DOI: 10.5061/dryad.vg7b1
title: Data from: Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity

description: 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.
description: 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.txt