Ecological opportunity spurred adaptive radiation of Central Mexican Silversides: Evidence from functional and morphometric traits
Data files
Sep 09, 2025 version files 3.66 MB
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alternative_calibration_treefile.tree
63.46 KB
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BAMM_speciation_outputs.RData
39.40 KB
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BAMMoutputs.RData
3.46 MB
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Bloom_etal_2013_trimmed_treefile.tre
2 KB
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functional_measurements_dataset.RData
23.40 KB
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R_Script.R
48.10 KB
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README.md
6.25 KB
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TableS1_catalog_numbers.txt
2.40 KB
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TableS2_measurements_rates.csv
19 KB
Abstract
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.
Dataset DOI: 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.
