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Background  The Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed.    Methods  Here, we describe a new species of  Scapholeberis  Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene.    Results   Scapholeberis yahuarcaquensis  n. sp. has a combination of characters present in  Scapholeberis kingi  Sars, 1888 and  Scapholeberis armata freyi   Dumont & Pensaert, 1983 . These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between  S. yahuarcaquensis  n. sp. and the closest species  S. freyi  from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on the DNA sequences. New methods of collecting and integrative biology will give important support to recognize the fauna from the Amazon Basin, one of the most important sources of fresh water in the world that remains unknown in many respects.

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A new species of <i>Scapholeberis</i> Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology

A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology