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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.
Although sedimentary ancient DNA (sedaDNA) has been increasingly used to study paleoecological dynamics (Schulte et al., 2020), the approach has rarely been compared with the traditional method of pollen analysis for investigating past changes in the vegetation composition and diversity of Arctic treeline areas. Here, we provide a history of latitudinal floristic composition and species diversity based on a comparison ofsedaDNA and pollen data archived in three Siberian lake sediment cores spanning the mid-Holocene to the present (7.6-0 cal ka BP), from northern typical tundra to southern open larch forest in the Omoloy region. Our results show that thesedaDNA approach identifies more plant taxa found in the local vegetation communities, while the corresponding pollen analysis mainly captures the regional vegetation development and has its limitations for plant diversity reconstruction. Measures of alpha diversity were calculated based onsedaDNA data recovered from along a tundra to forest tundra to open larch forest gradient. Across all sites,sedaDNA archives provide a complementary record of the vegetation transition within each lake's catchment, tracking a distinct latitudinal vegetation type range from larch tree/alder shrub (open larch forest site) to dwarf shrub-steppe (forest tundra) to wet sedge tundra (typical tundra site). By contrast, the pollen data reveal an open landscape, which cannot distinguish the temporal changes in compositional vegetation for the open larch forest site and forest-tundra site. IncreasingLarixpollen percentages were recorded in the forest-tundra site in the last millenium although noLarixDNA was detected, suggesting that thesedaDNA approach performs better for tracking the local establishment ofLarix. Highest species richness and diversity are found in the mid-Holocene (before 4.4 ka) at the typical tundra site with a diverse range of vegetational habitats, while lowest species richness is recorded for the forest tundra where dwarf-willow habitats dominated the lake's catchment. During the late Holocene, strong declines in species richness and diversity are found at the typical tundra site with the vegetation changing to relatively simple communities. Nevertheless, plant species richness is mostly higher than at the forest-tundra site, which shows a slightly decreasing trend. Plant species richness at the open larch forest site fluctuates through time and is higher than the other sites since around 2.5 ka. Taken together, there is no evidence to suggest that the latitudinal gradients in species diversity changes are present at a millennial scale. Additionally, a weak correlation between the principal component analysis (PCA) site scores ofsedaDNA and species richness suggests that climate may not be a direct driver of species turnover within a lake's catchment. Our data suggest thatsedaDNA and pollen have different but complementary abilities for reconstructing past vegetation and species diversity along a latitude.
Lakes cover large parts of the climatically sensitive Arctic landscape and respond rapidly to environmental change. Arctic lakes have different origins and include the predominant thermokarst lakes, which are small, young and highly dynamic, as well as large, old and stable glacial lakes. Freshwater diatoms dominate the primary producer community in these lakes and can be used to detect biotic responses to climate and environmental change. We used specific diatom metabarcoding on sedimentary DNA, combined with next-generation sequencing and diatom morphology, to assess diatom diversity in five glacial and 15 thermokarst lakes within the easternmost expanse of the Siberian treeline ecotone in Chukotka, Russia. We obtained 163 verified diatom sequence types and identified 176 diatom species morphologically. Although there were large differences in taxonomic assignment using the two approaches, they showed similar high abundances and diversity of Fragilariceae and Aulacoseiraceae. In particular, the genetic approach detected hidden within-lake variations of fragilarioids in glacial lakes and dominance of centric Aulacoseira species, whereas Lindavia ocellata was predominant using morphology. In thermokarst lakes, sequence types and valve counts also detected high diversity of Fragilariaceae, which followed the vegetation gradient along the treeline. Ordination analyses of the genetic data from glacial and thermokarst lakes suggest that concentrations of sulfate (SO42-), an indicator of the activity of sulfate-reducing microbes under anoxic conditions, and bicarbonate (HCO3-), which relates to surrounding vegetation, have a significant influence on diatom community composition. For thermokarst lakes, we also identified lake depth as an important variable, but SO42- best explains diatom diversity derived from genetic data, whereas HCO3- best explains the data from valve counts. Higher diatom diversity was detected in glacial lakes, most likely related to greater lake age and different edaphic settings, which gave rise to diversification and endemism. In contrast, small, dynamic thermokarst lakes are inhabited by stress-tolerant fragilarioids and are related to different vegetation types along the treeline ecotone. Our study demonstrated that genetic investigations of lake sediments can be used to interpret climate and environmental responses of diatoms. It also showed how lake type affects diatom diversity, and that such genetic analyses can be used to track diatom community changes under ongoing warming in the Arctic.
Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Furthermore, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line ecotone. Using a space-time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.