Flatfishes (order Pleuronectiformes) are divided into two suborders: Psettodoidei, with one family, one genus (Psettodes); and Pleuronectoidei (hereafter pleuronectoids), with 13 families, approximately 128 genera. The eyes of these adult fishes are uniquely located on one side of the body. The absence of transitional species of flatfishes offered an early challenge to theories of evolutionary change through the accumulation of a series of small steps .
The study of flatfish fossils has been ongoing. Schwarzhans  documented the recent and fossil otoliths of the order. Chanet  summarized studies regarding the fossils of this order. Friedman  named †Heteronectes and re-studied †Amphistium. Friedman  placed the Eocene crown-group flatfish †Joleaudichthys in Psettodoidei and two other Eocene crown-group fossils, †Numidopleura and †Eobothus, within Pleuronectoidei. .
Two distinct views regarding the origin of flatfishes have been presented . One, proposed by Kyle  and Chabanaud , considers that all major flatfish lineages were independent offshoots of an evolving “pre-perciform” lineage and treats Psettodes as the descendant of a recent percoid ancestor. However, Chapleau  and a number of ichthyologists believe that flatfishes have a “lower-percoid” origin. Psettodes has been suggested to be the most “primitive” flatfish [9,10,11]. The “lower-percoid” origin of flatfishes was recently confirmed by molecular data and is now widely accepted by teleost ichthyologists [12,13,14,15,16,17].
Moreover, recent studies have confirmed that the most closely related organisms to flatfishes are percomorph taxa, predominantly carangiforms and istiophoriforms, including latids, carangoids, billfishes, moonfish, swordfish, barracudas, archerfishes, snook and threadfins (this group is referred to as the cara group hereafter) [12,13,14,15, 18,19,20,21,22,23,24]. These taxa and flatfishes were initially collectively referred to as clade L by Chen et al. . Li et al.  named this clade Carangimorpha, which was soon after referred to as Carangimorphariae (hereafter, carangimorphs) by Betancur-R et al. [19, 20], and conferred upon it a new taxonomic rank in a revised classification of bony fishes.
While the monophyly vs. polyphyly of the pleuronectiforms remains disputed, much molecular research on teleostean phylogenies has involved the flatfishes [12, 14, 15, 17, 21,22,23, 25]. Most studies focus on the phylogenetic status of flatfishes among teleosteans (especially percomorphs), but only representatives of pleuronectiforms have been included [13, 22]. Recently, molecular studies with broader taxonomic representation for this prominent group have been performed [12, 18, 19, 26], but the results are highly divergent, especially those presented by two major research groups, Betancur-R. et al. [19, 27] and Campbell et al. [18, 28], who strongly debate flatfish monophyly. Campbell et al.  used whole mitochondrial genome sequences to examine the phylogenetic affinities of the flatfishes (Pleuronectiformes) and obtained only weak support for the monophyly of Pleuronectiformes.
In the last ten years, several large-scale fish phylogenetics projects broadly representing the carangimorphs have been performed, which strongly support the monophyly of Pleuronectoidei [18,19,20, 27]. However, whether the other suborder of flatfishes, Psettodoidei, with close relationship to Pleuronectoidei remains unclear [12, 20, 23, 24, 29]. Betancur-R. et al.  conducted a thorough investigation of the phylogeny of flatfishes and their position among percomorphs by combining high genetic coverage (20 loci; ca. 20 kbp) with dense taxonomic breadth (214 taxa), including all putative flatfishes and a diverse percomorph outgroup. The majority of concatenation topologies provide evidence that flatfish has a single evolutionary origin, although a minority of analyses have inferred a non-monophyletic Pleuronectiformes, with varying placement of Psettodes and pleuronectoid clades among carangimorphs. As mentioned above, these authors support the monophyly of flatfishes. However, Campbell et al.  rapidly cast doubt on the monophyly of flatfishes based on six nuclear genes and extensive taxonomic sampling, including flatfishes and potential close relatives (approximately 90 taxa). Their results were most consistent with a non-monophyletic Pleuronectiformes, with Psettodes consistently excluded from other flatfishes and placed among other carangimorphs. Soon thereafter, Campbell et al.  and Betancur-R. et al.  launched a continuous debate based on more comprehensive data or complete (mitochondrial genome) mitogenome data. This issue has become a hot topic, and there is no consensus. Harrington et al.  presented a high-resolution phylogeny using a sequence dataset comprising more than 1000 ultraconserved DNA element loci covering 45 carangimorphs that unequivocally supports flatfish monophyly and a single origin of asymmetry. It remains unclear why so many phylogenetic analyses based on different datasets still have failed to clarify the issue of flatfish monophyly.
Currently, the key problem challenging the monophyly of flatfishes is the phylogenetic placement of Psettodes. What factors are responsible for the inconsistent phylogenetic position of the Psettodes clade? In this study, the mitogenomes of five flatfishes, Psettodes erumei, Samaris cristatus, Achirus lineatus, Trinectes maculatus and Cynoglossus nanhaiensis, were determined, and species data from all 13 flatfish families were compiled. Select mitogenomes of representative carangimorph species were employed for phylogenetic and molecular clock analyses. Based on our evaluation of the evolutionary history of carangimorphs, particularly the evolutionary events during the period of emergence of the Psettodes ancestor, we explain why different molecular phylogenetic studies are so divided on the issue of flatfish monophyly.