The Genetic Diversity and the Divergence Time in Extant Primitive Mayfly, Siphluriscus chinensis Ulmer, 1920 Using the Mitochondrial Genome

Abstract

In this study, the mitochondrial (mt) genomes of Siphluriscus chinensis (Ephemeroptera: Siphluriscidae) were evaluated in specimens collected from two sites in China: Niutou Mountain, Zhejiang Province (S. chinensis NTS) and Leigong Mountain, Guizhou Province (S. chinensis LGS) and were successfully sequenced. The lengths of the mt genomes of S. chinensis NTS and S. chinensis LGS were 15,904 bp (ON729390) and 15,212 bp (ON729391), respectively. However, an in-depth comparison of the two mt genomes showed significant differences between the specimens collected from the two sites. A detailed analysis of the genetic distance between S. chinensis NTS and S. chinensis LGS was undertaken to further achieve an accurate delimitation of S. chinensis. The genetic distance between S. chinensis NTS and the other three species within Siphluriscidae was a high value, above 12.2%. The two mt genomes were used to reconstruct phylogenetic relationships and estimate divergence time. The results demonstrated robust differences between S. chinensis NTS and S. chinensis LGS, which revealed that a kind of cryptic species existed. Maximum likelihood (ML) and Bayesian inference (BI) analyses produced well-supported phylogenetic trees that showed evolutionary relationships between Siphluriscidae (((S. chinensis HQ875717 + S. chinensis MF352165) + S. chinensis LGS) + S. chinensis NTS). The most recent common ancestor (MRCA) of four species within Siphluriscidae began to diversify during the Neogene [11.80 million years ago (Mya); 95% highest posterior densities (HPD) = 6.17–19.28 Mya], and S. chinensis NTS was first to diverge from the branches of S. chinensis LGS. In short, based on mitochondrial genomes, our results showed that the specimens collected from Leigong Mountain, Guizhou Province (S. chinensis LGS) belonged to S. chinensis, and the specimens collected from Niutou Mountain, Zhejiang Province (S. chinensis NTS) were a cryptic species of S. chinensis.

Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera)

“…Both trees supported that Isonychiidae diverged next to Siphluriscidae, a result that was also supported by Cao et al and Xu et al in reconstructing the phylogenetic relationships of Ephemeroptera based on the 13 PCGs [76,109], but Baetidae was supported as the sister clade to other families of mayflies, excluding Siphluriscidae [24]. Teloganodidae was clustered with Baetidae, which was consistent with other research [26,57,76,77], but this result may have been caused by the long branch attraction. Both trees recovered the monophyly of Potamanthidae and suggested a relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae), which was consistent with Wang et al [25].…”

“…Thereafter, based on over 400 targeted genomic protein coding regions, Odgen et al suggested that Potamanthidae was the sister clade of all remaining burrowing mayflies [24], and this result was consistent with the work of Miller et al [14]. In recent years, Wang et al supported the phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae), whereas Tong et al suggested the phylogenetic relationship of (Potamanthidae + Ephemeridae) + Polymitarcyidae [25,26]. Of note, most researchers have been involved in morphological studies and other aspects of Potamanthidae rather than molecular research [11,[27][28][29][30][31].…”

“…Eighty mt genomes were used for phylogenetic relationship analyses, including the 7 mt genomes newly reported in this paper, and 73 mt genomes downloaded from the NCBI for Ephemeroptera in 15 families (Baetidae, Heptageniidae, Neoephemeridae, Leptophlebiidae, Isonychiidae, Ephemerellidae, Ephemeridae, Viemamellidae, Potamanthidae, Caenidae, Siphluriscidae, Polymitarcyidae, Ameletidae, Siphlonuridae, and Teloganodidae) [26,43,51,[70][71][72][73][74][75][76][77][78][79][80][81][82][83]. Siphluriscidae is typically regarded as occupying a basal position within the Ephemeroptera [82,84].…”

Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species

“…Many tick species share great morphological similarities and therefore group into species complexes until differentiating characters can be described [ 22 ]. The mitochondrial genome (mitogenome) is a reliable marker for cryptic species identification, phylogenetic studies, and population genetics analysis, and has been widely used in animals [ 23 , 24 , 25 , 26 , 27 , 28 ], including in ticks [ 7 , 21 , 29 ]. In recent years, the number of sequenced mitogenomes of Ixodidae species has increased significantly, but the mitogenome studies on parasitic ticks of giant pandas have only been performed for three Haemaphysalis species [ 30 , 31 , 32 ].…”

The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes

“…There are 38,874 described species of Cerambycidae (Coleoptera: Polyphaga) to date, according to the "Titan database about Cerambycidae" (http://titan.gbif.fr/sel_sous_famille.php, accessed on pha using PCGs, tRNA, and rRNA genes of mitochondrial genomes [28]. Additionally, mitochondrial genomes have also been used as molecular markers in the phylogeny of Mantodea [29,30], Phasmatodea [31,32], Archaeognatha [33], Ephemeroptera [34], etc., with remarkable results.…”