Phylogenetic analysis provides insights into the evolution of Asian fireflies and adult bioluminescence

• Published in: Molecular phylogenetics and evolution 2019-11, Vol.140, p.106600-106600, Article 106600
• Main Authors: Chen, Xing, Dong, Zhiwei, Liu, Guichun, He, Jinwu, Zhao, Ruoping, Wang, Wen, Peng, Yanqiong, Li, Xueyan
• Format: Article
• Language: English
• Subjects: Animals; Asian fireflies; DNA, Ribosomal - genetics; Fireflies - classification; Genes, Mitochondrial; Genetic Variation; High-Throughput Nucleotide Sequencing; Internode certainty; Luminescence; Mitogenomes; Nuclear ribosomal DNA repeat unit; Phylogeny; Reproducibility of Results; Species Specificity; Tree certainty
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2019.106600

Using the genome skimming method, we sequenced and assembled mitochondrial genomes (mitogenomes) and nuclear ribosomal DNA (rDNA) repeat unit of 23 species (Lampyridae: 14 genera in five subfamilies; Rhagophthalmidae: one genus), together with 145 published Elateroidea species, to recover firefly phylogenies with the least tree conflict. We then clarified the phylogenetic position of 10 Asian genera and inferred the adult bioluminescence state of the Lampyridae ancestor. Graphical Figure. Pipeline of firefly phylogeny reconstruction using Next-generation sequencing data and their adult bioluminescent inference. A. We extracted total DNA from fireflies with data less than three Gb in size (i.e., genome skimming method). We then captured small proportional reads mapped to a reference gene available in GenBank. The captured reads allowed effective assembly of longer contigs with only 3–20 iterations (i.e., the by-capture method). Combined with public data, we selected different taxa and coding regions to reconstruct the phylogeny using maximum likelihood (ML) and Bayesian inference (BI) methods. We then adopted tree certainty (TC) and internode certainty (IC) methods to evaluate ML tree conflict to guide re-selection of other combinations of taxa and gene sets. Finally, we inferred the origin of bioluminescence using basic ancestral state reconstruction (ASR). We used ML to calculate the loss and gain rates of bioluminescence, which were verified using the Markov Chain Monte Carlo (MCMC) method. B. Ancestor bioluminescent state of adult was inferred from the 144-species phylogeny using the all-rates-different model. Results showed the common ancestor of Lampyridae had the adult bioluminescent trait, with nine subsequent loss events. [Display omitted] •We reported 22 mitogenomes and 22 nuclear rDNA repeat unit for the first time.•Our firefly phylogeny clarified position of 10 Asian firefly genera.•Our phylogenies recovered the monophyly of each of the three luminous families.•The common ancestor of Lampyridae possessed adult bioluminescence. Fireflies are one of the best-known examples of luminescent organisms. The limited geographic distribution and rarity of some firefly genera have hindered molecular phylogenetic analysis, resulting in uncertainty in regard to firefly phylogeny. Here, using genome skimming next-generation sequencing, we sequenced 23 Asian firefly species from 15 genera (Lampyridae: 14; Rhagophthalmidae: one) and assembled their mitochondria