Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes

Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order in the world following Coleoptera and Diptera, Lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such a charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly resolved. Compared to earlier phylogenomic studies, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa) and acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling with significant increases in the number of included genes on tree topology by considering a series of systematic errors using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias giving rise to unstable positions of ditrysian groups in phylogenomic reconstruction. Phylogenetic inference showed the most comprehensive framework to reveal the relationships among lepidopteran superfamilies, and presented some newly relationships with strong supports (Papilionoidea was sister to Gelechioidea and Immoidea was sister to Galacticoidea, respectively), but limited by taxon sampling, the relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly resolved, which need to increase taxon sampling for further phylogenomic reconstruction. The present study demonstrates that taxon sampling is an important determinant for an accurate lepidopteran tree of life and provides some essential insights for future lepidopteran phylogenomic studies.

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae)

Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.

Isolation and phylogenetic analysis of a new Porcine parvovirus strain GD2013 in China

Porcine parvovirus (PPV), a causative agent of an infectious reproductive disorder causing stillbirth, mummification, embryonic death and infertility (SMEDI) syndrome in swine, is a threat to both domestic pigs and wild boars regardless of age and gender. Recent studies found that the observed average substitution rate in the PPV genome was close to those of the RNA viruses and new strains showing serological neutralization activities different from that of the vaccine strain NADL-2 have been reported. These observations have increased the need for the development of new commercial vaccine strains. In this study, a new PPV strain, GD2013, was isolated from Guangdong, China, and its entire genome sequenced. A phylogenetic tree based on the complete coding region of the genomes of 32 PPV strains was constructed using the Bayesian Markov Chain Monte Carlo (MCMC) method. The results showed that strain GD2013 fell into the same phylogenetic cluster as the classical vaccine strains NADL-2 and POVCAP, suggesting a close relationship to the vaccine strains. Multiple sequence alignments and amino acid mutation analyses of the PPV VP2 gene revealed a new amino acid polymorphism site at Thr45 on VP2 that could be used to identify low virulence strains as vaccine candidates. Selective pressure analysis of the NS1 and VP2 genes by calculating the mean rates of non-synonymous substitutions (dN) over synonymous substitutions (dS) implied that both of these genes were under negative selection. Therefore, by using phylogenetic and amino acid mutation analyses, a likely candidate strain suitable for evaluation as an attenuated vaccine strain was identified.