Mining megadiverse genera of flowering plants

Here in this article, we show how to use the package’s function megaGen for mining the megadiverse genera for any family of flowering plants. Frodin (2004) in Taxon suggests 500 species as the threshold for a genus to be considered megadiverse. The function megaGen uses any integer numeric value in the argument thld to define the threshold for a megadiverse genus.


Setup

Install the latest development version of expowo from GitHub:

#install.packages("devtools")
devtools::install_github("DBOSlab/expowo")
library(expowo)


Mining megadiverse genera for any angiosperm family

The function megaGen uses a specified threshold number to return a dataframe or save a CSV file listing all megadiverse genera for any family of flowering plants and their associated number of accepted species. In this example, we performed a search for three plant families using a threshold of 500 species, but the output only contains results for Aristolochia and Begonia of Aristolochiaceae and Begoniaceae families.

ABM <- megaGen(family = c("Aristolochiaceae", "Begoniaceae", "Martyniaceae"),
               thld = 500,
               verbose = TRUE,
               save = FALSE,
               dir = "results_megaGen/",
               filename = "Arist_Begon_Martyniaceae_search")
TABLE 1. A general megaGen search to mining the megadiverse genera for some specific angiosperm families, based on a specified threshold of 500 species.
family genus authors scientific_name species_number kew_id powo_uri
Aristolochiaceae Aristolochia L. Aristolochia L. 534 330834-2 http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:330834-2
Begoniaceae Begonia L. Begonia L. 1992 327437-2 http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:327437-2


Mining megadiverse genera accross all angiosperm families

To mine a global checklist of megadiverse genera for all families of flowering plants, including their associated species number, we recommend to load the dataframe-formatted data object called POWOcodes that comes associated with the expowo package. The POWOcodes data object already contains the URI addresses for all angiosperms families recognized in the POWO database, you just need to call it to your R environment.

The example below shows how to mine a global checklist of all most speciose genera of flowering plants by using the vector of all angiosperm families and associated URI addresses stored in the POWOcodes object.

data(POWOcodes)

ALL_megaGen <- megaGen(POWOcodes$family,
                       thld = 500,
                       verbose = TRUE,
                       save = FALSE,
                       dir = "results_megaGen/",
                       filename = "all_megadiverse_angiosperm_genera")