Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

Abstract

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA—metabarcoding—focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long‐range PCR‐generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome‐scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.

Environmental palaeogenomic reconstruction of an Ice Age algal population

“…The low relative frequencies of sequences mapping to other non-Nannochloropsis eukaryotic taxa are likely to be artifacts resulting from the spurious mapping of short and damaged ancient DNA molecules coupled with the vast diversity of sequences present in sedaDNA 22,23 . We note that the low overall proportions of sequences identified by our metagenomic analyses are broadly consistent with other shotgun metagenomic studies from sedaDNA 10,13,14 suggesting that the vast majority of taxonomic diversity in the sediment record is currently unidentifiable.…”

“…Our complete N. limnetica chloroplast palaeogenome reconstructions represent the first derived from sedaDNA to the best of our knowledge, although a near-complete chloroplast sequence has recently been reported for a vascular plant 14 . Mitochondrial palaeogenomes have previously been reconstructed from cave sediments 12 , and archaeological middens and latrines 24,25 , but ours are, as far as we know, the first derived from lake sediments.…”

“…alaeogenomics, the genomic-scale application of ancient DNA, is revolutionizing our understanding of past evolutionary and ecological processes, including population dynamics, hybridization, and the effects of drivers of change [1][2][3][4] . Despite extensive application to, and innovations using, body fossils [5][6][7] , its use on another major source of ancient DNA-the environment-has been almost entirely limited to inventorying taxa through time [8][9][10][11][12][13][14][15] . However, a nuanced understanding of ecological and evolutionary dynamics requires population genomic information.…”

“…Lake sedaDNA is used to infer the taxonomic composition of past communities 27,28 , regardless of whether those taxa preserve in the body fossil record. While techniques such as DNA metabarcoding allow for the inventorying of groups of organisms 29,30 , either deep shotgun sequencing or target enrichment of sedaDNA is required for palaeogenomic reconstruction, which would allow for robust species-level identification 12,14,24 and the potential exploration of population genomic variation.…”

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

“…This data can be used for the assembly of chloroplast genomes (cpGenomes) and nuclear ribosomal DNA (nrDNA) sequences within which plant barcodes and other gene loci can be recovered [13,34,42]. The ability of genome skimming to go beyond generating standard plant barcodes is highly advantageous as the resulting genomic data can be used for other applications including species delimitation [16,22,43], population genomics [44], development of capture probes [45][46][47], evolutionary and phylogenetic studies [21,34,40,41,[48][49][50][51], and metagenomics eDNA studies [52][53][54]. Hence, genome skimming is increasingly seen as the way forward to build large-scale curated DNA reference databases from taxonomically identified voucher specimens [13,14].…”