The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles

Abstract

Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.Genes 2020, 11, 181 2 of 17 a sister group of Trachypachidae [17]. Studies on morphology of defense glands [18][19][20] and those on karyotypes [21,22] of some carabid species also contributed to understanding of the phylogeny of Carabidae.Molecular data can be used to address problems when morphological evidence have been conflicting or difficult to interpret. Based on 18S rDNA sequences, Maddison et al. (1999) supported Carabidae (including cicindelines, rhysodines and paussines) as monophyletic and that Brachinini probably was a sister group to Harpalinae [23]. Their results also assumed Harpalinae, Cicindelinae, Rhysodinae and Paussinae to be closely related to each other. However, their further analyses based on expanding molecular data (18S rDNA, 28S rDNA and wingless gene) recovered Carabidae as non-monophyletic, with respect to the trachypachid beetles [24]. Gough et al. (2019) recovered Cicindelinae as a sister group to the subfamily Rhysodinae, and placed the tribe Megacephalini nested within Platychilini in Cicidelinae [25]. Maddison et al. (2019) inferred the phylogeny of the supertribe Trechitae based on two nuclear ribosomal genes (18S rDNA and 28S rDNA) and four nuclear protein-coding genes (wingless gene, carbamoyl phosphate synthetase domain of the rudimentary gene, arginine kinase gene and muscle-specific protein 300 gene) [26]. In addition, some molecular studies had attempted the phylogenetic reconstructions at the genus or subgenus levels (Bembidion: Maddison, 2012; Carabus: Deuve et al., 2012; Ohomopterus: Sota and Vogler, 2003; Pamborus: Sota et al., 2005; Paraphaenops: Ortuño et al., 2017; Pterostichus: Sasakawa and Kubota, 2007) [27-32]. Recent studies on the suborders of Coleoptera or on the whole Coleoptera phylogeny also involved the exemplars of Carabidae. Hunt et al. (2007) [33] suggested that the monophyletic Geadephaga (comprising Trachypachidae, Rhysodidae...

Illumina Short-Read Sequencing of the Mitogenomes of Novel Scarites subterraneus Isolates Allows for Taxonomic Refinement of the Genus Scarites Fabricius 1775, within the Carabidae Family

“…The overall mitogenome sequence had an average nucleotide composition of A = 41%, T = 38%, C = 13%, and G = 8%. This high AT percentage (79%) is similar to what has been seen in other Carabidae mitogenomes [22]. A very similar genomic organization was found for the Arkansas species (Table S1 and Figure 3B), with an identical total of 37 genes, with 13 coding sequences (CDS), 2 rRNA genes, and 22 tRNAs.…”

“…All protein coding genes start with the typical ATN codons, except for cox1, which was initiated with an unconventional TCG start codon. Unconventional start codons for cox1 have been observed in other insect species as well [22,40,41]. All protein coding sequences use either TAA or TAG stop codons.…”

“…Unfortunately, there is only limited molecular data available for Scarites, and for the Scaritinae subfamily in general. Molecular DNAbased phylogenetic studies typically rely on ribosomal RNA sequences or mitogenomes (or a combination thereof) [16,17,[20][21][22]. However, the use of these in taxonomic placement of the Scarites species has been hampered due to the lack of available data.…”

Convergent evolution of specialized generalists: Implications for phylogenetic and functional diversity of carabid feeding groups

“…However, our phylogenetic reconstruction placed the generalist carnivore Abax parallelepipedus as a sister taxon to all Harpalinae. This position is questionable since the genus is well known to be a member of the Pterostichini (Li, Li, Song, Tang, & Yin, 2020) and might be a result of the very limited data, with only one sequence available for this species. Collembolan specialists belong to three tribes, each forming monophyletic groups with other feeding groups: Loricerini, Nebrini, and Notiophilini.…”

Diversity of Geadephaga (Coleoptera: Carabidae and Cicindelidae) in Colombia: an approach from existing literature

“…Geadephaga, the group of terrestrial Adephaga formed by Carabidae (ground beetles), Cicindelidae (tiger beetles) and Trachypachidae, with about 40 000 described species worldwide, represents nearly 10 % of the species so far described in the order Coleoptera (Bouchard et al, 2017;. Within this monophyletic group (López-López & Vogler, 2017), the position of tiger beetles is still under debate, whether as Cicindelidae at family rank (López-López & Vogler, 2017;Duran & Gough, 2020) or as Cicindelinae within Carabidae (Gough et al, 2019;Li et al, 2020). In this study, we provisionally placed tiger beetles at family rank without prejudice to future advances in genomic studies, because in most studies they have been treated separately from ground beetles.…”