The Ethiopian highlands represent a remarkable biodiversity “hotspot” with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot-spots. Here, we analyze the most comprehensive genetic dataset of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled acrysross most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated  divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most likely caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the Ethiopian highland’s fauna.

The files contain pair-end reads that were submitted to ipyrad (Eaton & Overcast, 2020) for denovo assembly of ddRAD loci. The reads were demultiplexed and barcodes removed in Skewer (Jiang, Lei, Ding & Zhu, 2014) and pre-processing of read ends in PEAR (Zhang, Kobert, Flouri & Stamatakis, 2014). Every pair of reads was merged (with minimum required overlap of 10 nucleotides) and cut in two halves. If they were not successfully merged, we trimmed off the last 10 nucleotides from the reverse read. The PEAR-treatment was necessary to avoid poor quality mergers in a substantial proportion of loci.

References:

Eaton, D. A. R., & Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq datasets. Bioinformatics, 36(8), 2592–2594. doi: 10.1093/bioinformatics/btz966
Jiang, H., Lei, R., Ding, S. W., & Zhu, S. (2014). Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics, 15(1), 182. doi: 10.1186/1471-2105-15-182
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014). PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics, 30(5), 614-20. doi: 10.1093/bioinformatics/btt593