO1_pos2, CO1_pos3, 28SrRNA, H3_pos3, H3_pos2; lset applyto=(1,2,5,6) nst=6 rates=invgamma; lset applyto=(3) nst=6 rates=invgamma; prset applyto=(3) statefreqpr=fixed(equal); lset applyto=(4) nst=1 rates=invgamma; lset applyto=(7) nst=6 rates=gamma; lset applyto=(8) nst=1 rates=propinv; prset applyto=(8) statefreqpr=fixed(equal);

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Analysis 11

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charset 16SrRNA = 1-583; charset tRNALeu = 584-653; charset ND1 = 654-1105; charset CO1_pos1 = 1106-1762\3; charset CO1_pos2 = 1107-1762\3; charset CO1_pos3 = 1108-1762\3; charset 28SrRNA = 1763 - 2986; charset H3_pos3 = 2987 - 3313\3; charset H3_pos1 = 2988 - 3313\3; charset H3_pos2 = 2989 - 3313\3; partition favored = 7: 16SrRNA tRNALeu, ND1, CO1_pos1 H3_pos1, CO1_pos2 H3_pos2, CO1_pos3, 28SrRNA, H3_pos3; lset applyto=(1,2,5,6) nst=6 rates=invgamma; lset applyto=(3) nst=6 rates=invgamma; prset applyto=(3) statefreqpr=fixed(equal); lset applyto=(4) nst=1 rates=invgamma; lset applyto=(7) nst=6 rates=gamma;

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