Data from: Species selection favors dispersive life histories in sea slugs, but higher per-offspring investment drives shifts to short-lived larvae

Krug PJ, Vendetti JE, Ellingson RA, Trowbridge CD, Hirano YM, Trathen DY, Rodriguez AK, Swennen C, Wilson NG, Valdés ÁA

Date Published: August 11, 2015

DOI: http://dx.doi.org/10.5061/dryad.88mv3.2

 

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Title Figure S1, 16S secondary structure model for Sacoglossa
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Description Secondary structure model for a portion of the mitochondrial large ribosomal subunit rRNA (16S) gene for Elysia crispata; positions conserved across Mollusca are bolded.
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Title Figure S2, Alignment of partial 16S gene sequences
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Description Alignment of partial 16S gene sequences for all taxa, annotated according to secondary structure. Regions of ambiguous alignment (indicated by green shaded boxes marked “X”) were manually deleted prior to analyses.
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Title Figure S3, Annotated alignment of partial 28S rDNA sequences
Downloaded 105 times
Description Alignment of a portion of the nuclear large ribosomal subunit rRNA (28S) gene for all taxa, showing annotated secondary structure based on features conserved across Metazoa. Regions of ambiguous alignment (indicated by green shaded boxes marked “X”) were manually deleted prior to analyses.
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Title Figure S4, Individual gene trees (a-d), BI consensus tree (e), and ML tree with two data partitions (f)
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Description Supplementary phylogenetic trees, including individual ML gene trees for each locus based on partial sequences of the (a) mitochondrial COI (658 bp), (b) mitochondrial 16S rRNA (404 bp), (c) nuclear 28S rRNA (1392 bp), and (c) nuclear H3 (328 bp) genes; (e) the BI consensus phylogram; and (f) the ML phylogram and significant bootstrap support values when using two data partitions as per PartitionFinder.
Download Fig S4a-f, gene trees, BI consensus, ML a...ed.pdf (6.652 Mb)
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Title Figure S5, Collapsed phylogeny showing distribution of species richness and development modes
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Description Distribution of species diversity among supported clades on the ML phylogeny of Sacoglossa. Traditional genera or genus-level clades were collapsed in proportion to known species richness, listed for each group. Species diversity and a pruned tree were used as inputs for ML tests of state-dependent speciation rates using the BiSSE model. Larval development mode for terminal taxa are coded as: P, planktotrophic; L, lecithotrophic; ?, unknown. The number of species with each development mode (or missing data) is given in parentheses for collapsed clades or terminals representing multiple taxa, in the same order (P,L,?). The sum of these values represents the total number of species known in a clade, including undescribed candidate species identified in the present work. Red branches indicate shifts in diversification detected by MEDUSA that are independent of larval development mode. Traditional families are named to the right of, and delimited by, colored horizontal bars; bolded family names are traditionally placed in superfamily Limapontioidea. Select higher clade names are given on branches.
Download Fig S5, BiSSE tree v4.pdf (27.84 Kb)
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Title Figure S6, Posterior distributions of rate parameters from dependent models of correlated trait evolution
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Description Posterior distributions of parameters from dependent models of trait evolution, allowing ECY and development mode to evolve in a correlated manner. Transition rates are labeled as in Fig. 2. Z = percentage of time a rate was in the zero bin.
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Title Table S1, Sampled taxa and collection details
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Description Species names, sample codes and collection details for sequenced taxa used in phylogenetic analyses. Blank cells reflect missing information for sequence data obtained from a public database.
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Title Table S2, Developmental character data for Sacoglossa
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Description Developmental character data for Sacoglossa including larval development mode, presence/absence and pattern of extra-capsular yolk (ECY), mean egg diameter (± SD), and mean larval shell width (± SD) at hatching. Taxa are listed alphabetically by traditional family within higher clades, and then by binomial name within family. Generic names in quotation marks denote taxa that do not group with most other members of the genus to which they are traditionally assigned.
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Title Table S3, NCBI accession numbers
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Description Accession numbers from the National Center for Bioinformatics database for sequences generated and/or analyzed in this study.
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Title Table S4, BiSSE model fit using a pruned input tree and global estimate of unsampled taxa
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Description Comparison of BiSSE models correcting for missing data with a pruned input tree and one overall estimate of the percentage of unsampled taxa (69%), with either (a) one rate of character change, or (b) rates of reversal (q10) constrained to be rare (<1%) relative to gains of lecithotrophy (q01).
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Title Table S5, BiSSE parameter estimates using a percentage of unsampled taxa to correct for missing data
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Description Maximum-likelihood parameter estimates for BiSSE models, correcting for missing data using an overall percentage of unsampled taxa (69%). The ML tree (Fig. 3) was pruned of terminals missing character data, and used as the input tree for BiSSE analyses with three phylogenetic partitions across Sacoglossa, and either (A) one rate of character change, or (B) rates of reversal to planktotrophy (q10) constrained to be rare (<1%) relative to forward rates (q01). Estimates from the preferred model are bolded, with alternatives shown in descending order of AIC scores.
Download Table S5, split BiSSE params, % missing taxa.doc (50.17 Kb)
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Title Table S6, References cited in Table 4
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Description References cited in Table 4, from which data on development modes were taken for select clades in Heterobranchia and Caenogastropoda.
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When using this data, please cite the original publication:

Krug PJ, Vendetti JE, Ellingson RA, Trowbridge CD, Hirano YM, Trathen DY, Rodriguez AK, Swennen C, Wilson NG, Valdés ÁA (2015) Species selection favors dispersive life histories in sea slugs, but higher per-offspring investment drives shifts to short-lived larvae. Systematic Biology 64(6): 983-999. http://dx.doi.org/10.1093/sysbio/syv046

Additionally, please cite the Dryad data package:

Krug PJ, Vendetti JE, Ellingson RA, Trowbridge CD, Hirano YM, Trathen DY, Rodriguez AK, Swennen C, Wilson NG, Valdés ÁA (2015) Data from: Species selection favors dispersive life histories in sea slugs, but higher per-offspring investment drives shifts to short-lived larvae. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.88mv3.2
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