ddRAD data of Polylepis spp
The culturally and economically significant Andean tree genus Polylepis—which forms the world's highest-elevation treelines—has long eluded a well-supported phylogenetic reconstruction, possibly due to extensive gene flow, hybridization, and polyploidization. To address this, we investigate sympatric populations of P. neglecta (Bolivia) and P. incana (Ecuador) using genomic (ddRADseq) and morphological data. Our goal is to provide empirical evidence for these evolutionary processes and to propose strategies for reconstructing the phylogeny of the genus. We hypothesize that, despite high levels of gene flow and hybridization, species boundaries remain distinct, and that ddRADseq data will provide high phylogenetic resolution. Samples underwent ddRAD analysis following Peterson et al. (2012, https://doi.org/10.1371/journal.pone.0037135) using EcoRI and MspI as restriction enzymes and a selected fragment length of 350-450 bp. Samples were sequenced on an Illumina Novaseq 6000 (PE150) , resulting in appr. 2 Mio. sequences per individual sample. Sequences were demultiplexed with process_radtags --paired -i gzfastq -y gzfastq --barcode_dist_1 2 --barcode_dist_2 2 --inline_index --renz_1 'ecoRI' --renz_2 'mspI' --disable_rad_check --retain_header.
The culturally and economically significant Andean tree genus Polylepis—which forms the world's highest-elevation treelines—has long eluded a well-supported phylogenetic reconstruction, possibly due to extensive gene flow, hybridization, and polyploidization. To address this, we investigate sympatric populations of P. neglecta (Bolivia) and P. incana (Ecuador) using genomic (ddRADseq) and morphological data. Our goal is to provide empirical evidence for these evolutionary processes and to propose strategies for reconstructing the phylogeny of the genus. We hypothesize that, despite high levels of gene flow and hybridization, species boundaries remain distinct, and that ddRADseq data will provide high phylogenetic resolution. Samples underwent ddRAD analysis following Peterson et al. (2012, https://doi.org/10.1371/journal.pone.0037135) using EcoRI and MspI as restriction enzymes and a selected fragment length of 350-450 bp. Samples were sequenced on an Illumina Novaseq 6000 (PE150) , resulting in appr. 2 Mio. sequences per individual sample. Sequences were demultiplexed with process_radtags --paired -i gzfastq -y gzfastq --barcode_dist_1 2 --barcode_dist_2 2 --inline_index --renz_1 'ecoRI' --renz_2 'mspI' --disable_rad_check --retain_header.