Abstract The Neotropical harvestman family Stygnidae, with its unique morphology and remarkable diversity, has long attracted taxonomic attention, yet its internal relationships and the traditional morphology‐based classification system remain largely untested by molecular data. Here, we use ultraconserved element loci from both fresh and historical specimens, together with a gigamatrix that integrates legacy marker data, to reconstruct a first family‐wide phylogenomic framework for Stygnidae. We recover a well‐supported Stygnidae clade comprising six main lineages. Although phylogenetic conflict driven by severe incomplete lineage sorting (ILS) at the short deep internodes complicates the definitive resolution of basal relationships, the classical division into two subfamilies is not supported in our downstream analyses. Instead, our results favour a three‐clade system consisting of Stygninae, Heterostygninae and Auraninae subfam. nov ., with the latter two forming a sister clade: (Stygninae, (Heterostygninae, Auraninae subfam. nov.)). Considering the potential homoplasy observed in traditional external traits, we integrated our molecular topology with a comprehensive examination of male genitalic morphology, proposing an updated classification of the three subfamilies and formally redefining the diagnostic characters for each. Furthermore, the gigamatrix analysis increases generic coverage, allowing us to resolve the phylogenetic placement of additional genera and provide robust molecular support for recent morphology‐based taxonomic revisions within the family. From an evolutionary perspective, the overall phylogenetic pattern suggests a possible Northern Amazonian origin of Stygnidae, while the presence of short deep internodes and long terminal branches may be indicative of an ancient rapid diversification in the Neotropics. The contrasting phylogenetic placements of small‐sized stygnid lineages could reflect either repeated evolution of miniaturization or the persistence of a small‐bodied ancestral morphology, although these alternatives will require further testing. By providing a stable phylogenetic framework, this study offers a basis for broader investigations of morphological and biogeographic evolution in these distinctive Neotropical harvestmen.
Kim et al. (Wed,) studied this question.