DOI: 10.5061/dryad.crjdfn31m
title: Cave-adapted evolution in the North American Amblyopsid fishes inferred using phylogenomics and geometric morphometrics

description: Cave adaptation has evolved repeatedly across the Tree of Life, famously
 leading to pigmentation and eye degeneration and loss, yet its
 macroevolutionary implications remain poorly understood. We use the North
 American amblyopsid fishes, a family spanning a wide degree of cave
 adaptation, to examine the impact of cave specialization on the modes and
 tempo of evolution. We reconstruct evolutionary relationships using
 ultraconserved element loci, estimate the ancestral histories of
 eye-state, and examine the impact of cave adaptation on body shape
 evolution. Our phylogenomic analyses provide a well-supported hypothesis
 for amblyopsid evolutionary relationships. The obligate blind cavefishes
 form a clade and the cave-facultative eyed spring cavefishes are nested
 within the obligate cavefishes. Using ancestral state reconstruction, we
 find support for at least two independent subterranean colonization events
 within the Amblyopsidae. Eyed and blind fishes have different body shapes,
 but not different rates of body shape evolution. North American
 amblyopsids highlight the complex nature of cave-adaptive evolution and
 the necessity to include multiple lines of evidence to uncover the
 underlying processes involved in the loss of complex traits.
description: <strong>Ultraconserved elements
 dataset</strong> We performed target-capture of
 ultraconserved element loci using the Acanthomorph MYbaits Probe Kit
 (2,600 probes for 1,341 UCE Loci). Cleaning and processing was performed
 through the PHYLUCE pipeline and ABySS was used for assembly. The
 concatenated dataset was made with a 75% complete datamatrix.
description: <strong>2020_Concatenated_alignments_amblyfull75_nexus.nex
 </strong> This dataset is a concatenated dataset
 for ultraconserved element (UCE) loci from the Amblyopsidae fish family.
 After DNA extraction and sonication shearing, a Kapa HyperPrep Library
 Preparation Kit was used to create libraries. Then target capture of the
 UCE loci was performed with the MYbaits Acanthomorph probe set and target
 capture kit targeting 1,314 loci. Sequencing was performed on an Illumina
 HiSeq300-PE150 platform at the Oklahoma Medical Research Foundation with
 ~30x sequencing coverage. Assembly was performed using ABySS. Cleaning and
 processing was completed through the Phyluce pipeline. This dataset was
 created with a 75% complete datamatrix and contains 897 UCE
 loci.
 <strong>Evolution19-0496_S1.docx</strong>
 Supplementary Materials 1. Specimen tables for both morphology
 and molecular samples.
 <strong>Evolution19-0496_S2.docx</strong>
 Supplementary Materials 2. Supplementary figures in a single
 document with figure legends.
 <strong>Evolution19-0496_S3.docx</strong>
 Supplementary Materials 3. Explanation of landmark positions for
 landmark-based geometric morphometrics.
 <strong>S2_FigS1.pdf</strong>
 Lateral GM landmark scheme for the amblyopsids based on Burress
 et al. (2017). LM descriptions can be found in Supplementary Material S3.
 Black filled circles = static landmarks, gray filled circles = sliding
 landmarks, unfilled circles = unbend landmarks.
 <strong>S2_FigS2.pdf</strong>
 Amblyopsid RAxML phylogenomic hypothesis with all individuals
 labeled. Species codes are: As = Amblyopsis spelaea, Asay = Aphredoderus
 sayanus, Ccor = <i>Chologaster cornuta</i>, Fa =
 <i>Forbesichthys agassizii</i>, Fp = <i>F.
 papilliferus</i>, Po = <i>Percopsis omiscomaycus</i>, Sp
 = <i>Speoplatyrhinus poulsoni</i>, Te = <i>Typhlichthys
 eigenmanni</i>, Tr = <i>Troglichthys rosae</i>, Ts =
 <i>Ty. subterraneus</i>. Locality codes are included for blind
 cavefishes and eyed spring cavefishes.
 <strong>S2_FigS3.pdf</strong>
 Amblyopsid ASTRAL-II coalescent species tree with all individuals
 labeled. Species codes are: As = Amblyopsis spelaea, Asay =
 <i>Aphredoderus sayanus</i>, Ccor = <i>Chologaster
 cornuta</i>, Fa = <i>Forbesichthys agassizii</i>, Fp =
 <i>F. papilliferus</i>, Po = <i>Percopsis
 omiscomaycus</i>, Sp = <i>Speoplatyrhinus poulsoni</i>,
 Te = <i>Typhlichthys eigenmanni</i>, Tr =
 <i>Troglichthys rosae</i>, Ts = <i>Ty.
 subterraneus</i>. Locality codes are included for blind cavefishes
 and eyed spring cavefishes.
 <strong>S2_FigS4.pdf</strong>
 Amblyopsid SVDQuartets consensus coalescent species tree with all
 individuals labeled. Species codes are: As = Amblyopsis spelaea, Asay =
 Aphredoderus sayanus, Ccor = <i>Chologaster cornuta</i>, Fa =
 <i>Forbesichthys agassizii</i>, Fp = <i>F.
 papilliferus</i>, Po = <i>Percopsis omiscomaycus</i>, Sp
 = <i>Speoplatyrhinus poulsoni</i>, Te = <i>Typhlichthys
 eigenmanni</i>, Tr = <i>Troglichthys rosae</i>, Ts =
 <i>Ty. subterraneus</i>. Locality codes are included for blind
 cavefishes and eyed spring cavefishes.
 <strong>S2_FigS5.pdf</strong>
 Summary of 1000 mapped character states using stochastic
 character mapping of eye-state. Nodes referenced in-text are numbered with
 roman numerals (I and II).
 <strong>S2_FigS6.pdf</strong>
 Biplots of PC scores per individual for the full GM dataset (N =
 146) colored by species. PC1 is located on the X axis and PC2 is located
 on the Y axis. Warp grids indicate the shape of the minimum and maximum
 specimen along that axis.
 <strong>S2_FigS7.pdf</strong> GM
 Phylomorphospace of the amblyopsid data subset (N = 18) with species
 colored and ellipses surrounding the eye-states (blue = blind, orange =
 eyed).