EXAMPLE 1: Lujan, N.K., J. Armbruster, N. Lovejoy, and H. López-Fernández. 2015. Multilocus molecular phylogeny of the Loricariidae (Pisces: Siluriformes) with a focus on subfamily Hypostominae. Molecular Phylogenetics and Evolution 82A:269–288.
Despite dozens of morphology and DNA based phylogenies of the Loricariidae, our understanding of the evolutionary history of this highly diverse and ecologically and commercially important family remains quite coarse. In 2015 I published the first comprehensive, genus-level molecular phylogeny for the Hypostominae, the most morphologically and taxonomically diverse subfamily of the Loricariidae. This study revealed the need for widespread systematic revision and dramatically changed our understanding of the family's morphological, ecological and biogeographic diversification. Specializations for eating wood, for example, were thought to have originated only twice based on phylogenies inferred from morphological traits, whereas molecular data strongly support a third independent origin. Also highly apparent in the molecular phylogeny is an abundance of Guiana Shield endemic clades and lineages, supporting the geologically ancient highlands of northern South America as an important region for the family's early diversification. This phylogeny is now being used with a variety of comparative methods to investigate morphological, ecological and biogeographical diversifications within the Loricariidae. I am also conducting combined analyses of molecular and morphological datasets with the goal of identifying morphological synapomorphies that can serve as the basis of a revised taxonomy. More taxonomically comprehensive species-level phylogenetic studies of several subclades are also in preparation or already in press (see below), as is a complete revisitation of results for the entire family using a NGS, targeted sequence capture approach.
EXAMPLE 2: Lujan, N.K., V. Meza-Vargas, V. Astudillo-Clavijo, R. Barriga-Salazar, H. López-Fernández. 2015. Multilocus molecular phylogeny for Chaetostoma Clade genera and species with a review of Chaetostoma (Siluriformes: Loricariidae) from the central Andes. Copeia 103:664–701.
Commonly known as the 'rubber-nosed plecos' because of their distinctively fleshy, unarmored snout, species in the genus Chaetostoma are common, locally abundant, and broadly distributed along the flanks of the Andes Mountains from Panama to Southern Peru. They are fished for food throughout their range and some species are commercially harvested for the aquarium fish hobby. With 47 valid species, this genus is the third most species-rich in Loricariidae, yet our knowledge of species interrelationships and boundaries has historically been very poor. Many species have not been studied since their original descriptions over a century ago. Since 2010, I have conducted comprehensive, systematic research on Chaetostoma, including field work to revisit type localities and take live color photographs (a first for many species), standardized collection of meristic and morphometric data, and generation of a species-level, multi-locus molecular phylogeny. Two papers on members of this genus and closely related genera from the Ecuadorian Andes have recently been published.
EXAMPLE 3: Lujan, N.K., C.A. Cramer, H. López-Fernandez. in prep. Evolutionary relationships and biogeographical patterns within the ornamental wood-eating genera Panaqolus and Panaque (Siluriformes, Loricariidae), with descriptions of four new taxa.
Panaque schaeferi Lujan et al. 2010
Wood-eating fishes are not only ecologically intriguing, they are also incredibly popular among aquarium fish hobbyists because of their bold colors, curious behaviors and bizarre morphologies. For this study of interspecific relationships within two genera of ornamental wood-eating loricariids, we sampled broadly across specimens being exported from South America for the aquarium fish trade. To our amazement, results revealed that species-level diversity within one genus (Panaqolus) exceeds the diversity recognized by current taxonomy by over 300%.