Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Abstract

Accurate identification is essential for any study exploring biodiversity. Unfortunately, museum type specimens preserved for more than a hundred years are often not informative enough for precise identification of the species represented by the name-bearing type. The use of ancient DNA can help solve taxonomic problems when name-bearing types no longer have diagnostic morphological features that allow for an accurate identification of the species involved. That is the case for Deuterodon pedri, an endemic species from a small drainage in the rio Doce basin in Minas Gerais, Brazil, for which the type material is in poor condition. Specimens of D. pedri were collected in 1865 by the Thayer Expedition to Brazil and fixed in spirits, enabling them to yield viable DNA. As the morphology alone of the type material does not allow for an accurate identification, we used both morphological and ancient DNA (aDNA) methods to decisively establish the identity of D. pedri. This identification allowed us to recognize the species among recently collected specimens and then, based on them, redescribe the species. A genetype for the lectotype of D. pedri is presented.Keywords: Lectogenetype, Mini-Barcode, Primers, Rio Doce, Thayer Expedition.Uma identificação acurada é fundamental para qualquer estudo que explora a biodiversidade. Infelizmente, espécimes de museu descritos há mais de cem anos, algumas vezes não são informativos o suficiente para uma identificação precisa da espécie representada pelo tipo. O uso de DNA antigo pode ajudar a resolver problemas taxonômicos, quando espécimes tipos não apresentam mais as características morfológicas diagnósticas que permitem a identificação precisa das espécies. Esse é o caso de Deuterodon pedri, uma espécie endêmica de uma pequena drenagem na bacia do rio Doce, em Minas Gerais, Brasil cujo material tipo encontra-se em condições precárias. Espécimes de D. pedri foram coletados em 1865 pela Expedição Thayer ao Brasil e fixados em "cachaça", o que permite apresentar DNA viável. Como apenas o exame morfológico do material tipo não permitiria a identificação precisa, nós usamos ambos os dados de análises morfológicas e DNA antigo (aDNA) para estabelecer decisivamente a identidade de D. pedri. Esta identificação permitiu reconhecer a espécie entre exemplares coletados recentemente e, com base neles, redescrever a espécie. É apresentado um genetipo para o lectótipo de D. pedri.

Mining museums for historical DNA: advances and challenges in museomics

“…The recognition that hDNA allows for sampling extinct species (e.g., [24][25][26][27]) and extirpated populations (e.g., [28]), as well as improving taxonomic coverage (e.g., [29]), has been borne out in new work (Table 2). Recent hDNA studies have helped to discover and delimit species (e.g., [27,30]), resolve phylogenetic relationships and investigate convergent evolution [31], infer biogeographic history [7], document genetic erosion in populations [9,32], clarify taxonomic confusion with type specimens [33][34][35][36], and investigate epigenetic effects such as cytosine methylation [37]. Historical specimens have also been used to pinpoint the biogeographic origins of domesticated crops, which often have highly complex anthropogenic histories.…”

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

“…For example, genetic data from museum specimens has been used to track temporal and spatial changes in species distributions (Lozier & Cameron 2009), investigate population genetics (Spurgin et al 2014;Schmid et al 2018), and evaluate conservation implications (Anco et al 2018;Brandt et al 2018). Additionally, accessing molecular sequence data from natural history collections may be an invaluable resource for resolving taxonomic questions (Cappellini et al 2014), including generating genetic data from type specimens (Hawksworth 2013;Silva et al 2017;McGuire et al 2018). Furthermore, DNA from historical museum specimens can provide novel insights into ambiguously identified collections (Chambers & Hebert 2016).…”

Comparison and optimization for DNA extraction of archived fish specimens

“…In taxonomy, the use of aDNA has been a powerful tool for solving problems wherein the type specimens, usually very old, no longer preserve diagnostic features for species identification [3,4]. However, the DNA extracted from this kind of sample is usually little and highly fragmented, restricting the success of further applications.…”