Aim Species distribution models (SDMs) based on current species ranges underestimate the potential distribution when projected in time and/or space. A multi-temporal model calibration approach has been suggested as an alternative, and we evaluate this using 13,000 years of data. Location Europe. Methods We used fossil-based records of presence for Picea abies, Abies alba and Fagus sylvatica and six climatic variables for the period 13,000 to 1000yr bp. To measure the contribution of each 1000-year time step to the total niche of each species (the niche measured by pooling all the data), we employed a principal components analysis (PCA) calibrated with data over the entire range of possible climates. Then we projected both the total niche and the partial niches from single time frames into the PCA space, and tested if the partial niches were more similar to the total niche than random. Using an ensemble forecasting approach, we calibrated SDMs for each time frame and for the pooled database. We projected each model to current climate and evaluated the results against current pollen data. We also projected all models into the future. Results Niche similarity between the partial and the total-SDMs was almost always statistically significant and increased through time. SDMs calibrated from single time frames gave different results when projected to current climate, providing evidence of a change in the species realized niches through time. Moreover, they predicted limited climate suitability when compared with the total-SDMs. The same results were obtained when projected to future climates. Main conclusions The realized climatic niche of species differed for current and future climates when SDMs were calibrated considering different past climates. Building the niche as an ensemble through time represents a way forward to a better understanding of a species' range and its ecology in a changing climate

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

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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.

In the European Alpine System, the Carpathian Mountains are recognized as one of the major centres of diversity and endemism. In the present study, we aimed to explain the spatial structure of plant endemism in its South‐Eastern subunit by the complementary use of diversity indices, parsimony analysis of endemicity (PAE), biotic element analysis (BEA), and barrier analysis. We analyzed the available information on 111 plant taxa confined to the South‐Eastern Carpathians, mapped using two different sets of operational geographical units (OGUs): 71 geomorphological units and 64 quadrats. Our results showed that centres of endemics diversity largely corresponded to the areas of endemism and biotic elements. PAE consensus cladogram outlined four major areas of endemism (with three nested ones): (1) Danubian; (2) western part of the Southern Carpathians; (3) eastern part of the Southern Carpathians; and (4) Pocutico‐Marmarossian. Out of the seven identified biotic elements, five were spatially clustered and overlapped the major areas of endemism, with one notable exception: the calcareous massifs from the Eastern Carpathians, not identified through PAE. Conversely, the latter outlined a nested area of endemism (Cozia – Buila‐Vânturarița), omitted by BEA. Barrier analysis identified three major breaks in the distribution of endemics: (1) south of the Retezat – Țarcu – Godeanu mountain group; (2) north of the Piatra Craiului – Bucegi – Ciucaș mountain group; and (3) north of the Rodna massif. The results obtained in here using different methods are generally spatially convergent, indicating highly structured patterns of endemism in the South‐Eastern Carpathians. These patterns mostly follow the present‐day distribution of alpine habitats and calcareous bedrock, which might have acted as isolating factors through insularity. Interestingly, three of the spatial clusters of OGUs obtained from the endemics distribution analyses (the Eastern Carpathians, as well as eastern and western parts of the Southern Carpathians) largely also correspond to the mid‐Miocene archipelago configuration of landmasses in this part of the Carpathians. This might suggest the existence of older migration barriers that emerged throughout the Neogene Period. Differences in the spatial patterns outlined by PAE and BEA could stem from partial sympatry of endemics caused by post‐speciation processes such as dispersal or extinction. Additionally, sympatric distribution of taxa with disjunct populations may be caused by the absence of divergence among segregated populations, such as the patterns of relict distributions seen in alpine plants. Finally, the complementary use of these methods may prove to be an efficient approach for better understanding the geographical structure of endemism and provide a starting point for further testing of hypotheses on evolutionary processes.