DOI: 10.5061/dryad.bk3j9kdbg
title: Data from: Periodic environmental disturbance drives repeated ecomorphological diversification in an adaptive radiation of Antarctic fishes

description: The ecological theory of adaptive radiation has profoundly shaped our
 conceptualization of the rules that govern diversification. However, while
 many radiations follow classic early burst patterns of diversification as
 they fill ecological space, the longer-term fates of these radiations
 depend on many factors, such as climatic stability. In systems with
 periodic disturbances, species-rich clades can contain nested adaptive
 radiations of subclades with their own distinct diversification histories,
 and how adaptive radiation theory applies in these cases is less clear.
 Here, we investigated patterns of ecological and phenotypic
 diversification within two iterative adaptive radiations of
 cryonotothenioid fishes in Antarctica’s Southern Ocean: crocodile
 icefishes and notoperches. For both clades, we observe evidence of
 repeated diversification into disparate regions of trait space between
 closely related taxa and into overlapping regions of trait space between
 distantly related taxa. We additionally find little evidence that patterns
 of ecological divergence are correlated with evolution of morphological
 disparity, suggesting that these axes of divergence may not be tightly
 linked. Finally, we reveal evidence of repeated convergence in sympatry
 that suggests niche complementarity. These findings reflect the dynamic
 history of Antarctic marine habitats, and may guide hypotheses of
 diversification dynamics in environments characterized by periodic
 disturbance.
description: <em>Descriptions of code scripts:</em>
 <strong>procD-pgls.R</strong> R
 script used to test for correlations among Procrustes body shape
 coordinates and major axes of ecological disparity using phylogenetic
 generalized least squares (PGLS) regression. These analyses were performed
 using the procD.pgls function implemented in the R package geomorph (Baken
 et al. 2021; Adams et al. 2021). 
 <strong>PGLS.R</strong> R script
 used to test for relationships among phenotypic (body size and PC axes 1-3
 of body shape variation) and ecological (buoyancy, depth, and PC axes 1-3
 of diet variation) variables using phylogenetic generalized least squares
 (PGLS) regression. These analyses were performed using the gls function
 implemented in the R package nlme (Pinheiro et al. 2017).
 <strong>DTT.R</strong> R script
 used to calculate relative subclade disparity through time (DTT; Harmon et
 al. 2003) in the traits of mean percentage buoyancy, mean depth, and
 maximum body size. These analyses were performed using the ddt function
 implemented in the R package geiger2 (Pennell et al. 2014). 
 <strong>PGLMM.R</strong> R script
 used to test the relationships among range overlap, clade age, and
 ecomorphological diversification for all pairwise comparisons of icefishes
 and notoperches using phylogenetic generalized linear mixed models
 (PGLMMs). These analyses were performed using the MCMCglmm function
 implemented in the R package MCMCglmm (Hadfield 2010). 
 <em>Descriptions of files:</em>
 <strong>all_chan.tps</strong>
 Landmark data for all icefish (Channichthyidae) species analyzed
 in this study. This file includes the coordinates of 28 landmarks (24
 fixed landmarks and 4 sliding semi-landmarks) placed on a total of 45
 specimens. The start of landmark information for each specimen is
 indicated by "LM=" and ends with the scale factor, labeled
 "SCALE=". The variable "LM" corresponds to the number
 of landmarks placed on each specimen, "IMAGE" refers to the file
 name of the specimen image on which landmarks were placed, "ID"
 corresponds to the species identity of each specimen image, and
 "SCALE" refers to the scale adjustment applied to each photo in
 tpsDig. 
 <strong>all_trem.tps</strong>
 Landmark data for all notoperch (Trematominae) species analyzed
 in this study. This file includes the coordinates of 28 landmarks (24
 fixed landmarks and 4 sliding semi-landmarks) placed on a total of 125
 specimens. The start of landmark information for each specimen is
 indicated by "LM=" and ends with the scale factor, labeled
 "SCALE=". The variable "LM" corresponds to the number
 of landmarks placed on each specimen, "IMAGE" refers to the file
 name of the specimen image on which landmarks were placed, "ID"
 corresponds to the species identity of each specimen image, and
 "SCALE" refers to the scale adjustment applied to each photo in
 tpsDig. 
 <strong>chan_classifiers.csv</strong>
 A 45 x 2 matrix containing information on species identity for
 each icefish specimen included in the landmark dataset. This file is used
 as input in the procD-pgls.R script.
 <strong>chan_diet.csv</strong>
 Diet data for all icefish (Channichthyidae) species analyzed in
 this study. For each species listed in this file, diet is represented by
 mean frequencies of occurrence of 39 different prey categories identified
 from 34 studies that performed stomach content analyses across both
 icefishes and notoperches. For each prey item, we calculated the mean prey
 frequency of occurrence weighted by the number of individual observations
 in each study for each prey item. Included in this file is the total
 number of specimens examined across all studies for each focal
 species. 
 <strong>chan_PairwiseTraits.csv</strong>
 Data matrix including data on sympatry, time since common
 ancestry, and Euclidean distances in phenotypic and ecological traits for
 all possible pairwise comparisons of icefish species. This is the input
 data file used for fitting phylogenetic generalized linear mixed models to
 test the relationships among range overlap, clade age, and
 ecomorphological divergence. The column label "lineage 1" refers
 to the "focal" species, and "lineage 2" refers to the
 species being compared to "lineage 1." The column
 "sympatry" indicates whether the species pair of interest is
 sympatric (1) or allopatric (0), and the column "age" indicates
 age of the most recent common ancestor shared by the species pair of
 interest. Columns labeled "dietPC1", "dietPC2",
 "dietPC3", "shapePC1", "shapePC2",
 "shapePC3", and "size" are the Euclidean distances in
 each of these traits for all pairwise comparisons of species.
 <strong>chan_ranges.csv</strong>
 Geographic range data for all icefish (Channichthyidae) species
 analyzed in this study. Species are coded as present (1) or absent (0)
 from each of four geographic regions: (1) the Antarctic Peninsula and
 nearby islands, including the South Shetland and South Orkney Islands; (2)
 South Georgia, Bouvet, and the South Sandwich Islands; (3) Kerguelen
 Island; and (4) the High Latitude Antarctic, defined as the region of
 marine habitats found at latitudes higher than 66 degrees South.
 <strong>chan_sympatry_matrix.csv</strong>
 Matrix classifying each pairwise comparison of icefish
 (Channichthyidae) species as sympatric (1) or allopatric (0). A given pair
 of species was considered sympatric if they were both present (1) in at
 least one of the areas listed in the geographic range data file
 ("chan_ranges.csv"). Otherwise, the pair was considered
 allopatric. 
 <strong>ice-trem_datafile</strong>
 Compilation of all trait data for all icefish and notoperch
 species examined in this study. This file includes data on maximum body
 size ("MaxSize", represented by Total Length, cm), mean depth
 distribution ("MeanDepth", given in meters), mean percentage
 buoyancy ("Buoyancy"), the first three PC axes of body shape
 variation ("BodyShapePC1", "BodyShapePC2", and
 "BodyShapePC3"), and the first three PC axes of diet variation
 ("DietPC1", "DietPC2", and "DietPC3"). Data
 on maximum body size were obtained from Eastman (2019) and references
 therein. Mean depths of occurrence were calculated from trawl records for
 adult specimens supplied by U.S. Antarctic Marine Living Resources Program
 Antarctic finfish surveys conducted between 1998 and 2012. Values
 representing mean percentage buoyancy were obtained from Near et al.
 (2012). PC axes 1-3 of body shape variation were obtained from a Principal
 Components Analysis of Procrustes body shape coordinates. PC axes 1-3 of
 diet variation were obtained from a Principal Components Analysis of the
 weighted mean frequency of prey occurrence data.
 <strong>noto_sliders.txt</strong>
 Matrix indicating the positions of the 4 sliding semi-landmarks
 placed on images of icefish and notoperch specimens. The column label
 "slide" indicates the number of the sliding semi-landmarks;
 "before" indicates the number of the fixed landmark placed
 immediately before the sliding landmark; and "after" indicates
 the number of the fixed landmark placed immediately after the sliding
 landmark.
 <strong>notothenioid_timetree.tre</strong>
 Time-calibrated phylogeny for notothenioids inferred using BEAST
 v2.4.7. This tree was inferred based on the DNA alignment from Near et al.
 (2018) that includes 104,709 loci captured from 80 species of
 notothenioids, including our 14 focal crocodile icefish species and our 16
 focal notoperch species.
 <strong>trem_classifiers.csv</strong>
 A 125 x 2 matrix containing information on species identity for
 each notoperch specimen included in the landmark dataset. This file is
 used as input in the procD-pgls.R script.
 <strong>trem_diets.csv</strong>
 Diet data for all notoperch (Trematominae) species analyzed in
 this study. For each species listed in this file, diet is represented by
 mean frequencies of occurrence of 39 different prey categories identified
 from 34 studies that performed stomach content analyses across both
 icefishes and notoperches. For each prey item, we calculated the mean prey
 frequency of occurrence weighted by the number of individual observations
 in each study for each prey item. Included in this file is the total
 number of specimens examined across all studies for each focal
 species.
 <strong>trem_PairwiseTraits.csv</strong>
 Data matrix including data on sympatry, time since common
 ancestry, and Euclidean distances in phenotypic and ecological traits for
 all possible pairwise comparisons of notoperch species. This is the input
 data file used for fitting phylogenetic generalized linear mixed models to
 test the relationships among range overlap, clade age, and
 ecomorphological divergence. The column label "lineage 1" refers
 to the "focal" species, and "lineage 2" refers to the
 species being compared to "lineage 1." The column
 "sympatry" indicates whether the species pair of interest is
 sympatric (1) or allopatric (0), and the column "age" indicates
 age of the most recent common ancestor shared by the species pair of
 interest. Columns labeled "buo", "depth",
 "dietPC1", "dietPC2", "dietPC3",
 "shapePC1", "shapePC2", "shapePC3", and
 "size" are the Euclidean distances in each of these traits for
 all pairwise comparisons of species.
 <strong>trem_ranges.csv</strong>
 Geographic range data for all notoperches (Trematominae) species
 analyzed in this study. Species are coded as present (1) or absent (0)
 from each of four geographic regions: (1) the Antarctic Peninsula and
 nearby islands, including the South Shetland and South Orkney Islands; (2)
 South Georgia, Bouvet, and the South Sandwich Islands; (3) Kerguelen
 Island; and (4) the High Latitude Antarctic, defined as the region of
 marine habitats found at latitudes higher than 66 degrees South.
 <strong>trem_sympatry_matrix.csv</strong>
 Matrix classifying each pairwise comparison of notoperch
 (Trematominae) species as sympatric (1) or allopatric (0). A given pair of
 species was considered sympatric if they were both present (1) in at least
 one of the areas listed in the geographic range data file
 ("trem_ranges.csv"). Otherwise, the pair was considered
 allopatric.