DOI: 10.5061/dryad.nvx0k6f4k
title: Ecological opportunity spurred adaptive radiation of Central Mexican Silversides: Evidence from functional and morphometric traits

description: Dispersal to a geographic area or colonizing a new habitat can lead to
 ecological opportunity, which predicts that in absent or reduced
 competition, lineages can diversify to exploit available resources,
 ultimately leading to adaptive radiation. We investigated the role of
 colonizing new environments with novel community contexts in Central
 Mexican Silversides, a putative adaptive radiation. We explored
 macroevolutionary dynamics of speciation and phenotypic evolution across
 New World Silversides in different community settings. We analyzed
 geometric morphometric, linear, and functional traits, three classes of
 morphological data rarely evaluated jointly in a single group. We found
 that Central Mexican Silversides, which occupy a region characterized by
 low species richness, and isolated freshwater habitats, experienced
 elevated rates of phenotypic evolution and speciation. In the absence of
 ecological opportunity, other lineages of Menidiinae experienced constant
 evolutionary rates through time and patterns consistent with non-adaptive
 diversification dynamics. We found that traits related to piscivory and
 burst-swimming have the highest rates of evolution in Central Mexican
 Silversides. We also show that functional traits and linear morphometrics
 better capture among lineage variation than body shape data. Our study
 shows that unique paleogeographic and ecological settings can promote
 adaptive radiation in clades that otherwise experience steady-state
 diversification dynamics.
description: # Ecological opportunity spurred adaptive radiation of Central Mexican
 Silversides: Evidence from functional and morphometric traits Dataset DOI:
 [10.5061/dryad.nvx0k6f4k](10.5061/dryad.nvx0k6f4k) ## Description of the
 data and file structure This dataset contains phylogenetic trees, trait
 data, BAMM analyses, specimen catalog numbers, and supporting scripts used
 in the study of adaptive radiation in Central Mexican Silversides. Data
 files are organized to correspond with the analyses presented in the
 manuscript, which investigates the role of ecological opportunity in
 shaping functional and morphological diversification of Central Mexican
 Silversides. ### Files and variables #### File:
 alternative_calibration_treefile.tree **Description:** Bloom et al. 2013
 phylogeny with alternative time calibration used in our comparative
 analyses. #### File: BAMM_speciation_outputs.RData **Description:** output
 files used in the speciation rate analyses. #### File:
 Bloom_etal_2013_trimmed_treefile.tre **Description:** Bloom et al. 2013
 phylogeny with original time calibration trimmed for our comparative
 analyses. #### File: functional_measurements_dataset.RData
 **Description:** functional and morphometric data used in the comparative
 trait analyses. #### File: R_Script.R **Description:** R script containing
 the pipeline for data processing, analysis, and visualization. #### File:
 BAMMoutputs.RData **Description:** output files used in the trait rate
 analyses. #### File: TableS1_catalog_numbers.txt **Description:** list of
 all specimens used in the study, including catalog numbers. #####
 Institutions acronyms: FMNH: Field Museum of Natural History, Chicago,
 Illinois, USA. JFBM: James Ford Bell Museum of Natural History, University
 of Minnesota, Minneapolis, Minnesota, USA. MNRJ: Museu Nacional,
 Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro,
 Brazil. UMMZ: University of Michigan Museum of Zoology, Ann Arbor,
 Michigan, USA. USNM: Smithsonian Institution, National Museum of Natural
 History, Washington, District of Columbia, USA. DDB: Western Michigan
 University, Kalamazoo, Michigan, USA. #### File:
 TableS2_measurements_rates.csv **Description:** This file contains
 phylogenetically size-corrected and log-transformed trait measurements,
 along with estimated evolutionary rates for Central Mexican Silversides. 
 Note: Units provided below refer to the original raw measurements prior to
 size-correction and log-transformation. Log-transformed values are
 dimensionless. ##### Variables * taxa: species name **Swimming morphology
 measurements:** * swimming_measurement_1: sl – Standard length (tip of
 snout to base of caudal fin) (mm) * swimming_measurement_2: body_depth –
 Maximum body depth (mm) * swimming_measurement_3: body_width – Maximum
 body width (mm) * swimming_measurement_4: pectoral_ma – Pectoral fin
 moment arm (distance from base of pectoral fin to center of mass) (mm) *
 swimming_measurement_5: dorsal_ma – Dorsal fin moment arm (distance from
 base of first dorsal fin to center of mass) (mm) * swimming_measurement_6:
 pelvic_ma – Pelvic fin moment arm (distance from base of pelvic fin to
 center of mass) (mm) * swimming_measurement_7: anal_ma – Anal fin moment
 arm (distance from base of anal fin to center of mass) (mm) *
 swimming_measurement_8: caudal_ma – Caudal fin moment arm (distance from
 base of caudal fin to center of mass) (mm) * swimming_measurement_9:
 first_dorsal_length – Length of first dorsal fin base (mm) *
 swimming_measurement_10: first_dorsal_height – Height of first dorsal fin
 (mm) * swimming_measurement_11: second_dorsal_length – Length of second
 dorsal fin base (mm) * swimming_measurement_12: second_dorsal_height –
 Height of second dorsal fin (mm) * swimming_measurement_13:
 pectoral_length – Length of pectoral fin (mm) * swimming_measurement_14:
 pelvic_length – Length of pelvic fin (mm) * swimming_measurement_15:
 anal_height – Height of anal fin (mm) * swimming_measurement_16:
 caudal_height – Height of caudal fin (mm) * swimming_measurement_17:
 peduncle_depth – Depth of caudal peduncle (mm) * swimming_measurement_18:
 peduncle_length – Length of caudal peduncle (mm) *
 swimming_measurement_19: first_dorsal_area – Surface area of first dorsal
 fin (mm²) * swimming_measurement_20: second_dorsal_area – Surface area of
 second dorsal fin (mm²) * swimming_measurement_21: pectoral_area – Surface
 area of pectoral fin (mm²) * swimming_measurement_22: pelvic_area –
 Surface area of pelvic fin (mm²) * swimming_measurement_23: anal_area –
 Surface area of anal fin (mm²) * swimming_measurement_24: caudal_area –
 Surface area of caudal fin (mm²) **Feeding morphology measurements:** *
 feeding_measurement_1: eye_width – Maximum eye width (mm) *
 feeding_measurement_2: mouth_width – Maximum mouth width (mm) *
 feeding_measurement_3: lower_jaw_length – Length of lower jaw (mm) *
 feeding_measurement_4: head_depth – Maximum head depth (mm) *
 feeding_measurement_5: head_length – Head length (snout tip to posterior
 operculum) (mm) * feeding_measurement_6: snout_length – Snout length (mm)
 * feeding_measurement_7: min_gill_rakers – Minimum gill raker count
 (count, unitless) * feeding_measurement_8: max_gill_rakers – Maximum gill
 raker count (count, unitless) * feeding_measurement_ref:
 gill_raker_reference – Reference specimen for gill raker counts **Trait
 evolutionary rates (lambda):** * trait_tip_rate_1: swimming.PC1 – Tip
 evolutionary rate for swimming traits PC1 * trait_tip_rate_2: swimming.PC2
 – Tip evolutionary rate for swimming traits PC2 * trait_tip_rate_3:
 feeding.PC1 – Tip evolutionary rate for feeding traits PC1 *
 trait_tip_rate_4: feeding.PC2 – Tip evolutionary rate for feeding traits
 PC2 * trait_tip_rate_5: body_shape.PC1 – Tip evolutionary rate for body
 shape PC1 * trait_tip_rate_6: body_shape.PC2 – Tip evolutionary rate for
 body shape PC2 **Speciation rates:** * speciation_tip_rate_1: lambda.avg –
 Mean speciation rate estimated per tip lineage (lambda) ## Code/software
 The analyses in this dataset require R (https://www.r-project.org/), a
 free and open-source statistical software environment.