How ecological opportunity drives asymmetric phenotypic diversity in the gartersnakes, watersnakes, and allies (Natricidae:Thamnophiini)
Data files
Mar 21, 2026 version files 2.91 MB
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All_Thamno_Traits.csv
5.38 KB
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All_Thamnophiini_Ana_Curves_UCE_CatNum.tps
2.72 MB
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Braincase_PACA.nex
3.71 KB
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Diet.nex
2.06 KB
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Geography.nex
2.06 KB
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Habitat.nex
2.06 KB
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Landmarks_Bilat_Curves.csv
132.63 KB
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Mandible_PACA.nex
3.71 KB
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Maxilla_PACA.nex
3.71 KB
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Palatopterygoid_PACA.nex
3.72 KB
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README.md
7.88 KB
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Skull_PACA.nex
3.72 KB
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Snout_PACA.nex
3.69 KB
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Specimens_Used.csv
3.99 KB
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Suspensorium_PACA.nex
3.72 KB
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Thamno_Morphology_Tree.tre
2.68 KB
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Thamnophiini_UCE_51_Taxa.nex
4.31 KB
Abstract
Adaptive radiation is a common explanation for asymmetric diversity within taxonomic groups. Adaptive radiation is often initiated by ecological opportunity which promotes rapid evolution as species fill unoccupied niche space. Ecological opportunity via colonization can occur on continents where lineages pass through a geographical/environmental barrier, resulting in accelerated rates of phenotypic evolution. North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are a clade of colubroid snakes that exhibit high levels of ecological variance and a wide variety of diet preferences inhabiting many disparate biomes. Additionally, Thamnophiini represents an asymmetric radiation where 57% of species diversity is represented by the gartersnakes (Thamnophis). Furthermore, the group is geographically unevenly distributed, apart from Storeria storerioides, Thamnophis is the only genus that naturally occurs west of the Western Continental Divide in North America. As a result, ecological specializations occur independently throughout the clade with convergence in morphology and ecology shared between western and eastern groups. However, it is unclear if this ecological convergence extends to skeletal morphological traits, which are key for understanding ecological adaptation. Morphology of the snake skull has been shown to be influenced by natural history traits such as habitat and diet. Using high-dimensional shape data collected from µCT-scans and a well-resolved, genome-scale phylogeny of Thamnophiini inferred from genomic data, we conducted geometric morphometrics to analyze the tempo and mode of trait evolution of the snake skull, a highly adaptive component of the snake skeleton. We conducted Bayesian phylogenetic comparative methods that explicitly incorporate background rate heterogeneity across the tree to assess the impact of natural history traits, such as diet and habitat, and geography on morphological evolution and convergence. Our results support morphological convergence of skull shape across different ecotypes. Importantly, our results provide evidence that morphological rate is influenced by habitat and geography, with the colonizing western taxa exhibiting higher rates of morphological evolution than eastern taxa. This suggests that a major part of Thamnophiini diversification is strongly influenced by ecological opportunity following the westward expansion of Thamnophis lineages.
https://doi.org/10.5061/dryad.ghx3ffc03
Description of the data and file structure
Files and variables
File: All_Thamno_Traits.csv
Description: Dataset of trait data for all Thamnophiini taxa.
Variables
- Name_in_Tree: Scientific binomial included in the Thamnophiini phylogeny.
- Lifestyle: Habitat categorization for each taxon.
- Diet: Diet categorization for each taxon.
- Clade: Clade categorization for each taxon.
- Side: Geography categorization for each taxon.
- Genus: Genus for each taxon.
File: Landmarks_Bilat_Curves.csv
Description: Datset of landmarks to be read into downstream geometric morphometrics scripts.
Variables
- num: Number across all total landmarks.
- lm: Number split across anatomical landmarks and curve semilandmarks.
- Bone: Bone on which the landmark is placed.
- type: If it is either anatomical landmark or cuver semilandmark.
- Name: Name of the landmark as defined from json files exported from 3D Slicer.
- Description: Abbreviation of position of the landmark.
- Position: Whether landmark is lateral, medial, or on the right bone.
File: Specimens_Used.csv
Description: List of specimens CT-scanned for this study.
Variables
- species: Taxon scientific binomial.
- catnum: Museum catalog number of specimen.
- sex: Sex of the specimen.
File: All_Thamnophiini_Ana_Curves_UCE_CatNum.tps
Description: Concatenated landmarks across all bones for all specimens.
File: Thamno_Morphology_Tree.tre
Description: Time-calibrated phylogeny of Thamnophiini used for all downstream comparative analyses in this study.
File: Braincase_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for braincase shape to be used for BayesTraits and MuSSCRat analyses.
File: Diet.nex
Description: Nexus file of diet categorizations to be used for MuSSCRat analyses.
File: Geography.nex
Description: Nexus file of geography categorizations to be used for MuSSCRat analyses.
File: Habitat.nex
Description: Nexus file of habitat categorizations to be used for MuSSCRat analyses.
File: Maxilla_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for maxilla shape to be used for BayesTraits and MuSSCRat analyses.
File: Palatopterygoid_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for palatopterygoid arch shape to be used for BayesTraits and MuSSCRat analyses.
File: Skull_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for skull shape to be used for BayesTraits and MuSSCRat analyses.
File: Snout_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for snout shape to be used for BayesTraits and MuSSCRat analyses.
File: Thamnophiini_UCE_51_Taxa.nex
Description: Nexus file of time-calibrated Thamnophiini phylogeny to be used for BayesTraits and MuSSCRat analyses.
File: Mandible_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for mandible shape to be used for BayesTraits and MuSSCRat analyses.
File: Suspensorium_PACA.nex
Description: Nexus file of the first four phylogentically aligned components for suspensorium shape to be used for BayesTraits and MuSSCRat analyses.
Code/software (Zenodo)
Geometric Morphometrics Scripts
- Sliding_Landmarks.R: R script to prepare landmark data for downstream geometric morphometric analyses.
- PCA_Script.R: R script to conduct principal components analyses on shape data.
- Convergence_Analyses.R: R script to conduct convergent evolution analyses on shape data.
Supplementary Functions
- read.markups.json.R: Supplementary functions to read into Sliding_Landmarks.R to read JSON files exported from 3D Slicer. Taken from Rolfe et al. (2021).
- MatchedLocalSuperimpositions.R: Supplementary functions to read into PCA_Script.R to perform local Procrustes superimposition. Taken from Rhoa et al. (2021).
MuSSCRat Scripts
- Geography_Braincase_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of braincase shape.
- Geography_Mandible_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of mandible shape.
- Geography_Maxilla_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of maxilla shape.
- Geography_Palatopterygoid_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of palatopterygoid arch shape.
- Geography_Skull_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of skull shape.
- Geography_Snout_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of snout shape.
- Geography_Suspensorium_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of geography on evolution of suspensorium shape.
- Habitat_Braincase_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of braincase shape.
- Habitat_Mandible_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of mandible shape.
- Habitat_Maxilla_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of maxilla shape.
- Habitat_Palatopterygoid_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of palatopterygoid arch shape.
- Habitat_Skull_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of skull shape.
- Habitat_Snout_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of snout shape.
- Habitat_Suspensorium_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of habitat on evolution of suspensorium shape.
- Diet_Braincase_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of braincase shape.
- Diet_Mandible_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of mandible shape.
- Diet_Maxilla_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of maxilla shape.
- Diet_Palatopterygoid_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of palatopterygoid shape.
- Diet_Skull_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of skull shape.
- Diet_Snout_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of snout shape.
- Diet_Suspensorium_relaxed_state_dependent_hypo_test.Rev: MuSSCRat script to test state-dependence of diet on evolution of suspensorium shape.
Access information
Other publicly accessible locations of the data:
Data was derived from the following sources:
