Understanding the Biogeographic Scope of Next-Generation Sequencing Methods in Genomic Studies of Montane Taxa

Aim: Next-generation sequencing has become a powerful tool for increasing the robustness and reliability of phylogeographic analyses. However, it is unclear how much the use of these techniques has grown quantitatively, and to what extent their use has been equitably distributed among regions. Heterogeneous access to and use of these tools could perpetuate knowledge gaps, especially in the tropics. In this study, we used bibliometric methods and piecewise structural equation modelling to explore the influence of factors that have been hypothesized to explain variation in the rate of publication of genomic studies using second-generation molecular markers.Location: Neotropical Montane Forests.Time period: Studies published between 2013 and 2024.Taxon: Montane taxa.Methods: After a careful systematic review of published genomic studies using three search engines following a PRISMA workflow, we detected 69 papers that used next-generation sequencing techniques on highland species. We then fit a theoretical path model consisting of six piecewise structural equations (generalized least squares) to explore factors that affect the publication of studies using novel sequencing techniques, and thus their biogeographic scope. After eliminating non-significant paths, the final path model consisted of four equations.Results: The most represented taxonomic group among genomic studies of highland taxa were birds and plants, and certain biogeographic provinces (e.g., the Transmexican Volcanic Belt) were more studied than others. The most utilized technique was ultraconserved elements. The piecewise structural equation model showed that the biogeographic scope of high-throughput sequencing methods was limited by social and distance-based drivers related to sequencing methods, researchers, and the taxa and biogeographic provinces they study. Additionally, the number of participating nations had an important influence on the biogeographic scope of second-generation sequencing tools.Main conclusions: Our findings suggest that there are external constraints on the use of next-generation molecular techniques that limit phylogeographic inferences. Science is increasingly collaborative, both in terms of the number of researchers and the number of countries contributing to phylogenetics and phylogeography. Hopefully, the knowledge gaps detected in this synthesis will guide future studies in the Neotropics and lead to more equitable and collaborative use of novel methods among biogeographers and systematists.