The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.
While soil ecosystems undergo important modifications due to global change, the effect of soil properties on plant distributions is still poorly understood. Plant growth is not only controlled by soil physico-chemistry but also by microbial activities through the decomposition of organic matter and the recycling of nutrients essential for plants. A growing body of evidence also suggests that plant functional traits modulate species' response to environmental gradients. However, no study has yet contrasted the importance of soil physico-chemistry, microbial activities and climate on plant species distributions, while accounting for how plant functional traits can influence speciesspecific responses. Using hierarchical effects in a multi-species distribution model, we investigate how four functional traits related to resource acquisition (plant height, leaf carbon to nitrogen ratio, leaf dry matter content and specific leaf area) modulate the response of 44 plant species to climatic variables, soil physico-chemical properties and microbial decomposition activity (i.e. exoenzymatic activities) in the French Alps. Our hierarchical trait-based model allowed to predict well 41 species according to the TSS statistic. In addition to climate, the combination of soil C/N, as a measure of organic matter quality, and exoenzymatic activity, as a measure of microbial decomposition activity, strongly improved predictions of plant distributions. Plant traits played an important role. In particular, species with conservative traits performed better under limiting nutrient conditions but were outcompeted by exploitative plants in more favorable environments. We demonstrate tight associations between microbial decomposition activity, plant functional traits associated to different resource acquisition strategies and plant distributions. This highlights the importance of plant-soil linkages for mountain plant distributions. These results are crucial for biodiversity modelling in a world where both climatic and soil systems are undergoing profound and rapid transformations.
Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouc hon/ORTHO SKIM.
A morphometric multivariate and univariate study involving all the three taxa within the Fritillaria tubaeformis species complex was carried out. A total of 86 individuals from 8 populations were studied in vivo, complemented by the analysis of 116 individuals from herbarium specimens. According to our results, some morphological characters clearly support the separation among F. burnatii, F. tubaeformis and F. moggridgei. Despite this, some morphological overlapping does exist among F. tubaeformis and F. moggridgei, which show contiguous, partially interdigitated, but not overlapping ranges, and we deem more opportune their separation at subspecies level. On the contrary, Fritillaria burnatii is a clearly distinct species, albeit it can occasionally co-occur in the same site with F. tubaeformis subsp.moggridgei. An identification key for both fresh and dry specimens is provided.
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