Integrating Phylogenomics and Biogeography of Spectracanthicus (Siluriformes: Loricariidae) Reveals Complex Evolutionary History in a Brazilian Shield Endemic Genus

ABSTRACT Loricariidae is the most diverse catfish family in the Neotropics. Within this group, the genus Spectracanthicus presents conflicting phylogenetic signals: morphological studies suggest monophyly, whereas previous molecular analyses often yield unresolved relationships and taxonomic uncertainty. To address these discrepancies, we applied an integrative framework combining ultraconserved elements (UCE) phylogenomics, morphological comparisons of all valid Spectracanthicus species, and biogeographic reconstruction. Our analyses, based on 2215 UCE loci, recover Spectracanthicus as a monophyletic clade within Spectracanthicini under concatenated inference. Conversely, coalescent‐based analyses yielded a conflicting but strongly supported topology, highlighting persistent gene tree discordance. Ancestral range estimation identified the Xingu River basin as the probable ancestral area for the genus, with crown diversification beginning near the Miocene–Pliocene boundary (~4.2 Ma) and extending into the Pleistocene (~2.4–1.0 Ma). Model comparisons strongly favoured founder‐event speciation; however, given the restrictive ecology of these rheophilic fishes, we interpret this signal as passive allopatric isolation rather than active colonization. Lineage diversification was primarily driven by episodic, transient connectivity via headwater captures among adjacent Brazilian Shield drainages (Xingu, Tapajós and Tocantins–Araguaia). This timeline coincides with the Neogene geomorphological remodelling and progressive incision of shield tributaries driven by the establishment of the transcontinental Amazon River, whereas recent divergences were likely shaped by Pleistocene climate‐induced habitat fragmentation. Although coalescent and concatenated analyses recovered conflicting topologies, the combined evidence from phylogenomics and morphology supports the current systematic interpretation of Spectracanthicus .