Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.

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Large‐bodied frugivorous birds play an important role in dispersing large‐sized seeds in Neotropical rain forests, thereby maintaining tree species richness and diversity. Conversion of contiguous forest land to forest fragments is thought to be driving population declines in large‐bodied frugivores, but the mechanistic drivers of this decline remain poorly understood. To assess the importance of fragment‐level versus local landscape attributes in influencing the species richness of large‐bodied (>100 g) frugivorous birds, we surveyed 15 focal species in 22 forest fragments (2.7 to 33.6 ha, avg. = 16.0 ha) in northwest Ecuador in 2014. Fragment habitat variables included density of large trees, canopy openness and height, and fragment size; landscape variables included elevation and the proportion of tree cover within a 1 km radius of each fragment. At both the individual species level, and across the community of 12 species of avian frugivore we detected, there was higher richness and probability of presence in fragments with more tree cover on surrounding land. This tendency was particularly pronounced among some endangered species. These findings corroborate the idea that partially forested land surrounding fragments may effectively increase the suitable habitat for forest‐dwelling frugivorous birds in fragmented landscapes. These results can help guide conservation priorities within fragmented landscapes, with particular reference to retaining trees and reforesting to attain high levels of tree cover in areas between forest patches.

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