A fossil-informed pattern of body size increase and local extinction in Basiceros dirt ants (Hymenoptera: Formicidae)
Data files
Feb 14, 2025 version files 492.99 KB
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Basiceros_constrained_relaxed
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Basiceros_constrained_relaxed_exponentialIGR
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Basiceros_constrained_relaxed_exponentialIGR.nex
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Basiceros_constrained_strict
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Basiceros_enana_complete_database.xlsx
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Basiceros_morphological_matrix_08-05-24.nex
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constrained_mixed_protaog_08-03-24.nex
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constrained_modeled_dated_relaxed_08-08-24.nex
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constrained_modeled_dated_strict_08-08-24.nex
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Molecular_data_only_tree_08-02-24.nex
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README.md
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Feb 14, 2025 version files 493 KB
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Basiceros_constrained_relaxed
719 B
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Basiceros_constrained_relaxed_exponentialIGR
24.10 KB
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Basiceros_constrained_relaxed_exponentialIGR.nex
84.40 KB
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Basiceros_constrained_strict
722 B
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Basiceros_enana_complete_database.xlsx
37.37 KB
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Basiceros_morphological_matrix_08-05-24.nex
1.59 KB
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constrained_mixed_protaog_08-03-24.nex
80.72 KB
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constrained_modeled_dated_relaxed_08-08-24.nex
84.40 KB
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constrained_modeled_dated_strict_08-08-24.nex
84.37 KB
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Molecular_data_only_tree_08-02-24.nex
77.37 KB
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README.md
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Feb 26, 2025 version files 479.11 KB
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Basiceros_bodysize_evo_rate.csv
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Basiceros_constrained_relaxed_exponentialIGR-tree.nex
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Basiceros_constrained_relaxed_exponentialIGR.nex
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Basiceros_constrained_relaxed-tree.nex
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Basiceros_constrained_strict-tree.nex
722 B
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Basiceros_geographic_data.csv
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Basiceros_morphological_matrix_08-05-24.nex
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Basiceros_qualitative_class.csv
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Character_matrix.csv
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constrained_mixed_protaog_08-03-24.nex
80.72 KB
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constrained_modeled_dated_relaxed_08-08-24.nex
84.40 KB
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constrained_modeled_dated_strict_08-08-24.nex
84.37 KB
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Molecular_data_only_tree_08-02-24.nex
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Morphological_characters.csv
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Phylogeny_divergence_dating.csv
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README.md
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Rhopalothrix_sp_gr_meas_small.csv
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RHOPALOTHRIX_SP_GR_measurements.csv
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Abstract
Basiceros dirt ants are morphologically distinct and widely distributed members of Neotropical communities. These ants possess features that aid in leaf litter camouflage and are larger than other closely related lineages with similar cryptic adaptations. Here, we report the first fossil of this genus-group, Basiceros enana sp. nov. from Miocene-aged Dominican amber, which reveals a pattern of body size evolution and disjunct biogeography. The fossil evidences the local extinction of Basiceros in the Caribbean, even as living Basiceros are known from Honduras to Southern Brazil. Using combined morphological and molecular datasets of all closely related lineages, we recover the evolutionary trajectory for body size within the group, demonstrating that body size was initially small in these ants and followed by a rapid expansion of body size in the common ancestor of all living species. Results reflect the capacity for early morphological evolution to influence perceived patterns of body size increase through a mosaic of ancestral legacy and continuous enlargement.
https://doi.org/10.5061/dryad.6q573n66p
Description of the data and file structure
Complete morphometric database available in Dryad (10.5061/dryad.6q573n66p)
All supplemental figures and 3D semgnetations available in Zenodo (https://doi.org/10.5281/zenodo.14748662)
R script available in Zenodo (https://doi.org/10.5281/zenodo.14748666)
Files and variables on Dryad
Phylogeny_divergence_dating.csv - Summary of divergence dating results by parameter.
Basiceros_bodysize_evo_rate.csv - Two separate tables outlining ancestral state reconstruction results used to reconstruct the body size shift through time. Table one demonstrates values representing PC1 (body size) change for each branch. Blank cells mean that the species does not have that amount of branches. Table 2 shows the calculation of PC1 change. Node (PC1 value at node), tip (PC1 value at tip), branch (branch length in mya), rate (PC1/mya).
Basiceros_qualitative_class.csv - Qualitative classification of Rhopalothrix genus group representatives.
Basiceros_geographic_data.csv - Dirstibution data of Basiceros species used for the map in figure 5. (Values represent latitude and longitude).
RHOPALOTHRIX_SP_GR_measurements.csv - Complete list of the Rhopalothrix genus group linear morphometric measurements. All measurements in mm. All morphological terminology and measurements summarized in Supplementary Table 1. Used in PCA.
Rhopalothrix_sp_gr_meas_small.csv - Rhopalothrix genus group linear morphometric measurements binned to smallest individuals. All measurements in mm. All morphological terminology and measurements summarized in Supplementary Table 1. Used in PCA.
Morphological_characters.csv - Overview of the morphological characters used for coding the morphological character matrix. Used in phylogenetic reconstruction.
Character_matrix.csv - Character matrix of Rhopalothrix genus group used for phylogenetic placement of Basiceros enana.
Tree files
File: Basiceros_constrained_relaxed_exponentialIGR.nex
Description: Tree file of majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a relaxed clock model using an exponential IGR informative prior implementing the fossilized birth–death branch length (FBD) for Rhopalothrix genus-group species included in this study.
File: Basiceros_constrained_relaxed.nex
Description: Tree file of majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a relaxed clock model using a flat IGR informative prior implementing the fossilized birth–death branch length (FBD) for Rhopalothrix genus-group species included in this study. Used in ancestral state reconstruction.
File: Basiceros_constrained_strict.nex
Description: Tree file of majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a strict clock model using a flat IGR informative prior implementing the fossilized birth–death branch length (FBD) for Rhopalothrix genus-group species included in this study. Used in ancestral state reconstruction.
Nexus Files
File: Basiceros_morphological_matrix_08-05-24.nex
Description: Nexus file of the phylogenetic reconstruction based on only morphological characters for Mr. Bayes software.
File: Molecular_data_only_tree_08-02-24.nex
Description: Nexus file of the phylogenetic reconstruction based on only molecular characters for Mr. Bayes software.
File: constrained_mixed_protaog_08-03-24.nex
Description: Nexus file of the phylogenetic reconstruction based on only morphological and molecular characters for Mr. Bayes software.
File: constrained_modeled_dated_relaxed_08-08-24.nex
Description: Nexus file of the phylogenetic reconstruction for Mr. Bayes software. Settings for relaxed clock running an IGR model with a uniform variance. Used in ancestral state reconstruction.
File: constrained_modeled_dated_strict_08-08-24.nex
Description: Nexus file of the phylogenetic reconstruction for Mr. Bayes software. Settings for strict clock running an IGR model with a uniform variance.
File: Basiceros_constrained_relaxed_exponentialIGR.nex
Description: Nexus file of the phylogenetic reconstruction for Mr. Bayes software. Settings for relaxed clock running an IGR model with an exponential variance.
Files and variables on Zenodo (Supplemental Information)
Supplementary Table S1. Summary of morphological terminology and measurements.
| HL1 | Head length. In full-face view, the maximum distance from the posterior margin of the head to the anterior margin of the clypeus |
|---|---|
| HL2 | Head length 2. All castes. In full face view, the maximum length of head from anterolateral clypeal margin to vertexal corner as a virtual line. |
| HW1 | Head width. In full-face view, the maximum width of the head, excluding the eyes |
| HW2 | Head width 2. Male only. In full face view, the maximum width of head including eyes in full-face view. |
| MdL | Mandible length. in full-face view, the maximum diagonal-line distance from the base of the external mandibular insertion to the apical tooth. |
| SL | Scape length. In frontal view, the maximum length of the scape excluding the basal condyle and neck |
| SL2 | Scape length 2. All castes. In dorsal view, distance from anterior angle of basal scape lobe to scape apex. In the case of males, length in medial view from scape base middle to scape apex. |
| PDL | Pedicel length. All castes. Maximum length of pedicel from virtual line drawn from dorsal and ventral basal curves to pedicel apex. |
| ASIII | Antennomere segment III length. in most appropriate view, the maximum length of the third antennal segment. |
| AFL | Apical flagellomere length. All castes. In medial view, the maximum length of distal segment of antenna, in medial view. |
| FuL | Funiculus length. Female castes. Length of antennal funiculus, including the pedicel, with flagellomeres in same plane of focus. |
| EL | Eye length. In lateral view, eye length is measured along its maximum length |
| EW | Eye width. All castes. Maximum width of eye at an axis orthogonal to Eye Length with head oriented as above. |
| WL | Weber’s length. In lateral view, the distance between the anterior margin of the pronotum, excluding the collar, to the posteroventral margin of the metapleuron |
| MFL | Metafemur length. All castes. Maximum distance of the metafemur in dorsal view, measured from the distal margin of the trochanter to the metafemur apex. |
| MTL | Metatibia length. All castes. Maximum length of the metatibia in dorsal view, just before the basitarsal condyle to the metatibial apex. |
| PH | Petiolar height. In lateral view, the perpendicular distance from the posteroventral lobe of the petiolar tergite to its maximum dorsal margin |
| PL | Petiolar length. In lateral view, the distance between the anterior margin of the petiole, including its anterolateral projection, to its posterior margin, excluding the posteroventral folded ridge that embraces the helcium |
| PW | Petiolar width. In dorsal view, the maximum width of the petiole |
| PPL | Post Petiolar length. In lateral view, the distance between the anterior margin of the petiole, including its anterolateral projection, to its posterior margin, excluding the posteroventral folded ridge that embraces the helcium |
| PPW | Post Petiolar width. In dorsal view, the maximum width of the petiole |
| GL | Gaster length. In profile, the length of the gaster from the anterior most point of first gastral segment (fourth abdominal segment) to the posterior most point of the last segment. |
| GW | Gaster width. All castes. Maximum transversal distance of abdominal segment IV in dorsal view. |
| TL | Total Length. All castes. Axial length of body, including closed mandibles; summed MdL + HL + ML + PTL + PPL + GL. |
File: Supplementary Figure S1.
Description: Comparative morphospace of smallest exemplar of Rhopalothrix genus-group. Principal component analysis of 19 morphological traits from 17 specimens representing 17 species, including all known species of Basiceros. Basiceros specimens are depicted in blue (manni species group), black (disciger species group), and orange (Basiceros enana sp. n. from Miocene age Dominican amber). Species from other Rhopalotrhix genus-group taxa (Eurhopalothrix, Talaridris, Octostruma, Protalaridris, and Rhopalothrix) are depicted in green.
File: Supplementary Table S2.
Description: List of taxa (with extractions codes), source, and DNA sequences included in this study (with respective accession numbers). Accession numbers are included for eight of the nine genes, except 12S (see Supplementary File S2).
File: Supplemental Figure S2.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological characters for Rhopalothrix genus-group species included in this study. Morphological data are derived from Probst (2015). Node values denote posterior probability support values (0-100).
File: Supplemental Figure S3.
Description: Majority-consensus tree recovered under Bayesian Inference of molecular characters for Rhopalothrix genus-group species included in this study. Molecular data are derived from Probst et al. (2019) and GenBank sequences comprising nine loci and 4.3 kb. Node values denote posterior probability support values (0-100).
File: Supplemental Figure S4.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters for Rhopalothrix genus-group species included in this study. The *Basiceros *clade was constrained based on high support values from the molecular only and morphology only tree searches. Node values denote posterior probability support values.
File: Supplemental Figure S5.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a relaxed clock model using a flat IGR informative prior implementing the fossilized birth-death branch length (FBD) for Rhopalothrix* genus-group species included in this study. The Basiceros clade was constrained to accommodate the fossil *Basiceros species. Node values denote posterior probability support values.
File: Supplemental Figure S6.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a strict clock model using a flat IGR informative prior implementing the fossilized birth-death branch length (FBD) for Rhopalothrix genus-group species included in this study. The* Basiceros *clade was constrained to accommodate the fossil species. Node values denote posterior probability support values.
File: Supplemental Figure S7.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a relaxed clock model using an exponential IGR informative prior implementing the fossilized birth-death branch length (FBD) for Rhopalothrix* genus-group species included in this study. The Basiceros *clade was constrained to accommodate the fossil species. Node values denote posterior probability support values.
File: Supplemental Figure S8.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a relaxed clock model using a flat IGR informative prior implementing the fossilized birth-death branch length (FBD) for Rhopalothrix* genus-group species included in this study. The Basiceros *clade was constrained to accommodate the fossil species. Node values denote node age. Error bars colored in blue.
File: Supplemental Figure S9.
Description: Majority-consensus tree recovered under Bayesian Inference of morphological and molecular characters dated with a strict clock model using a flat IGR informative prior implementing the fossilized birth–death branch length (FBD) for Rhopalothrix* genus-group species included in this study. The Basiceros *clade was constrained to accommodate the fossil species. Node values denote node age. Error bars colored in blue.
File: Supplemental Figure S10.
Description: Photomicrographs of Basiceros enana sp. nov. (Holotype, MNHNSD FOS 18.02). A. Head in frontal view. B. Body in dorsolateral view. C. Body in lateral view. Scale bars: A 0.5 mm; B, C 1 mm
File: Supplemental Figure S11.;
Description: Illustration of Basiceros enana sp. nov. (Holotype, MNHNSD FOS 18.02). Dotted grid represents lost cuticle from expanded bubble during fossilization. Scale bar 0.2 mm.
File: Video_1_Basiceros_enana_in_amber_vid.mp4
Description: Artistic reconstruction of *Basiceros enana *sp. nov. within the amber.
File: Bubble.stl
Description: Volume rendering of Basiceros enana sp. nov. bubble.
File: B_enana_full_body_nobubble.stl
Description: Volume rendering of Basiceros enana sp. nov. excluding bubble.
File: B_enana_profile.png
Description: Volume render in profile view of Basiceros enana sp. nov.
Code/software (Zenodo - Software)
Our study comprises 3 analyses: comparative morphospace, combined morphological-molecular phylogenetic reconstruction, and ancestral state reconstruction and body size evolutionary rates.
The comparative morphospace and ancestral state reconstruction and body size evolutionary rates were performed in R v.4.4.1 (R Core Team 2024) using the packages “corrplot” (v0.92; Wei & Simko 2017), “FactoMineR” (v2.11; Lê et al 2008), ggplot2 (v3.5.1; Wickham 2016), and “phytools” v.2.3-0 (Revell 2012). Combined morphological-molecular phylogenetic reconstruction was performed in Mr. Bayes 3.2.7a (Huelsenbeck 2001).
Change Log
- Feb 14, 2025: first version
- Feb 14, 2025: second version changed word in title
- Feb 26, 2025: Converted Excel file to separate CSVs
Our dataset is composed of data for 3 analyses: comparative morphospace, combined morphological-molecular phylogenetic reconstruction, and ancestral state reconstruction and body size evolutionary rates.
For the comparative morphospace, ant trait measurements were taken of all species within the genus Basiceros, as well as representatives from each genus within the Rhopalothrix genus group. Morphometric sampling included linear measurements of 19 morphological traits: 11 cephalic, three mesosomal, and five metasomal. We used a subset of measurements taken above for morphospace analysis to exclude measurements that cannot be obtained through photographs: HL1, HL2, HW1, MDL, SL1, SL2, PDL, AFL, FUL, EL, EW, ML, MFL, MTL, PTH, PTL, PTW, PPL, and PPW. We employed principal component analyses (PCA) on linear measurement data to reduce the dimensionality of the morphological dataset. All measurements can be found in the file Basiceros_enana_complete_database.xlsx.
For the combined morphological-molecular phylogenetic reconstruction, we compiled molecular data from Probst et al. 2019 as well as those available from GenBank, along with morphological characters from 17 species in the Rhopalothrix genus group. We then performed a series of phylogenetic reconstructions based on molecular and morphological data to assess the placement of Basiceros enana sp. nov. among extant congeners. All analyses were run on Mr. Bayes. The morphological matrix can be found in the file Basiceros_enana_complete_database.xlsx.
Finally, for the ancestral state reconstruction and body size evolutionary rates, we performed an ancestral state reconstruction of PCA scores. We extracted principal component 1 (PC1) scores from a PCA of 17 linear measurements taken from the smallest specimen for each species included as a terminal in our combined phylogenetic analysis. We reconstructed ancestral PC1 scores using a single rate method with fastAnc in “phytools” v.2.3-0 (Revell 2012).