2.2. Occurrence data
We used two sets of occurrence data, at the species and genetic analysis
levels. M. geocarpum records were collected from its location
points using data of self-collected material and the Global Biodiversity
and Informatics Facility (GBIF, www.gbif.org), an online available
database. We used both the original population location points and those
from GBIF in all subsequent analyses. As the different data sources and
a large dataset (>500 occurrence records) would likely
carry elevated geographical or environmental space biases
(Boria et al. 2014;
Peterson et al. 2011), the number
of records were decreased in Wallace package, an online workspace based
on R interface (Kass et al. 2020)
using four complementary approaches: 1) we first removed occurrences
collected before 1986 to match with environmental layers and soil
properties; 2) considerable ambiguity may exist in GBIF data over the
identity of the species due to synonymous names (M. geocarpumvar. geocarpum , M. geocarpum var. Tisserantii ;Kerstingiella geocarpa , Kerstingiella tisserantii ). To
avoid any confusion arising from this taxonomic ambiguity, we searched
through the online databases using the following keywords:Macrotyloma geocarpum , Kerstingiella geocarpa , var.geocarpa or var. geocarpum ; orphan legumes. We then
harmonized the GBIF database and discarded the reports on var.tisserantii and Kerstingiella tisserantii ; 3) we used
spatially filtering occurrences located ≤ 10 km from other occurrences
using the spThin, an R package
(Aiello-Lammens et al. 2015);
finally, 4) we manually checked isolated locations points in Africa (in
ArcGis ver. 10.7.1) and removed occurrences in areas where M.
geocarpum is not generally grown.
The defined genetic clusters data with their geographic coordinates were
also filtered separately to ensure the real distribution of each
population within agroclimatic zones. The filtered dataset comprised in
total 64 occurrences (Pop1 = 22; Pop2 = 25 and GBIF = 17) that was used
in subsequent analyses (Table S1).