Lost biodiversity in the genomic age: contributions from historical DNA to the systematics of rare and extinct frogs

• Grant number: 22/02789-0
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: August 01, 2022
• Status: Discontinued
• Field of knowledge: Biological Sciences - Zoology - Taxonomy of Recent Groups
• Principal Investigator: Taran Grant
• Grantee: Daniel Yudi Miyahara Nakamura
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 18/15425-0 - A multi-disciplinary approach to the study of amphibian diversification: phase 2, AP.JP2
• Associated scholarship(s): 24/03494-9 - Methodological advances in museomics and dynamic homology: Integrating assembly of historical DNA reads and tree-alignment, BE.EP.DD

Abstract

Amphibians are the most threatened group of vertebrates. As a result of its global decline, many species collected in the past are currently rare or even extinct. Although the so-called lost frogs are preserved in museums, they are usually ignored in molecular phylogenies due to the lack of fresh tissues to DNA sequencing. Owing to cumulative post-mortem damages (high fragmentation and contamination rates, low endogenous content, and base modifications such as cytosine deamination), historical DNA from formalin-fixed type specimens (hDNA) was hardly sequenced with PCR and Sanger sequencing. Recently, these limitations have been overcome using single-stranded DNA preparations, enzymatic treatments, clean laboratory, and Next-Generation Sequencing (NGS) that generates millions of short reads, which are subsequently assembled in silico. Here we will use NGS (Illumina HiSeq) to sequence hDNA from partial nuclear and mitochondrial genomes of 60 species of neotropical lost frogs, including historical specimens of Centrolenidae, Dendrobatidae, Hylidae, Hylodidae, and Phyllomedusidae. We carefully selected these groups due to (I) the higher affordability in obtaining tissues of type specimens and (II) the potential to elucidate challenging problems of species identity and phylogenetic position of neotropical historical specimens never included in molecular phylogenies, which otherwise could not be performed only with phenomic data. This project will provide a large amount of molecular data from type specimens of rare and extinct frogs for the first time in Brazil, which is an innovative advance in amphibian systematics. (AU)

Scientific publications

(4)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

NAKAMURA, DANIEL Y. M.; ORRICO, VICTOR G. D.; DA SILVA, ESDRAS M. G.; LYRA, MARIANA L.; GRANT, TARAN. Museomics reduces taxonomic inflation in the Dendropsophus araguaya complex (Hylinae: Dendropsophini) from the Cerrado. JOURNAL OF VERTEBRATE BIOLOGY, v. 74, p. 18-pg., 2025-02-01. (18/15425-0, 24/03494-9, 12/12500-5, 22/02789-0, 21/10639-5)

NAKAMURA, DANIEL YUDI MIYAHARA; KOFFLER, SHEINA; MELLO, MARCO AURELIO RIBEIRO; FRANCOY, TIAGO MAURICIO. Resin foraging interactions in stingless bees: an ecological synthesis using multilayer networks. Apidologie, v. 55, n. 3, p. 19-pg., 2024-06-01. (23/02881-6, 18/14994-1, 22/02789-0, 19/26760-8, 18/20695-7)

NAKAMURA, DANIEL YUDI MIYAHARA; ESCALONA, MOISES; PINHEIRO, PAULO DURAES PEREIRA. Body size, habitat, and sexual selection affect call evolution in Cophomantini treefrogs (Anura: Hylidae: Hylinae). Biological Journal of the Linnean Society, v. N/A, p. 18-pg., 2024-03-23. (18/15425-0, 22/02789-0, 18/18473-6, 21/13764-5)

ESCALONA, MOISES; SIMOES, PEDRO IVO; GONZALEZ-VOYER, ALEJANDRO; MENDOZA-HENAO, ANGELA M.; MELLO BEZERRA, ANDRESSA DE; PINHEIRO, PAULO D. P.; MORALES, BELEN; GUAYASAMIN, JUAN M.; CARVALHO, THIAGO; CHAPARRO, JUAN C.; et al. Allometric Constraint Predominates Over the Acoustic Adaptation Hypothesis in a Radiation of Neotropical Treefrogs. Integrative Zoology, v. N/A, p. 11-pg., 2024-12-10. (18/18473-6, 22/02789-0)