DOI: 10.5061/dryad.mw6m9062f
title: Data from: Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes

description: Phenotypic macroevolutionary studies provide insight into how ecological
 processes shape biodiversity. However, the complexity of phenotype-ecology
 relationships underscores the importance of also validating
 phenotype-based ecological inference with direct evidence of resource use.
 Unfortunately, macroevolutionary scale ecological studies are often
 hindered by the challenges of acquiring taxonomically and spatially
 representative ecological data for large and widely distributed clades.
 The South American cichlid fish tribe Geophagini represents a
 continentally distributed radiation whose early locomotor morphological
 divergence suggests habitat as one ecological correlate of
 diversification, but an association between locomotor traits and habitat
 preference has not been corroborated. Field notes accumulated over decades
 of collecting across South America provide first-hand environmental
 records that can be mined for habitat data in support of macroevolutionary
 ecological research. In this study, we applied a newly developed method to
 transform descriptive field note information into quantitative habitat
 data, and used it to assess habitat preference and its relationship to
 locomotor morphology in Geophagini. Field note-derived data shed light on
 geophagine habitat use patterns and reinforced habitat as an ecological
 correlate of locomotor morphological diversity. Our work emphasizes the
 rich data potential of museum collections, including often overlooked
 material such as field notes, for evolutionary and ecological research.
description: Previously published Maximum Clade Credibility (MCC) and sample
 of 1000 Bayesian posterior distirbution phylogenies (from López-Fernández
 et al. 2013). The associated code prunes these phylgenies to include only
 focal taxa for this study. Locomotor morphological data
 was collected from preserved specimens, using digital calipers for linear
 measurements and on photos for area and moment arms. The associated code
 log-transforms, corrects for body size, and reduces the dataset by
 removing traits with Variance Inflation Factors (VIF) &gt;
 10. Habitat data was collected from field notes, in the
 form of a presence matrix. The associated code applies our transformed to
 convert the presence matrix into a quantiative compositional
 dataset. 
description: R Microsoft Excel
description: # Overview of Publication and Associated Data/Scripts Citation to
 Associated Publication: Astudillo-Clavijo V., H.R. Varella, T. Mankis, H.
 López-Fernández. 2024. Historical field records reveal habitat as an
 ecological correlate of locomotor phenotypic diversity in the radiation of
 Neotropical Geophagini fishes. American Naturalist. Citation to Associated
 Data and Scripts: Astudillo-Clavijo V., H.R. Varella, T. Mankis, H.
 López-Fernández. 2024. Historical field records reveal habitat as an
 ecological correlate of locomotor phenotypic diversity in the radiation of
 Neotropical Geophagini fishes. American Naturalist [Dataset]. Dryad.
 [https://doi.org/10.5061/dryad.mw6m9062f](https://doi.org/10.5061/dryad.mw6m9062f). Authors: Authors: Viviana Astudillo-Clavijo[1,2*], Henrique Varella[3,4], Tobias Mankis[2], Hernán López-Fernández[1,5] \[1] Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, USA \[2] Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada \[3] Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil \[4] Laboratório de Biologia e Genética de Peixes, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, IBB/UNESP, Botucatu, SP, Brazil \[5] Museum of Zoology, University of Michigan, Ann Arbor, 48108, USA \[*] Corresponding Author: [viviana.astudillo@utoronto.ca](mailto:viviana.astudillo@utoronto.ca) Abstract: Phenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish subfamily, Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide first-hand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study we applied a newly developed method to transform descriptive field note information into quantitative habitat data, and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often overlooked material such as field notes, for evolutionary and ecological research. Habitat data collection and analyses were performed by VAC, HRV, and TM. Morphological data collection and analyses were performed by VAC and TM. Repository Description: The Dryad repository associated with the cited publication (see publication and data citations above) contains scripts and data used in the study. ## Software Requirements Data are available as .csv files, which can be opened with software such as Microsoft ExcelData, most text editors, and imported into most coding programs, including R. Data analyses were performed in R version 4.0.2. The following R packages were used in analyses ``` factoextra 1.0.7 FactoMineR 2.4 corrplot 0.92 vegan 2.5-6 fmsb 0.7.2 ape 5.4 phytools 0.7-47 ggplot2 3.3.3 ``` ## Repository Layout and Contents **GeophaginiHabitat_PresAbs_moreSp.csv**: Geophagini habitat dataset. Columns 1-7 provide collection information. Empty cells represent missing information. Columns 8-17 are binary and mark the presence of substrate or structural elements on which the habitat index is applied. Column 18 is categorical and represents the type of flow in which a sample was collected. | Column\_Name | Description | | :------------------------ | :-------------------------------------------------------------- | | Genus | Genus of row taxa | | Species | Species name of row taxa | | Species\_Lot | Lot number for row taxa | | No\_Specimens | Number of specimens in the lot | | CollectionYear | Year lot was collected | | Lat | GPS Latitudinal coordinates of field site | | Long | GPS longitudinal coordinates of field site | | Aquatic\_Veg | Aquatic vegetations | | Flooded\_Terrestrial\_Veg | Flooded non-tree terrestrial vegetation | | Flooded\_Trees | Flooded trees | | Rocks | Rocks | | Snags | Woody debris | | LeafLitter | Leaf Litter | | Sand | Sand | | Mud | Mud | | Clay\_Silt | Clay/Silt | | Gravel | Gravel | | CurrentType | Categorical designation of current type (from none=0 to fast=3) | **Log_Indv_Avgs_from_Morph_Measure_Geophagus**: Log-transformed morphological trait data for Geopahgini species. For most species, multiple individuals have been measured. Original measurement units (prior to log-transformation) are shown in parentheses. Fig. 1 in the manuscript indicates collection of trait data. | Column Name | Description | | :-------------------------------------- | :-------------------------------------------------------------------------------------------- | | Genus | Genus of row taxa | | Species | Species name of row taxa | | Ind\_ID | Species name of row taxa with designation for specific individual measured | | SL | Standard length, measured from upper lip to end of vertebra (mm) | | body\_depth | Ventral to dorsal depth, measured anterior to pelvic fin base (mm) | | body\_width  | Lateral body width, measured at laterally widest point along body (mm) | | pectoral\_fin\_length | Length, from base to tip, of longest pectoral fin ray (mm) | | pelvic\_fin\_length  | Length, from base to tip, of longest pelvic fin ray (mm) | | pectoral\_moment\_arm | Distance from centre of mass to base of pectoral fin (mm) | | pelvic\_moment\_arm | Distance from centre of mass to base of pelvic fin (mm) | | anal\_moment\_arm | Distance from centre of mass to midpoint of anal fin base (mm) | | dorsal\_moment\_arm | Distance from centre of mass to midpoint of dorsal fin base (mm) | | spiny\_dorsal\_fin\_height | Height of most posterior dorsal fin spine (mm) | | soft\_dorsal\_fin\_height | Height of longest dorsal fin ray (mm) | | caudal\_fin\_height | Ventral to dorsal height of caudal fin when fully extended (mm) | | spiny\_anal\_fin\_height | Height of most posterior anal fin spine (mm) | | soft\_anal\_fin\_height | Height of longest anal fin ray (mm) | | pectoral\_fin\_area | Area of pectoral fin when fully extended (mm^2) | | anal\_fin\_area | Area of anal fin when fully extended (mm^2) | | dorsal\_fin\_area  | Area of dorsal fin when fully extended (mm^2) | | caudal\_fin\_area | Area of caudal fin when fully extended (mm^2) | | pectoral\_fin\_aspect\_ratio | Aspect ratio of pectoral fin, calculated as fin length^2/fin area | | caudal\_fin\_aspect\_ratio | Aspect ratio of caudal fin, calculated as fin length^2/fin area | | peduncle\_depth | Ventral to dorsal depth of midpoint of caudal peduncle (mm) | | peduncle\_length  | Lateral length of caudal peduncle, measured from end of dorsal fin base to last vertebra (mm) | | peduncle\_depth\_to\_body\_depth\_ratio | Ratio of peduncle depth to body depth measurements (mm) | | frontal\_area | Area of fish when seen in frontal view | | fineness\_ratio | Measure of streamlining, calculated as ratio of standard length to body width (mm) | | body\_width\_to\_depth\_ratio | Ratio of body width to body depth (mm) | | pelv\_fin\_area | Area of pelvic fin when fully extended (mm^2) | | pelv\_fin\_AR | Aspect ratio of pelvic fin, calculated as fin length^2/fin area | **Cichlidae2015-FullTree.phy**: Newick format Maximum Clade Credibility phylogeny for Geopahgini from López-Fernández et al. 2013. **Cichlidae2015-FullTree1000.phy**: Bayesian posterior samples of Geopahgini phylogenies in Newick format from López-Fernández et al. 2013. ## Scripts **Habitat_analysis_Geophagini_Nov2023.R**: Code for applying habitat index on field note data, performing CA on habitat data, and performing CCA on habitat and morphological data, with and without phylogenetic-correction. ## How to Use Prior to running scripts do the following: (1) Download the repository directory from Dryad to your local computer (2) Unpack the repository directory and all subdirectories on your local computer (3) Open R and install/load required software for the script you are working with (see the "Prepare the workspace" section of the script you are working with for a list of required software) (4) All scripts should be run in R from within the downloaded repository directory. Navigate to the correct working directory in R with the setwd() function.