Escobari, B. | Search bioRxiv

bioRxiv2025

Utilizing large language models to construct a dataset of Württemberg's 19th-century fauna from historical records

Constructing datasets on past biodiversity from historical sources is crucial for understanding long-term ecological changes. Typically, compiling such datasets relies on prior knowledge of the sources composition and requires considerable manual effort. To overcome these challenges, we implement an automated approach based on prompted large language models (LLMs) to detect mentions of species in texts from 19th-century Wurttemberg and link these mentions to identifiers in the GBIF database. Based on our evaluation, we find that LLMs can reliably identify species in the texts with high recall (92.6%) and precision (95.3%), while providing estimates of the correct species identifier with considerable accuracy (83.0%).

ecology↗

bioRxiv2021

Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

PREMISEThe genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. METHODSWe sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. RESULTSOur results indicate that the inclusion of all plastid genome partitions is needed to infer fully resolved phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. CONCLUSIONSThe concatenation and combined analysis of all plastid genome partitions and the construction of manually curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of strongly supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence datasets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

plant biology↗