Databases
PaleoClim.org High-resolution, easily accessible paleoclimate data are essential for environmental, evolutionary, and ecological studies. Integrative studies of the impacts of climate change in the Early Pleistocene and Pliocene – periods in which recent speciation events are known to concentrate – have been hindered by the limited availability of downloadable, user-friendly climatic descriptors. This was before we introduced PaleoClim.org, a free database of high-resolution downscaled paleoclimate outputs at 2.5-minute resolution (~5 km at equator). As of now, the database contains climatic data for 9 key time periods spanning from 3.3 million to 300 years ago.
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Dendrobates.org is an online emporium of field based accounts of poison frog species.
Darwin's Game Night provides detailed reviews of evolution themed board games and information regarding their use in the classroom. The site also has teaching materials associated with our top picks!
The Brown Lab Bioinformatics Pipeline - Code for UCEs and phylogenomics
Software
SDMtoolbox is a python-based ArcGIS toolbox for spatial studies of ecology, evolution and genetics. SDMtoolbox consists of a series python scripts (91 and growing) designed to automate complicated ArcMap (ESRI) analyses. A large set of the tools were created to complement MaxEnt species distribution models (SDMs) or to improve the predictive performance of MaxEnt models. SDMtoolbox is not limited to analyses of MaxEnt models and many tools are also available for use on other data (i.e. haplotype networks) or the results of other SDM methods .
Humboldt is a comprehensive R package that performs spatial analyses of species' niche overlap in E-space (environment or climate space).
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To install, open R and type the following:
install.packages("devtools"); devtools::install_github("jasonleebrown/humboldt")
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If you are having issues with using a newer version of R and cannot install 'rgeos' and 'rgdal', use the following script (this script assumes 'devtools' is installed):
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packageurl2 <- "https://cran.r-project.org/src/contrib/Archive/rgeos/rgeos_0.6-4.tar.gz"
packageurl <- "https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-7.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
install.packages(packageurl2, repos=NULL, type="source")
devtools::install_github("jasonleebrown/humboldt")
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Note the software will be updated in the future so this workaround is no longer necessary
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Machuruku is an R package developed with Wilson X. Guillory for phylogenetic niche modeling and estimation of ancestral distributions. Machuruku, named after the Quechua word for 'ancient', uses a modified Bioclim niche-modeling method and ancestral character estimation to reconstruct ancestral niches. Output ancestral niche models can then be projected into paleoclimate data to visualize the potential distributions of evolving lineages across time and space.
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To install, open R and type the following:
install.packages(c("BiocManager", "devtools"))
BiocManager::install("ggtree")
devtools::install_github("wxguillo/machuruku")
MACHISPLIN is an R package for interpolation of noisy multi-variate data through comprehensive statistical analyses using thin-plate-smoothing splines and machine learning ensembling. This package is a free open-source machine learning analog to the expensive ANUSPLIN software.
To install, open R and type the following:
install.packages("devtools"); devtools::install_github("jasonleebrown/machisplin")
Tangible Niche & Genetic Simulator: TANAGERS is a GRASS GIS package where users sculpt 3D landscapes and simulate ecological and evolutionary processes. TANAGERS incorporates tactile learning with real-time ecology and evolution simulations in an interactive, visually dynamic way. Working with the Tangible Landscape infrastructure, which represents a real-time feedback cycle of hands-on interaction, 3D scanning, geospatial computation and projection, we have created a highly interactive way to explore how physical geography and species-specific life-history factors affect population ecology, genetic diversity, and speciation across a landscape.