title: Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.
abstract: BACKGROUND
  Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatus wenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome.
  
  
  RESULTS
  The eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes). Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus.
  
  
  CONCLUSIONS
  Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing, 100048, China. qinjie0912@163.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Qin
authors.affiliation: Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, P.R. China. zhangyz@ioz.ac.cn.
authors.forename: Yanzhou
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: China National GeneBank, BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, China. xinzhou@genomics.cn.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry Administration, No.1 Dongxiaofu, Haidian, Beijing, China. kongxbo@hotmail.com.
authors.forename: Xiangbo
authors.initials: X
authors.lastname: Kong
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. shujun268@163.com.
authors.forename: Shujun
authors.initials: S
authors.lastname: Wei
authors.affiliation: CSIRO Oceans and Atmosphere Flagship, GPO Box 1538, Hobart, Tasmania, 7001, Australia. Bob.Ward@csiro.au.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Ward
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing, 100048, China. zhangab2008@mail.cnu.edu.cn.|College of Life Sciences,Capital Normal University, Beijing, 100048, P. R. China. zhangab2008@mail.cnu.edu.cn.
authors.forename: Ai-bing
authors.initials: AB
authors.lastname: Zhang
mesh_terms: D000818:Animals; D020137:Base Pair Mismatch; D002681:China; D018387:Codon, Initiator / Q000235:genetics; D004272:DNA, Mitochondrial / Q000032:analysis / Q000302:isolation & purification; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D008928:Mitochondria / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000235:genetics / Q000378:metabolism; D009036:Moths / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D018387:Codon, Initiator; D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins; D012336:RNA, Ribosomal, 16S; D012343:RNA, Transfer