Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

Abstract

BackgroundA skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements.ResultsMitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in the tribe Diaphini although our analyses show it to be independently derived. Most tribes are resolved in accordance with adult morphology although Gonichthyini is found within a subclade of the tribe Myctophini consisting of ctenoid scaled species. Mitogenomic sequence data from this study recognize 10 reciprocally monophyletic lineages within Myctophidae, with five of these clades delimited from additional rearranged gene orders or intergenic non-coding sequences.ConclusionsMitogenomic results from DNA sequences and unique gene orders corroborate morphology in phylogeny reconstruction and provide a likely scenario for the phylogenetic history of Myctophiformes. The extent of gene order rearrangements found within the mitochondrial genomes of myctophids is unique for phylogenetic purposes.

Eye-Size Variability in Deep-Sea Lanternfishes (Myctophidae): An Ecological and Phylogenetic Study

“…Unfortunately, no fully resolved phylogeny is available for the family Myctophidae to date. Consequently, two different phylogenies, A and B (Figure 1), were built in the Mesquite program v. 2.75 [42] based on two published phylogenies [43], [44]. Paxton et al's phylogeny classified genera using derived character states of adult osteology and photophore patterns, as described by Paxton et al [43], and of larvae as described by Moser and Ahlstrom [45], [46], [47].…”

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

“…The traditional protocols to produce the mitochondrial genomes have relied on performing either standard/long PCR or cloning, followed by a series of Sanger sequencing (Moreira, Furtado & Parente, 2015; Gan, Schultz & Austin, 2014; Poulsen et al, 2013). The classic method is a time consuming and resource demanding task (Hahn, Bachmann & Chevreux, 2013).…”

Genetic support for the morphological identification of larvae of Myctophidae, Gonostomatidae, Sternoptychidae and Phosichthyidae (Pisces) from the western Mediterranean

“…Genetic analysis based on mtDNA has been useful in establishing phylogenetic relationships among mesopelagic and other deep-sea fishes (Miya and Nishida 1998, Miya et al 2001, Poulsen et al 2013. The results presented here identified two wide clusters corresponding to the recognized monophyletic orders Myctophiformes and Stomiiformes (e.g.…”

“…The results presented here identified two wide clusters corresponding to the recognized monophyletic orders Myctophiformes and Stomiiformes (e.g. Paxton 1972, Fink 1984, Poulsen et al 2013) using ML and BI methods ( Fig. 1 and Fig.…”

“…The genetic evidence for constructing the evolutionary history of lanternfishes and lightfishes that inhabit the Mediterranean Sea is lacking. Phylogenetic relationships within Myctophidae had been unresolved by genetic methods until a recent study by Poulsen et al (2013) combined sequencing of mitogenomes, coding and non-coding regions, and gene order rearrangement. The results of their study supported the classical morphological phylogeny recognized for myctophids (Paxton 1972.…”