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Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae \"Pelagia\" in reference to the common habitat preference that links the 15 families.

The Indo-West Pacific scombrid genus Rastrelliger Jordan & Starks is reviewed. Formerly, the genus was considered to contain three valid species, viz., R. brachysoma (Bleeker, 1851) known from the south-east coast of India to Samoa Islands; R. faughni Matsui, 1967 reported from the south-east coast of India to Fiji; and R. kanagurta (Cuvier, 1816), the most widespread species known from the east coast of Africa and the Persian/Arabian Gulf east to Tonga. Herein, R. chrysozonus (Rüppell, 1836), restricted to the Red Sea, is resurrected from the synonymy with R. kanagurta and both species are redescribed in detail, based on an integrative morphological and molecular assessment. Consequently, Scomber microlepidotus Rüppell, 1836 is moved from the synonymy with R. kanagurta to synonymy with R. chrysozonus. Rastrelliger chrysozonus differs from R. kanagurta primarily by a longer upper jaw. Rastrelliger brachysoma differs from the other three species by a deeper body, a deeper caudal peduncle, and a very long intestine. Rastrelliger faughni differs from the other three species in having a more slender body, usually X spines in the first dorsal fin (versus IX spines), shorter and fewer gill rakers, a shorter maxilla, and a shorter intestine. The phylogenetic analysis of mitochondrial genes of all Rastrelliger species also demonstrated that R. chrysozonus forms a well divergent evolutionary lineage, with R. kanagurta being its closest relative. In addition to the redescriptions of R. chrysozonus and R. kanagurta, brief species accounts for R. brachysoma and R. faughni and the key to the four species are provided.

The study of which life history traits primarily affect molecular evolutionary rates is often confounded by the covariance of these traits. Scombroid fishes (billfishes, tunas, barracudas, and their relatives) are unusual in that their mass-specific metabolic rate is positively associated with body size. This study exploits this atypical pattern of trait variation, which allows for direct tests of whether mass-specific metabolic rate or body size is the more important factor of molecular evolutionary rates. We inferred a phylogeny for scombroids from a supermatrix of molecular and morphological characters and used new phylogenetic comparative approaches to assess the associations of body size and mass-specific metabolic rate with substitution rate. As predicted by the body size hypothesis, there is a negative correlation between body size and substitution rate. However, unexpectedly, we also find a negative association between mass-specific metabolic and substitution rates. These relationships are supported by analyses of the total molecular data, separate mitochondrial and nuclear genes, and individual loci, and they are robust to phylogenetic uncertainty. The molecular evolutionary rates of scombroids are primarily tied to body size. This study demonstrates that groups with novel patterns of trait variation can be particularly informative for identifying which life history traits are the primary factors of molecular evolutionary rates.

We present an overview of all known fossil scombroid fishes (Scombroidei, Perciformes) of the former USSR, many taxa of which are described in a language other than Russian for the first time. Also new is the application of a cladistic framework for these taxa. For each taxon, short taxonomic synopses with the most relevant characteristics (synapomorphies, meristic counts) are presented in a form useful for future cladistic analysis. As an exception, we present an extensive systematic description of the billfish †Hemingwaya sarissa Sytchevskaya & Prokofiev, because we disagree with earlier interpretations. The ‘gempylid’ †Hemithyrsites maicopicus Daniltshenko retains its generic name, which is considered the valid name of what is also known as Promethichthys Gill. A new tribe, †Eocoelopomini, is erected to contain the genera †Eocoelopoma Woodward, †Palaeothunnus Bannikov, and †Micrornatus Monsch. It is questioned whether species previously described as belonging to Thunnus South should be classified in that genus. A new species of tribe Scomberomorini, †Neocybium parvidentatum, is described from the Bartonian of W Kazakhstan. A specimen of †Auxides (questionably Maastrichthian, Iran), also reported here, possibly extends the radiation of †Auxides, and scombroids as a whole, further back in time. The fossil record of the Blochiidae is probably extended downwards to the Thanetian.

We introduce a new method that uses generalized linear mixed models to infer the depth distribution of pelagic fishes. It uses existing data from research surveys and observers on commercial vessels to estimate changes in catchability when longline fishing gear is lengthened to access deeper water. We infer the depth distribution of catchability for 37 fish species that are caught on pelagic longlines in the Pacific Ocean. We show how the estimates of catchability can be used to correct abundance indices for variations in longline depth. Our method facilitates the inclusion of data from early surveys in the time series of commercial catch rates used to estimate abundance. It also resolves inconsistencies in the time series caused by a rapid switch to deep longlining in the 1970s. The catchability distribution does not always match depth preferences derived from tracking studies. Therefore, depth preferences from tracking studies should not be used to correct abundance indices without additional information on feeding behavior.

The 13 peptides encoded by vertebrate mitochondrial DNA (mtDNA) are essential subunits of oxidative phosphorylation (OXPHOS) enzymes. These genes normally experience purifying selection and also coevolve with nuclear-encoded subunits of OXPHOS complexes. However, the role of positive selection on mtDNA evolution is still unclear, as most examples of intergenomic coevolution appear to be the result of compensation by nuclear-encoded genes for mildly deleterious mtDNA mutations, and not simultaneous positive selection in both genomes. Organisms that have experienced strong selective pressures to increase aerobic capacity or adapt to changes in thermal environment may be better candidates in which to examine the impact of positively selected changes on mtDNA evolution. The tuna (suborder Scombroidei, family Scombridae) and billfish (suborder Scombroidei, families Xiphiidae and Istiophoridae) are highly aerobic fish with multiple specializations in muscle energetics, including a high mitochondrial content and regional endothermy. We examined the role of positively selected mtDNA substitutions in the production of these unique phenotypes. Focusing on a catalytic subunit of cytochrome c oxidase (COX II), we found that the rate ratio of nonsynonymous (d(N); amino acid changing)-to-synonymous (d(S); silent) substitutions was not increased in lineages leading to the tuna but was significantly increased in the lineage preceding the billfish. Furthermore, there are a number of individual positively selected sites that, when mapped onto the COX crystal structure, appear to interact with other COX subunits and may affect OXPHOS function and regulation in billfish.

The muscles serving the ventral portion of the gill arches ( = infrabranchial musculature) are poorly known in bony fishes. A comparative analysis of the infrabranchial muscles in the major percomorph lineages reveals a large amount of phylogenetically-relevant information. Characters derived from this anatomical system are identified and discussed in light of current hypotheses of phylogenetic relationships among percomorphs. New evidence supports a sister-group relationship between the Batrachoidiformes and Lophiiformes and between the Callionymoidei and Gobiesocoidei. Investigated data also corroborate the existence of two monophyletic groups, one including the Pristolepididae, Badidae, and Nandidae, and a second clade consisting of all non-amarsipid stromateiforms. New synapomorphies are proposed for the Atherinomorphae, Blenniiformes, Lophiiformes, Scombroidei (including Sphyraenidae), and Gobiiformes. Within the latter order, the Rhyacichthyidae and Odontobutidae are supported as the successive sister families of all remaining gobiiforms. The present analysis further confirms the validity of infrabranchial musculature characters previously proposed to support the grouping of the Mugiliformes with the Atherinomorphae and the monophyly of the Labriformes with the possible inclusion of the Pholidichthyiformes. Interestingly, most hypotheses of relationships supported by the infrabranchial musculature have been advanced by preceding anatomists on the basis of distinct data sources, but were never recovered in recent molecular phylogenies. These conflicts clearly indicate the current unsatisfactory resolution of the higher-level phylogeny of percomorphs.

Evoxymetopon moricheni n. sp. is described from the northern Gulf of Aqaba, Red Sea, on the basis of a single specimen. It is characterised within the genus by a convex upper head profile; the posterior confluence of the frontal ridges slightly elevated at the nape, resulting in the presence of a slight sagittal crest; eye 5.2 times in head length; the lower hind margin of opercle slightly pointed in its lower half; the pelvic fins reduced to a scale-like structure with two soft rays on the posterior process of the basipterygium, its origin below the eighth dorsal-fin element; the first anal spine single, oval, scale like, and originating a short distance behind the vent (opposite the 34th dorsal-fin soft ray), anterior anal-fin soft rays minute and embedded, barely penetrating the skin and not visible externally, while the posterior fin supporting the rays enlarged and visible externally; approximately 17 anal-fin rays externally visible; approximately 83 dorsal-fin elements, with first spine not elongate, shorter than second; 12 pectoral-fin rays (ii + 6 + iv), with shorter anterior (fourth ray shortest) and longer posterior rays extending above the lateral line; 10 upper and 13 lower gill rakers of the first gill arch; head and body silver white, with a blackish margin anteriorly on snout and head, continuing along the anterior half of the dorsal-fin base. The new finding represents a new record of the genus from the Red Sea.

Recent studies on the mitochondrial genome have suggested that the duplications of tRNA and tandem repeats in the control region are important changes that are related to species diversity. This paper reports the study of mitogenomes from five Pampus (Perciformes, Stromateidae) species with very similar morphology. A duplicated tRNA Met gene in the tRNA-IQM region is present in Pampus sp. and P. punctatissimus. In the conserved sequence blocks of the control region, a duplicated CSB3 and promoter are found in Pampus sp. but are absent in P. minor. Moreover, a duplicated TAS is found in P. punctatissimus and P. chinensis. Based on the complete mitogenome sequence of Pampus sp., the first sequence reported from Stromateidae and the longest (17,694 bp) among the Perciformes mitogenomes, we conducted phylogenetic analysis to show that Stromateoidei and Scombroidei are more closely related to each other than to other Perciformes suborders. However, we reject the reciprocal monophyly of these two suborders.