Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships

Phylogenetic relationships within decapod crustaceans are highly controversial. Even recent analyses based on molecular datasets have shown largely contradictory results. Previous studies using mitochondrial genomes are promising but suffer from a poor and unbalanced taxon sampling. To fill these gaps we sequenced the (nearly) complete mitochondrial genomes of 13 decapod species: Stenopus hispidus, Polycheles typhlops, Panulirus versicolor, Scyllarides latus, Enoplometopus occidentalis, Homarus gammarus, Procambarus fallax f. virginalis, Upogebia major, Neaxius acanthus, Calocaris macandreae, Corallianassa coutierei, Cryptolithodes sitchensis, Neopetrolisthes maculatus, and add that of Dromia personata. Our new data allow for comprehensive analyses of decapod phylogeny using the mitochondrial genomes of 50 species covering all major taxa of the Decapoda. Five species of Stomatopoda and one species of Euphausiacea serve as outgroups. Most of our analyses using Maximum Likelihood (ML) and Bayesian inference (BI) of nucleotide and amino acid datasets revealed congruent topologies for higher level decapod relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea), Thalassinida: Axiidea), (Astacidea, Polychelida), Achelata), Stenopodidea), Caridea), Dendrobranchiata). This result corroborates several traditional morphological views and adds new perspectives. In particular, the position of Polychelida is surprising. Nevertheless, some problems can be identified. In a minority of analyses the basal branching of Reptantia is not fully resolved, Thalassinida are monophyletic; Polychelida are the sister group to Achelata, and Stenopodidea are resolved as sister group to Caridea. Despite this and although some nodal supports are low in our phylogenetic trees, we think that the largely stable topology of the trees regardless of different types of analyses suggests that mitochondrial genomes show good potential to resolve the relationship within Decapoda.     

Mitogenomic analyses of eutherian relationships

Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70-100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place approximately 10 MYBP, a dating consistent with recent findings in primate paleontology.     

Mitogenomic analyses of caniform relationships

Extant members of the order Carnivora split into two basal groups, Caniformia (dog-like carnivorans) and Feliformia (cat-like carnivorans). In this study we address phylogenetic relationships within Caniformia applying various methodological approaches to analyses of complete mitochondrial genomes. Pinnipeds are currently well represented with respect to mitogenomic data and here we add seven mt genomes to the non-pinniped caniform collection. The analyses identified a basal caniform divergence between Cynoidea and Arctoidea. Arctoidea split into three primary groups, Ursidae (including the giant panda), Pinnipedia, and a branch, Musteloidea, which encompassed Ailuridae (red panda), Mephitidae (skunks), Procyonidae (raccoons) and Mustelidae (mustelids). The analyses favored a basal arctoid split between Ursidae and a branch containing Pinnipedia and Musteloidea. Within the Musteloidea there was a preference for a basal divergence between Ailuridae and remaining families. Among the latter, the analyses identified a sister group relationship between Mephitidae and a branch that contained Procyonidae and Mustelidae. The mitogenomic distance between the wolf and the dog was shown to be at the same level as that of basal human divergences. The wolf and the dog are commonly considered as separate species in the popular literature. The mitogenomic result is inconsistent with that understanding at the same time as it provides insight into the time of the domestication of the dog relative to basal human mitogenomic divergences.     

Mitogenomic phylogeny of the Naticidae (Gastropoda: Littorinimorpha) reveals monophyly of the Polinicinae

The Naticidae is a species-rich family of predatory marine gastropods with substantial interspecific morphological diversity. The classification of the Naticidae has been traditionally based on morphology data, but the phylogenetic relationships within the family are debated due to conflicting molecular results, especially regarding the monophyly of subfamilies Polinicinae and Naticinae. To further resolve the phylogenetic controversies within the Naticidae, we undertake a phylogenetic approach using 14 newly sequenced complete or nearly complete (only lacking a control region) mitochondrial genomes. Both the maximum likelihood and Bayesian inference analyses supported monophyly of the Polinicinae, but paraphyly of the Naticinae due to the placement of the enigmatic genus Notocochlis. The ancestral character reconstruction suggests that the operculum, a character that currently defines the two subfamilies, evolved from an ancestor with a calcareous operculum in the evolutionary history of naticids. In addition, the chronogram estimates that naticids was originated in late Triassic (about 227 million years ago), consistent with previous hypotheses. Our study highlights the importance of using complete mitochondrial genomes while reconstructing phylogenetic relationships within the Naticidae. The evolution scenario of the naticid operculum contributes new insights into the classification of Naticidae.     

Mitogenomic phylogeny of Typhlocybinae (Hemiptera: Cicadellidae) reveals homoplasy in tribal diagnostic morphological traits

The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister‐group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov.; but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, that is, Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided.     

Mitogenomic phylogeny of Nassarius (Gastropoda: Neogastropoda)

Nassariids (Family Nassariidae) are a group of marine snails that are distributed worldwide, with their maximum species diversity in tropical regions, particularly the Indo‐Pacific. However, the traditional taxonomy of Nassariidae defined by shell or radula characters is usually inconsistent with little phylogenetic signal. In the present study, the complete mitochondrial (mt) genomes of nine Nassarius species were sequenced and compared with other eight nassariid species previously reported. All nassariid mt genomes showed the same gene order as in most caenogastropods and shared a very similar pattern with respect to genome size, nucleotide composition and AT contents. A deletion of three nucleotides in nad6 gene was detected in Nassarius jacksonianus and Nassarius acuticostus, and this feature also provided implications for nassariid phylogeny. The genetic distance analysis and reconstructed phylogeny revealed a distant relationship between N. jacksonianus or N. acuticostus and other members in Nassarius. The mitogenomic phylogeny recovered the evolutionary relationships within Nassarius with high statistical support. In addition, a chronogram was reconstructed under an uncorrelated relaxed molecular clock, which dated the divergence among main lineages of Nassarius during ~31 MYA.     

Mitogenomic perspectives on the origin and phylogeny of living amphibians

Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for "missing" fossils, and can benefit comparative studies of amphibian evolution.     

Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

Background

Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.

Results

Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.

Conclusions

Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.     

Mitogenomic perspectives into sciaenid fishes' phylogeny and evolution origin in the New World

Sciaenid fishes are widely distributed throughout the coastal waters and estuaries of the world. A total of 23 genera of this family are endemic to the Old World. However, evolutionary relationships among Old World sciaenid fishes and their origin have remained unresolved despite their diversity and importance. Besides, hypotheses that explain the origin and biogeographical distribution of sciaenid fishes are controversial. In this study, the complete mitochondrial genome sequences of seven representative sciaenid species were determined and a well-resolved tree was recovered. This new timescale demonstrated that the sciaenid originated during the late Jurassic to early Cretaceous Period. The estimated origin time of sciaenid fish is 208 Mya, and the origin of Old World sciaenid is estimated at 126 Mya. Reconstruction of ancestral distributions indicated a plesiomorphic distribution and center of origin in the New World, with at least one lineage subsequently dispersed to the Old World. Moreover, we conclude that the common ancestors of Old World sciaenid fishes were derived from species of New World.     

Vesicle adhesion reveals novel universal relationships for biophysical characterization

Adhesion plays an integral role in diverse biological functions ranging from cellular transport to tissue development. Estimation of adhesion strength, therefore, becomes important to gain biophysical insight into these phenomena. In this study, we use curvature elasticity to present non-intuitive, yet remarkably simple, universal relationships that capture vesicle–substrate interactions. These relationships not only provide efficient strategies to tease out adhesion energy of biological molecules but can also be used to characterize the physical properties of elastic biomimetic nanoparticles. We validate the modeling predictions with experimental data from two previous studies.     

Mitogenomic relationships of placental mammals and molecular estimates of their divergences

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at approximately 102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5-10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between Gorilla and Pan/Homo at approximately 11.5 MYA and that between Pan and Homo at approximately 8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed approximately 270,000 years ago, i.e. approximately 100,000 years earlier than the traditional age of "Mitochondrial Eve". Comparison between the two new mt genomes of Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera Elephas, Mammuthus and Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.     

Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines

Complete or nearly complete nucleotide sequences of mitochondrial genomes (mtDNAs) were determined from eight species which, together with previous mtDNA data for two other taxa, cover most subfamilies of Iguanidae sensu lato. These iguanid mtDNAs were found to be rather conservative with respect to gene arrangements and molecular evolutionary rates, which contrasts with mtDNAs of Acrodonta (Agamidae and Chamaeleonidae) in which several gene rearrangements and highly accelerated molecular evolutionary rates have been known. Phylogenetic analyses consistently suggested the earliest shoot-off of a Malagasy subfamily Oplurinae and an affinity of Polychrotinae and Tropidurinae sensu stricto. However, even with the ample molecular characters derived from complete mtDNA sequences, phylogenetic relationships between iguanid subfamilies were poorly resolved in general, presumably due to the rapid ancient cladogenesis. Divergence time estimation without assuming the molecular clock suggested the Late Triassic/Early Jurassic divergence of Iguanidae from acrodonts and the Middle/Late Jurassic divergence of Oplurinae from the other iguanids. Together with geological and paleontological evidence, these results led us to propose Gondwanan vicariance for the origin of Malagasy oplurines without invoking a land bridge connection between South America/Antarctica and drifting Madagascar/India.     

Mitogenomic phylogeny of Trochoidea (Gastropoda: Vetigastropoda): New insights from increased complete genomes

Increased mitochondrial (mt) genomes can provide more sets of genome‐level characteristics for resolving deeper phylogeny. Limited information with respect to the Trochoidea mitochondrial genome organization is available; besides, monophyly and internal relationships of the superfamily still remain a matter of discussion. To resolve the monophyly and internal phylogenetic controversies of Trochoidea and expand our understanding for mt genomic characteristic evolution among Trochoidea, the phylogenetic trees were reconstructed using 13 newly sequenced complete mt genomes and 35 genomes from GenBank, and both the maximum likelihood and Bayesian inference analyses were highly supported. Vetigastropoda phylogenetic analyses recovered the monophyly of Trochoidea. Trochoidea phylogenetic analyses and genetic distances supported the non‐monophyly of Tegulidae and Tegula, indicating that the taxonomic status of several genera (Rochia, Tectus and Cittarium) should be revised and Tegula, Omphalius and Chlorostoma should be placed as a same genus. The close affinity between Tectus virgatus and Rochia was also revealed. Three‐nucleotide insertion in nad1, nine‐nucleotide insertion and six‐nucleotide deletion in nad5 are detected in Tegulidae, Tectus and Rochia, respectively. Gene orders within Trochoidea are stable, with gene rearrangements exclusive to tRNA genes observed. Homoplasious convergences because of trnT rearrangement display translocation in Turbinidae and reversion in Trochidae and Calliostomatida. For trnE and trnG, we identify 11 arrangement types, suggesting that the gene rearrangement history needs to be further evaluated. Our study emphasizes the importance of mt genomes in resolving phylogenetic relationships within Trochoidea. In addition, the mt genomic characters would contribute new insights into the classification of Trochoidea.     

Molecular phylogeny reveals a core clade of Rhytismatales

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.     

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.     

Molecular phylogeny of RNA polymerase II gene reveals the relationships of tetraploid species with St genome (Triticeae: Poaceae)

To evaluate phylogeny of tetraploid with St genome, phylogenetic analyses of RNA polymerase II (RPB2), a member of the nuclear gene family encoding the second largest subunit, were performed. Our results showed that: (1) Roegneria magnicaespes and Roegneria alashanica are related to Pseudoroegneria. (2) Roegneria elytrigioides has StStStSt genomes and should therefore be classified as Pseudoroegneria elytrigioides. (3) Pseudoroegneria tauri and Pseudoroegneria deweyi which have StStPP genomes should be transferred to Douglasdeweya and be renamed as Douglasdeweya wangii and Douglasdeweya deweyi, respectively. (4) Pseudoroegneria geniculata ssp. scythica is related to Pseudoroegneria and Lophyrum, and hence should be identified as a species of Trichopyrum. (5) Pseudoroegneria libanotica might be a parental donor for Elytrigia caespitosa rather than Elytrigia caespitosa ssp. nodosa. It is unreasonable to recognize El. caespitosa ssp. nodosa as a subspecies of El. caespitosa. (6) Interspecific and intergeneric variations are detected in St genome of these tetraploid species.     

A Mitogenomic Phylogeny of Living Primates

Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels.     

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.