Phylogenetic position of a whale-fall lancelet (Cephalochordata) inferred from whole mitochondrial genome sequences

Abstract

BackgroundThe lancelet Asymmetron inferum (subphylum Cephalochordata) was recently discovered on the ocean floor off the southwest coast of Japan at a depth of 229 m, in an anaerobic and sulfide-rich environment caused by decomposing bodies of the sperm whale Physeter macrocephalus. This deep sulfide-rich habitat of A. inferum is unique among the lancelets. The distinguishing adaptation of this species to such an extraordinary habitat can be considered in a phylogenetic framework. As the first step of reconstruction of the evolutionary processes in this species, we investigated its phylogenetic position based on 11 whole mitochondrial genome sequences including the newly determined ones of the whale-fall lancelet A. inferum and two coral-reef congeners.ResultsOur phylogenetic analyses showed that extant lancelets are clustered into two major clades, the Asymmetron clade and the Epigonichthys + Branchiostoma clade. A. inferum was in the former and placed in the sister group to A. lucayanum complex. The divergence time between A. inferum and A. lucayanum complex was estimated to be 115 Mya using the penalized likelihood (PL) method or 97 Mya using the nonparametric rate smoothing (NPRS) method (the middle Cretaceous). These are far older than the first appearance of large whales (the middle Eocene, 40 Mya). We also discovered that A. inferum mitogenome (mitochondrial genome) has been subjected to large-scale gene rearrangements, one feature of rearrangements being unique among the lancelets and two features shared with A. lucayanum complex.ConclusionOur study supports the monophyly of genus Asymmetron assumed on the basis of the morphological characters. Furthermore, the features of the A. inferum mitogenome expand our knowledge of variation within cephalochordate mitogenomes, adding a new case of transposition and inversion of the trnQ gene. Our divergence time estimation suggests that A. inferum remained a member of the Mesozoic and the early Cenozoic large vertebrate-fall communities before shifting to become a whale-fall specialist.

The history of a developmental stage: Metamorphosis in chordates

“…3b) (Stokes and Holland, 1995;Willey, 1894). Some other amphioxus species from the genus Asymmetrons and Epygonichthys (Kon et al, 2007) stay asymmetric even as adults. However, very little is known about their postembryonic development.…”

Chordate evolution and the three-phylum system

“…The morphological similarity of extant lancelets is striking. This may not be attributable to their recent diversification, because the divergence time of the last common ancestor of the three extant genera is estimated to be 162 million years ago (Ma) [79] and that of the genus Asymmetron around 100 Ma [80]. These extant forms are reminiscent of some fossils with similar body plans, including Cathaymyrus [81] and Pikaia [82] dating back to earlier than 500 Ma.…”

A New Find of the Whale-fall Lancelet <i>Asymmetron inferum</i> (Cephalochordata) near a Hydrothermal Vent at Oomuro-dashi Submarine Volcano in the Izu Islands, Pacific Coast of Japan, as a Possible Case to Prove the Stepping-stone Hypothesis

“…For molecular phylogenetic analysis, obtained from DDBJ were 54 published sequences of Asymmetron lucayanum s. str. (accession numbers AB201335-AB201353, AP009354; see Kon et al 2006Kon et al , 2007, A. lucayanum complex sp. A (AB201315-AB201325, AP009353; see Kon et al 2006Kon et al , 2007, A. lucayanum complex sp.…”

“…(accession numbers AB201335-AB201353, AP009354; see Kon et al 2006Kon et al , 2007, A. lucayanum complex sp. A (AB201315-AB201325, AP009353; see Kon et al 2006Kon et al , 2007, A. lucayanum complex sp. B (AB201326-AB201334, AB240554-AB240565; see Kon et al 2006), A. inferum (AP009352) (see Kon et al 2007), and further, as an outgroup, Branchiostome japonicum (AB078191, registered initially as B. belcheri; see Nishikawa 2017).…”