Synbranchus (swamp eel) specimens exhibiting remarkable variation were collected from different habitats during recent fieldwork in the Xingu Basin, Brazil. For this study, those specimens were first sorted into about six morphotypes based on external morphology, especially color pattern. Representatives of each morphotype and additional specimens extralimital to the Xingu Basin were then sequenced for three mitochondrial genes (ATPase 8/6, 16s, and Cytb) and one nuclear (Rag1). Molecular phylogenetic analyses using Maximum Parsimony and Bayesian methods supported the recognition of five distinct lineages of Synbranchus in the middle to lower Xingu Basin and up to 10 species-level lineages across all samples. Two of the Xingu lineages were subsequently identified as the nominal S. marmoratus and S. madeirae, and another two were provisionally treated as Synbranchus spp. 5 and 7. The fifth lineage is formally described here as Synbranchus royal, distinguished by its extremely pronounced nuchal hump with dorsal head profile distinctly concave and rising steeply from above middle of eye vs. nuchal region moderately bulbous with dorsal profile ascending more gradually, straight or with shallow concavity behind eye (S. marmoratus) or nuchal hump lacking, dorsal profile ascending modestly, straight to scarcely concave behind eye (S. lampreia and S. madeirae); and relatively deep body, maximum depth at middle of TL 4.7–5.4% TL (vs. 3.2–4.8% TL in congeners). Synbranchus royal and Synbranchus sp. 7 were found in rocky rapids of main channels of the middle Xingu on the Brazilian Shield uplands, a sharp departure from the lentic habitats commonly associated with synbranchid (swamp) eels.
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