DOI: 10.5061/dryad.8cz8w9h3x
title: From Asia to the Americas: a new cross-continental perspective on viper biogeography and habitat dynamics

description: 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.
description: # From Asia to the Americas: a new cross-continental perspective on viper
 biogeography and habitat dynamics [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.8cz8w9h3x) [Primary
 article](https://doi.org/10.1111/jbi.15153) 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.