Flora Alpina: Atlas des 4500 Plantes Vascularies des Alpes

Schmid, Rudolf; Price, Michelle; Aeschimann, David; Lauber, K.; Moser, Daniel; Theurillat, Jean‐Paul

doi:10.2307/25065454

Cited by 17 publications

(29 citation statements)

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“…We base classifications on cleaned spatial occurrences from GBIF because they are largest in number and most widely used. Validation data comes from the highly regarded Flora Alpina of Aeschimann et al (2004), to which numerous experts contributed. The Flora is an authoritative synthesis of different national floras, presenting all 4491 vascular plant taxa of the European Alpine Arc, one of the floristically best-known areas in the world.…”

Section: Experimental Designmentioning

confidence: 99%

Avoiding impacts of phylogenetic tip‐state‐errors on dispersal and extirpation rates in alpine plant biogeography

Bätscher,

de Vos

2024

Journal of Biogeography

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AimMany biogeographic analyses require some form of automated state assignment to tips of phylogenetic trees, reflecting a species presence or absence in a particular area, e.g., a biome. As datasets get exponentially larger, such procedures may increasingly induce errors (here called tip‐state‐error), but the specific algorithmic cause and consequence on downstream estimation of dispersal and extinction rates remains poorly known. We aim to improve automated tip‐scoring methods in the context of the alpine biome by leveraging elevation information. We document the profound effect of tip‐state‐errors on Dispersal‐Extirpation‐Cladogenesis (DEC) models.LocationThe European Alpine Arc.TaxonThree thousand three hundred seventeen vascular plant species, emphasizing six focal genera: Campanula, Carex, Festuca, Ranunculus, Saxifraga, and Viola.MethodsWe use GBIF data to classify whether species occur above the upper climatic treeline using a newly developed algorithm ElevDistr or a gridded landscape model of thermal belts, under various filtering thresholds. We compared classification performance using the Flora Alpina as validation data. To determine if tip‐state‐error biases the dispersal and extirpation rate estimation, we fit DEC models for selected clades using tip‐states from different classification models.ResultsElevDistr is less error prone than other approaches. Filtering thresholds lower the false positive rate but increase the false negative rate. Inflated false positive rates bias the dispersal rate estimation upward, while inflated false negative rates lead to upward bias in extirpation rate estimation.Main ConclusionsEven moderate tip‐state‐error may lead to profound systematic bias in dispersal and extinction rate estimation if an unbalanced ratio between false positive and false negative rates occurs. Therefore, careful validation is imperative, though ElevDistr alleviates this problem in the context of the alpine environment. Overall, our results suggest contrasting rates of alpine biome shifts across the studied genera and have major implications for studies addressing the likelihood of niche evolution versus geographic dispersal.

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Section: Experimental Designmentioning

confidence: 99%

Avoiding impacts of phylogenetic tip‐state‐errors on dispersal and extirpation rates in alpine plant biogeography

Bätscher,

de Vos

2024

Journal of Biogeography

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“…More specifically, to extract GBIF information and merge all datasets, a large list of synonyms of all the plant species occurring in the European Alps was generated by compiling and web-scraping information from different sources: The Catalogue of Life (http://www.catalogueoflife.org/), the Plant List (http://www.theplantlist.org/) and the French National Alpine Botanical Conservatory (CBNA). To generate this list, a search was undertaken across 4490 accepted names referenced in the Flora Alpina Atlas 44 to obtain a total of 131.660 synonyms that were used as search inputs in GBIF to retrieve our online observations using the gbif.range R package 45 . Only observations with a 100% confidence name matching and accurate to 11.1 meters were kept.…”

Section: Observationsmentioning

confidence: 99%

“…It is important to note that for species with > 10'000 observations, we sampled randomly without replacement a subset of 10'000 observations for better computation efficiency 47,48 . Additionally, an independent and unbiased test dataset, reporting the empirical and distributional range of our 3'167 plant species over the European Alps, was constructed from expert-based information available in the Flora Alpina (FA) 44 and the extraction of the 5-95 th percentiles elevation values of each species (see Fig. S20 for more information)…”

Section: Observationsmentioning

confidence: 99%

Transnational conservation to anticipate future plant shifts in Europe

Chauvier

Pollock

Verburg

et al. 2023

Preprint

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To meet the COP15 biodiversity framework in Europe, one target is to protect 30% of land by 2030 through a resilient transnational conservation network 1,2. The European Alps are a key hub of this network hosting one of the most extensive natural areas and hotspots of plant biodiversity in Europe 3,4. Here, we assess the robustness of the conservation network to safeguard the European Alps’ flora by 2080 using semi-mechanistic simulations. Overall, we predict a shift in conservation need from lower to higher elevations through time as plants migrate upslope and shrink their distribution. While increasing species, trait, and evolutionary diversity, migration could also threaten 70% of the resident flora. Future expansions of the protected area network should ensure strong elevational connections, even those that span borders.

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“…Taxonomic assignment of OTUs was performed by comparison with a custom-made reference database including trnL DNA sequences for most of the Alpine seed plants (Spermatophyta). This local database was built starting from a previously developed trnL database (Leontidou et al, 2018), which was focused on the flora of a southeastern Italian Alpine region, subsequently complemented with public sequences (NCBI GenBank database; National Center for Biotechnology Information, www.ncbi.nlm.nih.gov/ genbank) for the other most frequent species of the Alpine flora (Aeschimann et al, 2004).…”

Section: Bioinformatics Analysis and Post-processing Of Metabarcoding...mentioning

confidence: 99%

Ancient DNA from speleothems: opportunity or challenge?

Marchesini

Festi²,

Girardi³

et al. 2022

Quat. res.

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Ancient environmental DNA retrieved from sedimentary records (sedaDNA) can complement fossil-morphological approaches for characterizing Quaternary biodiversity changes. PCR-based DNA metabarcoding is so far the most widely used method in environmental DNA studies, including sedaDNA. However, degradation of ancient DNA and potential contamination, together with the PCR amplification drawbacks, have to be carefully considered. Here we tested this approach on speleothems from an Alpine cave that, according to a previous palynomorphological study, have shown to contain abundant pollen grains. This offers a unique opportunity for comparing the two methods and, indirectly, trying to validate DNA-based results. The plant taxa identified by sedaDNA are fewer than those by pollen analysis, and success rate of PCR replicates is low. Despite extensive work performed following best practice for sedaDNA, our results are suboptimal and accompanied by a non-negligible uncertainty. Our preliminary data seem to indicate that paleoenvironmental DNA may be isolated from speleothems, but the intrinsic weakness of PCR-based metabarcoding poses a challenge to its exploitation. We suggest that newly developed methods such as hybridization capture, being free from PCR drawbacks and offering the opportunity to directly assess aDNA authenticity, may overcome these limitations, allowing a proper exploitation of speleothems as biological archives.

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Flora Alpina: Atlas des 4500 Plantes Vascularies des Alpes

Cited by 17 publications

References 0 publications

Avoiding impacts of phylogenetic tip‐state‐errors on dispersal and extirpation rates in alpine plant biogeography

Avoiding impacts of phylogenetic tip‐state‐errors on dispersal and extirpation rates in alpine plant biogeography

Transnational conservation to anticipate future plant shifts in Europe

Ancient DNA from speleothems: opportunity or challenge?

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