Over the last few centuries, millions of plant specimens have accumulated within herbaria and biocultural collections. These include type specimens, used to define species, and populations that are rare, extinct or difficult to access. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and become increasingly difficult to characterise their genetic signatures, even considering exponential advancements in sequencing technologies. Here, we tested the genotyping performance on highly degraded samples using a commonly used high-throughput sequencing (HtS) technique, genome skimming, against a recent alternative target capture kit, the universal set Angiosperm-353. We performed phylogenomic analyses of modern leaf and historical barks of Cinchona, including 23 historical barks and six fresh leaf specimens. DNA within historical barks is highly degraded, therefore a customised DNA extraction method was developed before library preparation. We show that sample degradation over time directly impacted the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we find that both approaches generate enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. Within historical barks, the target capture kit is more advantageous than genome skimming in profiling Cinchona species since it was possible to retrieve nuclear and plastid data to infer phylogenies. This study showcases the value of historical samples in genetic studies and paves the way for further experiments across different taxonomic groups with varying levels of genetic variation or hybridisation.

Fungi are a key component of tropical biodiversity. Due to their inconspicuous and largely subterranean nature, they are however usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomies) emerges as the strongest factor in explaining fungal community composition. Naturally open areas – campinas – are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi–plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short-reads can suffice for diversity and community comparison, long-reads add taxonomic precision and have the potential to reveal population diversity.

The assembly of the world’s most biodiverse region, the Neotropics, was traditionally considered the result of long-term environmental stability. Studies gathered during the last decades suggest that environmental “instability” instead, specially the dramatic modifications caused by the uplift of the Andes, was responsible of the Neotropical diversity. Yet a comprehensive understanding has been hindered by a lack of large-scale comparative data across wide phylogenetic and ecological contexts. Here, we evaluate the timing and drivers of Neotropical diversification in a large sample of Neotropical clades: 150 phylogenies (12,524 species) of seed plants and major tetrapods (amphibians, mammals, squamates, and birds). We unveil five trends: (1) biodiversity levels before the Quaternary were comparable (or higher) to those of the present,; (2) half of the clades diversified at constant rates; (3) past environmental variations correlate with diversification changes in 37% of the lineages, but with contrasting responses: (4) birds and mammals diversified extensively during warm periods and global cooling resulted in synchronized slowdowns of diversification; plant diversification generally increased during cooling; and (5) the rise of the Andes mostly impacted amphibians and squamates. Our study suggests that environmental instability over macroevolutionary scales may in fact act as a driving force of Neotropical diversification.