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Supplemental Information

Ancestral state reconstruction of tide pool occupancy for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

The most recent common ancestor (MRCA) of Oligocottinae and the MRCA of the Leiocottus lineage are each indicated with an arrow. See text for details.

DOI: 10.7287/peerj.preprints.2981v1/supp-1

Phenogram showing the inferred evolutionary history of maximum length of extant oligocottine species and the outgroup taxon Chitonotus pugetensis

The most recent common ancestor (MRCA) of Oligocottinae is indicated with an arrow. Phylogenetic relationships are represented by white edges and bifurcation points represent inferred speciation events. Phylogenetic topology is from Bayesian MCC tree shown in Figure 1. Relative time is indicated on the horizontal axis and maximum length in millimeters indicated on the vertical axis. The tips and nodes of the phylogeny are positioned on the vertical axis to reflect the maximum length or inferred maximum length of each taxon or hypothetical ancestor (respectively). Ancestral states for each node were inferred using maximum likelihood and 95% confidence intervals for each state are represented with blue lines. See text for details.

DOI: 10.7287/peerj.preprints.2981v1/supp-2

Ancestral state reconstruction of the presence of squamation for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

The most recent common ancestor (MRCA) of Oligocottinae, the MRCA of the subgenus Clinocottus (Blennicottus), and the MRCA of the clade composed of Oligocottus snyderi, O. rubellio, and O. maculosus are each indicated with an arrow. See text for details.

DOI: 10.7287/peerj.preprints.2981v1/supp-3

Ancestral state reconstruction of the presence of copulation for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

The most recent common ancestor (MRCA) of Oligocottinae is indicated with an arrow. Tips and nodes without a pie symbol are taxa for which no data are available or the state is not reconstructable due to missing data (respectively). See text for details.

DOI: 10.7287/peerj.preprints.2981v1/supp-4

Morphospace of significant principal component axes showing inferred phenotypic optima for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

Taxa (small circles, labeled by species name) are color-coded to match their inferred phenotypic optimum (large circles). Optima inferred using “surface” (Ingram & Mahler, 2013). See text for details.

Reference:

Ingram T., Mahler DL. 2013. SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion. Methods in Ecology and Evolution 4:416–425.

DOI: 10.7287/peerj.preprints.2981v1/supp-5

Morphological variation in enlarged male genital papillae

Species and museum lot numbers are as follows, A) Artedius harringtoni, OSIC 04533, 91mm SL; B) Clinocottus acuticeps, UAM 47713, 30mm SL; C) Oligocottus maculosus, OSU 07467, 73mm SL; D) Chitonotus pugetensis, OSU 14872, 76mm SL; E) Clinocottus analis, OSU 3241, 72mm SL; F) Clinocottus globiceps, OSU 00275, 104mm SL. Lot numbers begin with a three letter code which indicates the location of the specimen: OSU = Oregon State University, UAM = University of Alaska Museum. Scale bar = 2mm.

DOI: 10.7287/peerj.preprints.2981v1/supp-6

Modification of the anteriormost rays of the anal in males of the genus Oligocottus

Illustration of anal fin is shown for all species: A) O. rimensis, SIO 67-151; B) O. maculosus, OS 287; C) O. rubellio, OS 8133; D) O. snyderi, OS 4366. Cladogram indicating phylogenetic relationship of species is indicated below anal fin illustrations, adapted from Figure 3. Museum codes are SIO = Scripps Institute of Oceanography, OS = Oregon State University.

DOI: 10.7287/peerj.preprints.2981v1/supp-7

GenBank accession numbers for all sequences used in this study from the dataset assembled in Buser and Lopez (2015)

Comma separated values (CSV) format. See Buser and Lopez (2015) for collection locality data and DNA isolation and amplification methodology.

DOI: 10.7287/peerj.preprints.2981v1/supp-8

GenBank accession numbers for all sequences used in this study from the dataset assembled in Buser and Lopez (2015)

Microsoft Excel (xlsx) format. See Buser and Lopez (2015) for collection locality data and DNA isolation and amplification methodology.

DOI: 10.7287/peerj.preprints.2981v1/supp-9

Museum collection data for all 16 species of the subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

Comma seperated values (CSV) format.

DOI: 10.7287/peerj.preprints.2981v1/supp-10

Museum collection data for all 16 species of the subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis

Microsoft Excel (xlsx) format. Museum records where "tide pool" or the like is explicitly stated as the collection locality are highlighted in light green.

DOI: 10.7287/peerj.preprints.2981v1/supp-11

Verbatim descriptions of depth ranges for members of the sculpin subfamily Oligocottinae (ingroup) and the outgroup taxon Chitonotus pugetensis

Microsoft Excel (xlsx) format. Verbatim descriptions of depth ranges, primary literature references for tide pool occurrence, and museum lots where "tide pool" or the like is listed as the collection locality. List of museum codes and references are below the table.

DOI: 10.7287/peerj.preprints.2981v1/supp-12

Verbatim descriptions of depth ranges for members of the sculpin subfamily Oligocottinae (ingroup) and the outgroup taxon Chitonotus pugetensis

Comma separated values (csv) format. Verbatim descriptions of depth ranges, primary literature references for tidepool occurrance, and museum lots where "tide pool" or the like is listed as the collection locality. List of museum codes and references are below the table.

DOI: 10.7287/peerj.preprints.2981v1/supp-13

Summary of collection depth data for museum records of oligocottine sculpins and the outgroup taxon Chitonotus pugetensis

Microsoft Excel (xlsx) format. Catalog numbers, depth, and locality data are provided in Supplementary Table 2.

DOI: 10.7287/peerj.preprints.2981v1/supp-14

Summary of collection depth data for museum records of oligocottine sculpins and the outgroup taxon Chitonotus pugetensis

Comma separated values (csv) format. Catalog numbers, depth, and locality data are provided in Supplementary Table 2.

DOI: 10.7287/peerj.preprints.2981v1/supp-15

Folder containing R script, data matrix, shape data, and phylogenetic tree

The R script is titled "LitorallyAdaptiveScript.R" and contains a heavily annotated list of commands for importing the data matrix ("LitorallyAdaptive_datamatrix.csv"), shape data ("MorphoJcoords.csv"), and phylogenetic tree ("sculpin_birthdeath_mcc_starbeast.tree"), and performing all R-based analyses described in the manuscript. The script also contains descriptions of data contained in each file.

DOI: 10.7287/peerj.preprints.2981v1/supp-16

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Thaddaeus J Buser conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Michael D Burns conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

J. Andrés López conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The raw data has been supplied as a supplementary file.

Funding

Financial support for this work was provided by NSF grant DEB 0963767 to J.A. López and a NSF CASE GK-12 Fellowship, Oregon State University Provost's Distinguished Graduate Fellowship, Munson Wildlife Graduate Scholarship, Oregon Council Federation of Fly Fishers Scholarship, M. A. Ali Graduate Chair Award in Fisheries Biology, and Carl Bond Memorial Scholarship to T.J. Buser. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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