title: Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences.
abstract: Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of 'traditional markers' (e.g. mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small, and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support >95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the 'traditional markers', and show great potential to expedite resolution of many parts in the Beetle Tree of Life.
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Li-Heng
authors.identifier: http://orcid.org/0000-0001-8358-5574
authors.initials: LH
authors.lastname: Che
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Shao-Qian
authors.initials: SQ
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Pang
authors.affiliation: Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia.
authors.forename: Adam
authors.initials: A
authors.lastname: Ślipiński
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, Guangdong Province, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001517:Coleoptera / Q000145:classification* / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D049750:Genome, Insect; D009687:Nuclear Proteins / Q000235:genetics*; D010802:Phylogeny
chemical_list: D005819:Genetic Markers; D009687:Nuclear Proteins
keywords: coccinellidae; coleoptera; exons; phylogenomics; phylogeny; primers