A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations

Supplementary data to article entitled A hotspot of groundwater
amphipod diversity on a crossroad of evolutionary radiations Groundwater
harbours an exceptional fauna and provides invaluable ecosystem services,
yet is among the least explored and consequently least protected
ecosystems. Successful protection of its biodiversity depends on complete
species inventories, knowledge of species spatial distribution, and
quantification of biodiversity patterns, as well as disentanglement of the
processes that shaped biodiversity patterns. We studied the hyper-speciose
amphipod genus Niphargus as a model system within a global
subterranean biodiversity hotspot, the Western Balkans (Europe). We linked
the biodiversity patterns with possible underlying processes and discuss
the needs to include information on different origins of biodiversity into
conservation approaches. We analysed biodiversity patterns
of Niphargus using two biodiversity metrics, species
richness and phylogenetic diversity, on a grid-based approach. To account
for high cryptic diversity, we replaced nominal species with taxonomic
units identified in unilocus delimitations (MOTUs). We built a
time-calibrated multilocus phylogeny of 512 Niphargus MOTUs from
within and outside the study area, and calculated Faith's
phylogenetic diversity, standardized effect sizes of phylogenetic
diversity, and residual of phylogenetic diversity regressed onto species
richness. Within the study area, we recognized 245 MOTUs, belonging to
different Niphargus clades. Species richness is highest in a
north-western hotspot, although some species-rich cells were detected also
in the south-east. High phylogenetic diversity coincides with high species
richness in the north-west, while in the south-east it is lower than
expected. We have shown that species richness does not predictably
correlate with phylogenetic diversity. This difference suggests that
different processes have led to the formation of species-rich areas in the
Western Balkans: through a combination of dispersal and speciation in the
north-west, and local radiation in the south-east, respectively. This
calls for caution in conservation strategies relying solely on number of
species and may change the view on conservation priorities within this
region. The dataset includes R-script, together with all raw data needed
to reproduce the analyses: File "beast_analysis.xml" includes
alignments and settings used for BEAST2 analysis. R script
"20220124_niphargus_wbalkans.R" includes the code used in
production of diversity pattern analyses. To run the script set working
directory (commented) and unzip the "data" folder in the working
directory. Folder "data.zip" includes raw data needed to run the
script: species_occurence.csv, map shape files and beast.tree
file.