From Asia to the Americas: a new cross-continental perspective on viper biogeography and habitat dynamics

Pontes-Nogueira, Matheus 1 2 ; Alencar, Laura3; Sawaya, Ricardo1

Published Oct 01, 2025 on Dryad. https://doi.org/10.5061/dryad.8cz8w9h3x

Data files

Oct 01, 2025 version files 1.73 GB

jbi_15153.zip

1.73 GB
README.md

6.11 KB

Abstract

Aim: We investigate the biogeographical history of the family Viperidae focusing on how habitat use influenced the geographical range evolution of the group. We tested key hypotheses on origins and biogeographical processes of major clades within Viperidae, including the colonisation of the New World.

Location: Worldwide.

Taxon: Vipers (Serpentes: Viperidae).

Methods: We used four recently published phylogenies of Viperidae and applied Maximum Likelihood (ML) models with trait-specific parameters (habitats) in BioGeoBEARS to estimate ancestral geographical ranges and habitat use.

Results: Our results support an Asian origin for the Viperidae family, with a likely trans-Pacific dispersal to Central America instead of the Beringian land bridge route. The subfamily Viperinae must have originated in Africa, while the genus Lachesis likely emerged in South + Central America. Habitat reconstructions showed varied impacts of forested and open habitats on diversification and biogeographical processes when comparing the first three phylogenies with the last one.

Main conclusions: We highlight the significant role of habitat use in viper diversification and range evolution. Differently from what previously suggested, our findings indicate a trans-Pacific dispersal route for New World vipers.

Access this dataset on Dryad
Primary article

You can find the distribution data utilized in the Main Text to achieve the results found in the original paper inside jbi_15153.zip, and also the scripts (workflow to generate the results) and outputs (the results themselves). For the phylogenetic trees (required to run the analysis) and the shapefiles (if you want to recreate the figures in the Main Text), please refer to the Main Text in order to check sources and procedures we followed.

Data:

Distribution data (inputs__distrb)

See Main Text for the sources utilized for the construction of the GEOG.txt and CARAC.txt files. All of these files are used by the BioGeoBEARS_script_JBI-24-0395.R script as inputs to generate the results.

GEOG.txt files: distribution files

Files are constructed as following: number_of_species number_of_units (units [separated by tab]), followed by all species in the phylogeny and codification for presence (1) or absence (0) in each unit.
ALENCAR2016_GEOG.txt: distribution file for the species included in the Alencar et al. (2016) phylogeny.
TITLE2024_GEOG.txt: distribution file for the species included in the Title et al. (2024) phylogeny.
ZAHER2019_GEOG.txt: distribution file for the species included in the Zaher et al. (2019) phylogeny.
ZHENG2016_GEOG.txt: distribution file for the species included in the Zheng and Wiens (2016) phylogeny.

CARAC.txt files: habitat files

Files are constructed as following: number_of_species number_of_habitats (habitats [separated by tab]), followed by all species in the phylogeny and codification for having (1) or not having (0) that habitat. [NOTE: "X" is Fh, "Y" is Oh, and "Z" is "FOh" habitat type, please check Main Document for more explanation.]
ALENCAR2016_CARAC.txt: Habitat codification file for the species included in the Alencar et al. (2016) phylogeny.
TITLE2024_CARAC.txt: Habitat codification file for the species included in the Title et al. (2024) phylogeny.
ZAHER2019_CARAC.txt: Habitat codification file for the species included in the Zaher et al. (2019) phylogeny.
ZHENG2016_CARAC.txt: Habitat codification file for the species included in the Zheng and Wiens (2016) phylogeny.

Time-stratified matrix and time-slices

VIP_matriz.txt: time-stratified matrix.
VIP_tempo.txt: time-slices.

Outputs:

(outputs_MODEL_RESULTS): 240 files.

Result objects generated by each model using R for each tree (.RData).

Figures generated by the R script (later edited in GIMP 2.10.36) (outputs_PLOT_FIGURES)

ALENCAR2016_VIPERS_Circular_FINAL_HABITATS_ALL.pdf: Habitat estimation under best model (see main text) for the Alencar et al. (2016) phylogeny.
ALENCAR2016_VIPERS_Circular_FINALAICc_ALL.pdf: Range estimation under best model (see main text) for the Alencar et al. (2016) phylogeny.
TITLE2024_VIPERS_Circular_FINAL_HABITATS_ALL.pdf: Habitat estimation under best model (see main text) for the Title et al. (2024) phylogeny.
TITLE2024_VIPERS_Circular_FINALAICc_ALL.pdf: Range estimation under best model (see main text) for the Title et al. (2024) phylogeny.
ZAHER2019_VIPERS_Circular_FINAL_HABITATS_ALL.pdf: Habitat estimation under best model (see main text) for the Zaher et al. (2019) phylogeny.
ZAHER2019_VIPERS_Circular_FINALAICc_ALL.pdf: Range estimation under best model (see main text) for the Zaher et al. (2019) phylogeny.
ZHENG2016_VIPERS_Circular_FINAL_HABITATS_ALL.pdf: Habitat estimation under best model (see main text) for the Zheng and Wiens (2016) phylogeny.
ZHENG2016_VIPERS_Circular_FINALAICc_ALL.pdf: Range estimation under best model (see main text) for the Zheng and Wiens (2016) phylogeny.

(outputs_PLOT_RESULTS): 240 files.

Ancestral range reconstruction PDF's generated by each model using R (.pdf).

(outputs_TABLES_RESULTS): 32 files.

AIC and AICc results generated by each model using R (.RData and .txt).
[phylogeny]_restable_AIC_rellike_ALLAICC_MPN.txt: AIC results for all the 60 models for each phylogeny.
[phylogeny]_restable_AIC_rellike_formatted_ALLAICC_MPN.txt: AIC results (rounded numbers and removed NAs) for all the 60 models for each phylogeny.
[phylogeny]_restable_AICc_rellike_ALLAICC_MPN.txt: AICc results for all the 60 models for each phylogeny.
[phylogeny]_restable_AICc_rellike_formatted_ALLAICC_MPN.txt: AICc results (rounded numbers and removed NAs) for all the 60 models for each phylogeny.
[phylogeny]_restable_ALLAICC_MPN.txt: Only contains the parameter estimations for all the 60 models for each phylogeny.
[phylogeny]_teststable_ALLAICC_MPN.txt: p-value comparisons between base models vs models with +j parameter.

[phylogeny]_restable_ALLAICC_MPN.RData: restable object saved in the R environment.
[phylogeny]_teststable_ALLAICC_MPN.RData: teststable object saved in the R environment.

Code:

BioGeoBEARS_script_JBI-24-0395.R: main script used to generate all the results in the work.
calc_loglike_for_optim_edited.R: edited functions from the BioGeoBEARS package, OPTIONAL: see Main Script.
calc_loglike_for_optim_stratified_edited.R: edited functions from the BioGeoBEARS package, OPTIONAL: see Main Script.
get_trait_from_traitgeog_results_edited.R: edited functions from the BioGeoBEARS package, OPTIONAL: see Main Script.

Usage notes:

R is required to run BioGeoBEARS_script_JBI-24-0395.R, calc_loglike_for_optim_edited.R, calc_loglike_for_optim_stratified_edited.R and get_trait_from_traitgeog_results_edited.R. The main script was created using version 4.3.2. .RData objects in the outputs folder can also be opened with R to retrieve objects saved (i.e., past environments). No further software is needed to open any of the inputs here provided.

Licence:

All files uploaded here are licensed under CC0.