Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling

Abstract

Changes in species’ distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species’ range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.

Hybridization capture of larch (LarixMill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

“…In the case of the population history of L. sibirica and L. gmelinii in their contact zone, Semerikov et al (2013) found evidence for the asymmetric introgression of L. sibirica mitotypes in a population carrying only L. gmelinii chlorotypes, confirming the natural invasion of L. gmelinii into the range of L. sibirica. Here we corroborate these findings with a distinct discrepancy between relatively high rates of L. sibirica mitotypes as reported before (Epp et al, 2018) and low rates of L. sibirica in the chloroplast reads found in this study. This points to an invasion of L. gmelinii in a former population of L. sibirica prior to the date of our oldest sample (6700 cal-BP).…”

“…When comparing the ancient reads to chloroplast reference genomes from L. gmelinii and L. sibirica, the great majority of reads carry the L. gmelinii variants with a low frequency of L. sibirica variants in all four samples. In contrast, the analysis of one mitochondrial marker derived from the same core by Epp et al (2018), showed a mixture of both species, with relatively high rates of L. sibiricaexcept for the most recent sample, which showed clear dominance of the L. gmelinii mitotypepointing to a co-occurrence of both species across most of the sediment core. In the genus Larix, chloroplasts are predominantly inherited paternally (Szmidt, Aldén, & Hällgren, 1987) whereas mitochondrial DNA is inherited maternally (DeVerno, Charest, & Bonen, 1993), a phenomenon which has been reported for almost all members of the conifers (Neale & Wheeler, 2019).…”

“…Here we used kraken2 (Wood, Lu, & Langmead, 2019), a new version of kraken, which is a particularly conservative tool compared to others, reporting less false-positive but also less true-positive hits than others tools, even with default values (Harbert, 2018). We used it with a high confidence threshold as we found it gives the best results in terms of vegetation composition based on our knowledge of the vegetation history (Epp et al, 2018), but with the consequence of very low overall assignment rates. Indeed, when we use the default values of kraken2, we could assign 10-16% of the reads.…”

“…Sampling, DNA extraction and library preparation Core sub-sampling and DNA extraction were performed as described in Epp et al (2018). Five µL of each DNA extraction were used in the library preparation.…”

“…The lake is situated in the treeline ecotone with scattered patches of L. gmelinii occurring in the area (Klemm, Herzschuh, & Pestryakova, 2016). A sediment core of the lake has already been extensively studied using pollen analysis, DNA metabarcoding and mitochondrial variants (Epp et al, 2018;Klemm et al, 2016) making it an ideal site to study ancient larch population dynamics based on chloroplast DNA.…”