Data from: Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.Afro-alpine taxonomic reference library version 1.0This file contains the sequences of the taxonomic reference library version 1.0 for the African alpine flora. Sequences cover the P6 loop of the trnL. Header lines contain the species names followed by identity numbers (O-DP numbers) that correspond to specimen numbers in the herbarium of the Natural History Museum, University of Oslo, Norway. Sampling for the afro-alpine taxonomic reference library was carried out during 2007-2009 in Ethiopia, Kenya, Tanzania, and Uganda. Details on DNA extractions, PCRs, sequencing, and formatting of the final database can be found in the associated publication. Contact author: Sanne Boessenkool (sanneboessenkool@gmail.com)Afro-alpine_taxonomic_ref_library_v1.fastaSequences from dataset 1 with identification using the Afro-alpine reference libraryThe unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using the Afro-alpine reference library v.1. Further details can be found in the ReadMe file.sequences_dataset1_afro-alpine_identification.txtSequences from dataset 1 with identification using emblThe unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using a reference library formatted from embl. Further details can be found in the ReadMe file.sequences_dataset1_embl_identification.txtSequences from dataset 2 with identification using the Afro-alpine reference libraryThe unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using the Afro-alpine reference library v.1. Further details can be found in the ReadMe file.sequences_dataset2_afro-alpine_identification.txtSequences from dataset 2 with identification using emblThe unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using a reference library formatted from embl. Further details can be found in the ReadMe file.sequences_dataset2_embl_identification.tx