The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes

Abstract

With efficient sequencing techniques, full mitochondrial genomes are rapidly replacing other widely used markers, such as the nuclear rRNA genes, for phylogenetic analysis but their power to resolve deep levels of the tree remains controversial. We studied phylogenetic relationships of leaf beetles (Chrysomelidae) in the tribes Galerucini and Alticini (root worms and flea beetles) based on full mitochondrial genomes (103 newly sequenced), and compared their performance to the widely sequenced nuclear rRNA genes (full 18S, partial 28S). Our results show that: (i) the mitogenome is phylogenetically informative from subtribe to family level, and the per‐nucleotide contribution to nodal support is higher than that of rRNA genes, (ii) the Galerucini and Alticini are reciprocally monophyletic sister groups, if the classification is adjusted to accommodate several ‘problematic genera’ that do not fit the dichotomy of lineages based on the presence (Alticini) or absence (Galerucini) of the jumping apparatus, and (iii) the phylogenetic results suggest a new classification system of Galerucini with eight subtribes: Oidina, Galerucina, Hylaspina, Metacyclina, Luperina, Aulacophorina, Diabroticina and Monoleptina.

Higher‐level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences

“…The DNA from all 46 samples was pooled in approximately equal concentrations and four Illumina TruSeq libraries were prepared with an average insert size of 450 bp (following Gillett et al, 2014;Nie et al, 2017). Each library was sequenced using the Illumina Hiseq2500 platform at BerryGenomics (China) with 250-bp paired-end reads setting.…”

“…The site-heterogeneous CAT model implemented in phylobayes is a Dirichlet process mixture of profiles of equilibrium frequencies combined with general exchange rates (Lartillot et al, 2009). Recent studies have shown CAT-based models reduce the susceptibility of analyses to long-branch attraction, resulting in more robust topologies (Lartillot et al, 2009;Li et al, 2015Li et al, , 2017Timmermans et al, 2015;Feuda et al, 2017;Nie et al, 2017;Liu et al, 2018).…”

How many genera and species of Galerucinae s. str. do we know? Updated statistics (Coleoptera, Chrysomelidae)

“…(see e.g., Wilcox 1975; Medvedev 2012; Lee et al 2016). However, its position is still questionable (Nie et al 2017). …”

“…1). Among these tree hypotheses, a sister group relationship of Galerucinae and Alticinae was supported by the most molecular or morphological analyses (Seeno and Wilcox 1982; Doguet 1994; Farrell 1998; Gómez-Zurita et al 2007; Hunt et al 2007; Bouchard et al 2011; Ge et al 2011, 2012; Nie et al 2017). Some of the recently established groupings, based on DNA sequences, still need further in-depth analysis because they are phylogenetically and biogeographically incomplete (Biondi and D´Alessandro 2012).…”

“…Some genera are called “problematic genera” with the presence or absence of a MET and not fitting other characters. Recently, some researchers found that the MET may have multiple origins, evolving at least two or three times (Ge et al 2011; 2012; Nie et al 2017). …”