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Ginglymodians (e.g. gars) are a group of holostean fishes with a rich fossil history in the Mesozoic. The resolution of interrelationships among extinct ginglymodians is central to the problem of understanding the origin of this clade. Here, a new fossil ginglymodian, Diandongichthys ocellatus gen. et sp. nov. is described based on 13 well-preserved specimens from the Early-Middle Triassic (Anisian) marine deposits exposed in Luoping, eastern Yunnan, China. The discovery documents one of the oldest and smallest ginglymodians hitherto known from the Middle Triassic, with a maximum standard length of 41 mm. Diandongichthys , although displaying several synapomorphies of ginglymodians, retains some primitive states with respect to other early ginglymodians (e.g. a short snout without anterior infraorbitals, a maxilla ending below the orbit, and a median gular); consequently, it is nested at the base of the Ginglymodi in this phylogenetic study. Besides body shape, some autapomorphies on the cranial bones and caudal fin easily distinguish Diandongichthys from other members of this clade. The discovery provides new insights into the origin and early diversification of ginglymodian fishes. [ABSTRACT FROM AUTHOR]

The previously alleged ‘perleidid’ genus Peltoperleidus is a stem-neopterygian fish taxon with two or three horizontal rows of notably deepened flank scales. Until recently, members of this genus were known only from the Ladinian (late Middle Triassic) or near the Anisian/Ladinian boundary (~242 Ma) in southern Switzerland and northern Italy. Here, I report the discovery of a new species of the genus, Peltoperleidus asiaticus sp. nov., based on three well-preserved specimens from the Anisian (early Middle Triassic, ~244 Ma) of Luoping, eastern Yunnan, China. The discovery extends the geological range of Peltoperleidus by approximately two million years and documents the first record of the genus in Asia. Similar to its relatives (represented by P. macrodontus) from Europe, P. asiaticus sp. nov. is likely a small-sized durophagous predator with dentition combining grasping and crushing morphologies. Results of a cladistic analysis unite four species of Peltoperleidus as a monophyletic group within the Louwoichthyiformes, and suggest that the presence of two horizontal rows of notably deepened scales was independently evolved in Peltoperleidus and another stem-neopterygian taxon Altisolepis. P. asiaticus sp. nov. is nested at the base of Peltoperleidus, and a new family Peltoperleididae is proposed for the genus, contrasting the previous placement of Peltoperleidus in the poorly defined, paraphyletic ‘Perleididae’. Comparative studies of the basal peltoperleidid from China with its younger relatives from Europe provide new insights into the evolutionary origin and paleogeographic distribution of this clade.

Neopterygii is a taxonomically diverse clade of ray-finned fishes, including Teleostei, Holostei and closely related fossil taxa. The Colobodontidae is a stem group of large-sized neopterygians with a durophagous feeding adaption from the Middle to Late Triassic marine ecosystems in Europe and South China. Here, we report the discovery of a new colobodontid, Feroxichthys panzhouensis sp. nov., based on a well-preserved specimen from the early Middle Triassic (Anisian) of Panzhou (formerly known as Panxian), Guizhou, China. The discovery extends the geographical distribution of Feroxichthys from eastern Yunnan into western Guizhou, and demonstrates a more rapid diversification of early colobodontids than previously thought. The new species possesses diagnostic features of Feroxichthys (e.g., a fused lacrimal-maxilla), but it is easily distinguished from the type species Feroxichthys yunnanensis and other colobodontids by some derived features on the skull and, especially, the relatively short and deep body with a prominent postcranial hump. This body form, previously unknown in colobodontids, implicates a morphological adaptation to structurally complex habitats in light of ecological studies of modern ray-finned fishes with a similar body form. In addition, the feeding apparatus suggests a more obligate durophagous diet for F. panzhouensis sp. nov. than other colobodontids. Results of a cladistic analysis recover the new species as a sister taxon of F. yunnanensis within the Colobodontidae, and suggest that a hump-backed body form has independently evolved multiple times in Triassic neopterygians. As such, the new finding provides an important addition for our understanding of the morphological and ecological diversity of neopterygian fishes from the Triassic marine ecosystems in South China.

Neopterygii is a large group of ray-finned fishes which underwent a rapid radiation in the Middle Triassic. Until recently, 11 stem neopterygians have been recovered from the early Middle Triassic Luoping Biota in eastern Yunnan, China, and they are small to medium-sized fishes. Here, I report the discovery of a new stem neopterygian, Feroxichthys yunnanensis gen. et sp. nov. from the Luoping Biota, which represents the first evidence of large-sized stem neopteygians in this biota with a total length of ~340 mm (290 mm in standard length). The skull of the new taxon is exceptionally well-preserved, showing some peculiar features rarely known in other stem neopterygians, for example fusion of paired premaxillae, fusion of lacrimal with maxilla, and a fused parieto-dermopterotic with a strong posterior process. Phylogenetic studies recover Feroxichthys as a basal colobodontid, and a revised diagnosis of this family is presented. The feeding apparatus indicates that Feroxichthys might have been predominantly durophagous, resembling other colobodontids. However, the anterior peg-like teeth in the jaws of Feroxichthys are much longer and stronger than other colobodontids, enabling a more powerful initial prey capture before food was passed posteriorly to molariform teeth for crushing in the oral cavity. As a mysterious large durophagous predator previously unknown from the Luoping Biota, the new finding is important not only for understanding the early diversification of neopterygians during this age but also for investigating the trophic structure in this marine ecosystem.

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and "semionotiforms." In particular, the phylogenetic relationships between the widely distributed "semionotiforms," and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 "semionotiform" genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson's observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas.

Background & objectives: Comparative genomics and evolutionary analyses of conserved genes have enabled usto understand the complexity of genomes of closely related species. For example: -globin gene present inhuman hemoglobin is one such gene that has experienced many genetic changes in many related taxa andproduced more than 600 variants. One of the variant, HBS causes sickle-cell anemia in humans but offersprotection against severe malaria due to Plasmodium falciparum. In the present study, we characterized andperformed evolutionary comparative analyses of the -globin gene in different related and unrelated taxa tohave a comprehensive view of its evolution.Methods: DNA and protein sequences of -globin gene were downloaded from NCBI and characterized in detailin nine eutherian (Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus, Bostaurus, Canis familiaris, Equus caballus, Oryctolagus cuniculus), a dinosaurian (Gallus gallus) and a neopterygii(Danio rerio) taxa. Three more eutherian (Papio anubis, Ovis aries and Sus scrofa) taxa were included for ananalysis at the protein level but not included at the gene level owing to lack of genomic information. Computationaland phylogenetic analyses were performed using evolutionary comparative approach.Results: Results of comparative and phylogenetic analyses revealed less conservation of genetic architecture of-globin compared to its protein architecture in all eutherian taxa. Both dinosaurian and neopterygii taxa servedas outgroups and varied at gene and protein levels.Interpretation & conclusion: Most remarkably, all primates from eutherian taxa including P. anubis showedonly nine codon position differences and an absolute similarity between H. sapiens and P. troglodytes. Absoluteconservation of coding region in Equus caballus (horse) was observed. The results were discussed with aninference on the role of evolutionary forces in maintaining such close similarities and variations across closelyrelated taxa. Further, the need to utilize more comparative approaches in understanding the disease causinggenes’ evolution in closely related taxa is hoped for.

Dapedium pholidotum(Agassiz, 1832) (Actinopterygii, Neopterygii) is redescribed based on new material from the Posidonia Shale (Early Jurassic: Early Toarcian) of Germany. Dapediiformes ord. nov. is introduced forDapediumLeach, 1822 and other deep-bodied Mesozoic neopterygians. The species diagnosis ofD. pholidotumis amended. Comparison withD. stollorumThies & Hauff, 2011 andD. caelatumQuenstedt, 1858, also from the Lower Jurassic Posidonia Shale, shows thatD. pholidotumis unique in having: (1) a length/height ratio of the operculum ofc. 0.73, whereas inD. stollorumandD. caelatumthis value reaches onlyc. 0.58; (2) a length/width ratio of the gular plate ofc. 1.6, whereas inD. stollorumandD. caelatumthis value is 1.3; (3) 27 or more caudal fin lepidotrichia, whereas inD. stollorumandD. caelatumthere are 24 and 25 lepidotrichia, respectively; (4) at least 26 dorsal fin lepidotrichia, whereasD. stollorumandD. caelatumpossess only 24 dorsal fin lepidotrichia each; and (5) a length/height ratio of the flank scales immediately behind the operculum of 0.37, whereas inD. stollorumandD. caelatumthis ratio ranges around 0.31 and 0.5, respectively. A cladistic analysis based on modification of a previously published taxon–character matrix shows thatDapediumis the sister group of the ginglymodian fishes [Semionotiformes + Lepisosteiformes]. The generic diagnosis ofDapediumLeach, 1822 is amended. [ABSTRACT FROM AUTHOR]

The actinopterygian fish †Hemicalypterus weiri Schaeffer, 1967 is herein redescribed and rediagnosed based on new information collected from reexamination of museum specimens as well as examination of recently collected specimens from the Upper Triassic Chinle Formation of San Juan County, Utah, United States. †Hemicalypterus is distinguishable by its deep, disc-shaped compressed body; ganoid-scaled anterior half and scaleless posterior half; spinose, prominent dorsal and ventral ridge scales anterior to dorsal and anal fins; hem-like dorsal and anal fins with rounded distal margins; small mouth gape; and specialized, multicuspid dentition. This type of dentition, when observed in extant fishes, is often associated with herbivory, and †Hemicalypterus represents the oldest known ray-finned fish to have possibly exploited an herbivorous trophic feeding niche. A phylogenetic analysis infers a placement of †Hemicalypterus within †Dapediiformes, with †Dapediiformes being recovered as sister to Ginglymodi within holostean actinopterygians. [ABSTRACT FROM AUTHOR]

Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged ‘perleidiform’ families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China.

A new semionotiform fish, Isanichthys palustris gen. et sp. nov., is described from the Late Jurassic – Early Cretaceous Phu Kradung Formation, north-east Thailand. I. palustris is known from a single, nearly complete specimen found alongside abundant Lepidotes specimens at the Phu Nam Jun locality. I. palustris shows a mixture of semionotid-like characters, such as the pattern of cheek ossifications, and lepisosteid-like characters, such as the body shape and a dorsal fin opposed by an anal fin. I. palustris possesses only some of the characters currently used to define the Semionotidae. Cladistic analyses including various semionotid and gar taxa, together with Amia calva and Leptolepis coryphaenoides, suggest that the Semionotiformes (Lepisosteidae and ‘Semionotidae’) form a monophyletic clade, but the ‘Semionotidae’ taxa form an unresolved polytomy. The relationships between Semionotiformes, Halecomorphi and Teleostei are unresolved. When restricted to the best-known taxa, however, the analysis shows the monophyly of the Semionotidae sensu stricto ( Semionotus + Lepidotes) and a sister-group relationship between halecomorphs and teleosts. These last two results are regarded as the preferred hypothesis for further studies. I. palustris is the only known example of a predaceous, probably piscivorous, ‘semionotid’. It illustrates the great diversity and ecological adaptation of the semionotiforms during the Late Jurassic – Early Cretaceous. We question the phylogenetic relationships of ‘ancient fishes’ founded on molecular-based trees because we suspect that the use of very few Recent taxa as representatives of previously diverse lineages is an inevitable, but important, bias in the construction of such trees. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of the recently described genus †Ticinolepis from the Middle Triassic of the Monte San Giorgio are explored through cladistic analyses of the so far largest morphological dataset for fossil actinopterygians, including representatives of the crown-neopterygian clades Halecomorphi, Ginglymodi and Teleostei, and merging the characters from previously published systematic studies together with newly proposed characters. †Ticinolepis is retrieved as the most basal Ginglymodi and our results support the monophyly of Teleostei and Holostei, as well as Halecomorphi and Ginglymodi within the latter clade. The patterns of relationships within these clades mostly agree with those of previous studies, although a few important differences require future research. According to our results, ionoscopiforms are not monophyletic, caturids are not amiiforms and leptolepids and luisiellids form a monophyletic clade. Our phylogenetic hypothesis confirms the rapid radiation of the holostean clades Halecomorphi and Ginglymodi during the Early and Middle Triassic and the radiation of pholidophoriform teleosts during the Late Triassic. Crown-group Halecomorphi have an enormous ghost lineage throughout half of the Mesozoic, but ginglymodians and teleosts show a second radiation during the Early Jurassic. The crown-groups of Halecomorphi, Ginglymodi and Teleostei originated within parallel events of radiation during the Late Jurassic.

The piggyBac transposable element was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and specificity compared to the other Class II elements, the diversity and evolution of this superfamily have been only partially analyzed. Two main types of elements can be distinguished: the piggyBac-like elements (PBLE) with terminal inverted repeats, untranslated region, and an open reading frame encoding a transposase, and the piggyBac-derived sequences (PGBD), containing a sequence derived from a piggyBac transposase, and which correspond to domesticated elements. To define the distribution, their structural diversity and phylogenetic relationships, analyses were conducted using known PBLE and PGBD sequences to scan databases. From this data mining, numerous new sequences were characterized (50 for PBLE and 396 for PGBD). Structural analyses suggest that four groups of PBLE can be defined according to the presence/absence of sub-terminal repeats. The transposase is characterized by highly variable catalytic domain and C-terminal region. There is no relationship between the structural groups and the phylogeny of these PBLE elements. The PGBD are clearly structured into nine main groups. A new group of domesticated elements is suspected in Neopterygii and the remaining eight previously described elements have been investigated in more detail. In all cases, these sequences are no longer transposable elements, the catalytic domain of the ancestral transposase is not always conserved, but they are under strong purifying selection. The phylogeny of both PBLE and PGBD suggests multiple and independent domestication events of PGBD from different PBLE ancestors. [ABSTRACT FROM AUTHOR]

The Sirtuin (SIRT1-7) family comprises seven evolutionary-conserved enzymes that couple cellular NAD availability with health, nutrition and welfare status in vertebrates. This study re-annotated the sirt3/5 branch in the gilthead sea bream, revealing three paralogues of sirt3 (sirt3.1a/sirt3.1b/sirt3.2) and two of sirt5 (sirt5a/sirt5b) in this Perciform fish. The phylogeny and synteny analyses unveiled that the Sirt3.1/Sirt3.2 dichotomy was retained in teleosts and aquatic-living Sarcopterygian after early vertebrate 2R whole genome duplication (WGD). Additionally, only certain percomorphaceae and gilthead sea bream showed a conserved tandem-duplicated synteny block involving the mammalian-clustered sirt3.1 gene (psmd13-sirt3.1a/b-drd4-cdhr5-ctsd). Conversely, the expansion of the Sirt5 branch was shaped by the teleost-specific 3R WGD. As extensively reviewed in the literature, human-orthologues (sirt3.1/sirt5a) showed a high, conserved expression in skeletal muscle that increased as development advanced. However, recent sirt3.2 and sirt5b suffered an overall muscle transcriptional silencing across life, as well as an enhanced expression on immune-relevant tissues and gills. These findings fill gaps in the ontogeny and differentiation of Sirt genes in the environmentally adaptable gilthead sea bream, becoming a good starting point to advance towards a full understanding of its neo-functionalization. The mechanisms originating from these new paralogs also open new perspectives in the study of cellular energy sensing processes in vertebrates. [ABSTRACT FROM AUTHOR]

Vasoactive intestinal polypeptide (VIP) was isolated in two molecular forms from an extract of the gastroenteropancreatic system of the pallid sturgeon Scaphirhynchus albus (Acipenseriformes). VIP-1 was identical to the peptide previously isolated from the rainbow trout Oncorhynchus mykiss and the bowfin, Amia calva, consistent with the proposed sister group relationship of the Acipenseriformes and the Neopterygii. Sturgeon VIP-2 contained the amino acid substitution (Ala4 to Ser) at a site previously regarded as invariant. The isolation of two distinct VIP gene products provides some support for the hypothesis that S. albus, with approximately 120 chromosomes, is functionally tetraploid but the alternative view that the species is functionally diploid and the two peptides arose from a local duplication of the VIP gene within the Scaphirhynchus lineage cannot be rejected. [ABSTRACT FROM AUTHOR]

Growth hormone (GH), prolactin, and their relatives constitute a multigene family which is considered to have evolved from a common ancestor. The structural and functional domains of GH appear to be highly conserved among vertebrates. In order to investigate the phylogenetic relationships among GHs in the Actinopterygii and Sarcopterygii, we have cloned and sequenced GH from the pituitary of the primitive bony fish, Amia calva. Bony fishes (teleosts) and Amia (Halecomorphi) are purported sister-groups within the Neoptergii, hence studies on this perspective group of fish can provide insights into the evolution of GH. The deduced amino acid (aa) sequence from A. calva GH (amGH) cDNA revealed that the mature GH consists of 190 residues. Phylogenetic comparisons with GH aa sequences from blue shark, sturgeon, four teleosts (eel, carp, porgy, flounder), and two sarcopterygians (African lungfish and bullfrog) indicated, in the most parsimonious cladogram, that amGH clusters as the sister-group to the teleosts, that sturgeon is the sister-group to the Neopterygii, and that the African lungfish and bullfrog are in the same clade.

Ampullary sense organs are distributed in groups over the head of Hydrolagus colliei with their pores in clusters and innervated by the buccal, hyomandibular and superficial ophthalmic branches of the anterior lateral line nerve. The ampullae contain ciliated sense cells in an alveolate-shaped epithelium, which communicates to the surface through a jelly-filled tube. The sense cells synapse at their bases with the afferent nerve fibers that terminate in the dorsal nucleus of the anterior lateral line lobe of the medulla. The anatomy and ultrastructure support the homology with the ampullae of Lorenzini of elasmobranchs. Single units recorded from the buccal branch of the anterior lateral line nerve are either lateral line or ampullary in character, the former being sensitive only to mechanical stimuli, the latter to both mechanical and to weak electric stimuli. They are also distinguished by the positions of their receptive fields. The electroreceptive units are spontaneously active and are excited by a cathode placed near the opening of their pore and inhibited by an anode. Compound evoked potentials are recorded from beneath the lateral aspect of the tectum in response to weak electric fields in the bath. Each recording locus has a best position and orientation of the electric field. The electric fields are effective if their duration is longer than ca. 2 ms; longer than 10 ms makes no difference until an OFF effect becomes distinct at ca. 50 ms. The reception is tuned to low frequencies but is not sensitive to maintained current (DC). Evoked potentials summating moderate numbers of responses are clear at < 1 microV/cm. Ratfish were conditioned in a ring-shaped tank to reverse the direction of swimming when an electric field was switched ON. The stimulus was a 5 Hz square wave or the onset of a DC of 1-10 microA between a pair of electrodes on the floor of the tank. The fish responded to fields as weak as 0.2 microV/cm. A specialized sense modality for electroreception, similar to that in elasmobranchs and most other groups of nonteleost fishes, except for Myxini and Neopterygii (holosteans), is present in the subclass Holocephali. The notion is supported that this modality and its central as well as peripheral apparatus arose early in the evolution of vertebrates. Only two losses of the whole system need be hypothesized, on this idea, once in the ancestors of the hagfishes and once in the ancestors of the neopterygians, which include the teleosts. Some orders of teleosts then evolved a new system of electroreception independently. The ciliary receptor cells are probably primitive; microvillar sense cells evolved independently.

To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.

The hump-backed ginglymodian fishKyphosichthys grandei, from the Anisian (Middle Triassic) of South China, is re-described. The revised description presents much previously unknown or misidentified anatomical information, such as the presence of a median gular plate; a short, broad, squarish rostral; two pairs of extrascapulars, of which the lateral one is fused with the parietal bone; parasphenoid having relatively large, dorsoposteriorly oriented ascending processes which articulate with the sphenotics; a complete row of scales bordering the body lobe; and supracleithrum with a concave facet for articulation with the posttemporal, etc. Taxonomical comparison clearly distinguishesKyphosichthysfrom other known hump-backed ginglymodians – that is,Luoxiongichthys,Lophionotus,SemiolepisandParalepidotus– and a potential stem-group ginglymodianDapedium. A more comprehensive cladistic analysis of the Ginglymodi is conducted herein based on incorporation of more morphological characters and taxa, and rectification of the character states of some taxa used in previous analyses after re-description ofKyphosichthys grandeiand better knowledge ofLuoxiongichthys hyperdorsalisandSangiorgioichthys suibased on our observations of specimens at the Geological Museum of Peking University, Beijing, China. The results of our analysis produce the most completely resolved and best-supported hypothesis for the monophyletic group Semionotiformes to date, and also support a new hypothesis that the Middle Triassic ginglymodiansLuoxiongichthys,SangiorgioichthysandKyphosichthysform a monophyletic group at the base of the Ginglymodi, of whichKyphosichthys grandeiis the sister group ofSangiorgioichthys sui. The new family Kyphosichthyidae is introduced. The present contribution supplements previous analyses of the Ginglymodi, especially for basal taxa and the clade Semionotiformes, and sheds new light on the origin and early diversification of the Ginglymodi. http://zoobank.org/urn:lsid:zoobank.org:pub:C8ACA263-8658-4A66-BFF9-99F6D5C84E91 [ABSTRACT FROM PUBLISHER]

Flying fishes are extraordinary aquatic vertebrates capable of gliding great distances over water by exploiting their enlarged pectoral fins and asymmetrical caudal fin. Some 50 species of extant flying fishes are classified in the Exocoetidae (Neopterygii: Teleostei), which have a fossil record no older than the Eocene. The Thoracopteridae is the only pre-Cenozoic group of non-teleosts that shows an array of features associated with the capability of over-water gliding. Until recently, however, the fossil record of the Thoracopteridae has been limited to the Upper Triassic of Austria and Italy. Here, we report the discovery of exceptionally well-preserved fossils of a new thoracopterid flying fish from the Middle Triassic of China, which represents the earliest evidence of an over-water gliding strategy in vertebrates. The results of a phylogenetic analysis resolve the Thoracopteridae as a stem-group of the Neopterygii that is more crown-ward than the Peltopleuriformes, yet more basal than the Luganoiiformes. As the first record of the Thoracopteride in Asia, this new discovery extends the geographical distribution of this group from the western to eastern rim of the Palaeotethys Ocean, providing new evidence to support the Triassic biological exchanges between Europe and southern China. Additionally, the Middle Triassic date of the new thoracopterid supports the hypothesis that the re-establishment of marine ecosystems after end-Permian mass extinction is more rapid than previously thought. [ABSTRACT FROM AUTHOR]

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The review addresses the history and current state of ideas about the phylogenetic relationships and the evolutionary history of Acipenseriformes and outlines the main results of the studies on the key aspects of their development and morphology. On this basis, the hypothesis of paedomorphosis as a systemic mechanism underlying not only the formation of the unique structural type of the sturgeon skull, but also playing an essential role in the further morphological diversification of the group is formulated. [ABSTRACT FROM AUTHOR]

As part of the transition from Holostei to Teleostei, †Pachycormiformes represent a key group of fishes. However, the anatomy and phylogenetic relationships of the group in the context of the neopterygians are far from being understood. In this contribution we describe a new pachycormiform, †Kaykay lafken gen. et sp. nov., from the Upper Jurassic of Argentina. We made an exhaustive review of morphological characters of holostean and teleostean fishes and explore through a cladistic analysis the phylogenetic relationships of the new species. †Kaykay gen. nov. is retrieved among †Pachycormiformes as being the sister taxon of the macrocarnivorous clade composed of †Orthocormus and †Hypsocormus. Among †Pachycormiformes the pattern of relationships mostly agrees with previous hypotheses, although our study highlights the still poor knowledge of the anatomy of this group. According to our results †Saurostomus is the sister taxon of other toothed pachycormids. †Orthocormus species are recovered as a monophyletic group. The unsolved position of †Pachycormus and †Sauropsis might be a consequence of poor preservation, revealing a lack of understanding of their anatomy. Our phylogenetic analysis also confirms the rapid radiation of holosteans and teleosteomorphs in the Early Triassic and the radiation of pholidophoriforms in the Middle Triassic. †Aspidorhynchoidei radiate in the Early Jurassic. The large ghost ranges (e.g. between †Aspidorhynchoidei and Teleosteomorpha) evidence biases in the fossil record. [ABSTRACT FROM AUTHOR]

Wushaichthys exquisitus, a small fish from the Ladinian of Xingyi, Guizhou Province, southern China, was named a few years ago and interpreted as the most primitive species in the Thoracopteridae (Triassic 'flying' fishes with a Euro-Asian distribution). However, this hypothesis was questioned, because Wushaichthys also shares features with Peltopleuridae. A detailed morphological re-description of Wushaichthys was conducted based on new specimens, plus a revision of previously studied ones, as well as of members of Peripeltopleurus and thoracopterids, and their relationships were tested with a phylogenetic analysis based on 137 characters and 54 taxa. The results suggest that Wushaichthys is a member of a clade that is interpreted here as the new superfamily Thoracopteroidea, which contains Wushaichthyidae fam. nov. (Wushaichthys + Peripeltopleurus) and Thoracopteridae and is the sister taxon of the non-monophyletic Peltopleuridae among Peltopleuriformes. Thoracopteroidea superfam. nov. is strongly supported by numerous synapomorphies (e.g. frontal (= parietal) bone slightly expanded laterally; posttemporal contacts the extrascapular anterolaterally separating it from its counterpart; suspensorium is vertically oriented; narrow and deep rectangular preopercle, vertically oriented; preopercle sutured with the rear edge of the maxilla throughout the maxillary process; enlarged pectoral fins in most genera; and deeply forked hypocercal caudal fin). Although Thoracopteridae is monophyletic, one of its genera, Thoracopterus, is not. Consequently, the content of Thoracopteridae was re-evaluated and now includes Thoracopterus, Gigantopterus, Potanichthys comb. nov. and Italopterus gen. nov. Wushaichthyidae is supported by a unique combination of characters, and the results confirm it as a thoracopteroid, but not a thoracopterid. The characters of Wushaichthys are relevant for understanding the taxonomy and systematics of thoracopteroids, especially the evolutionary morphological modifications of the pectoral and pelvic fins and the lower lobe of the caudal fin, which are some of the main characters of these fishes. [ABSTRACT FROM AUTHOR]

A new species of the actinopterygian fish genus Saurichthys is described on the basis of several spe-cimens from the Sceltrich beds (Meride limestone Formation) of the UNESCO World Heritage area of Monte San Giorgio. The new species shows among other characters, unsegmented lepidotrichia in all fins and elongated and wide paired fins, suggesting a different adaptation for swimming and catching preys with respect to other Saurichthys species of Monte San Giorgio. Phylogenetic analysis suggests that the new species is closely related to the Saurorhynchus species group. The new finding adds further knowledge to the plasticity and functional adaptations of the genus Saurichthys, which was one of the most successful actinopterygians of the Triassic. [ABSTRACT FROM AUTHOR]

The new genus Thiollierepycnodus is erected here to accommodate ' Gyrodus ' wagneri or ' Proscinetes ' wagneri , a taxon known since the 19th century from the marine Kimmeridgian Plattenkalk of Cerin (France) and since 2014 at the excavation site of the Naturkunde-Museum Bamberg in Wattendorf (Germany). Thiollierepycnodus is placed in Pycnodontidae (Upper Jurassic to Eocene), which is the most advanced family of Pycnodontiformes. With 154–152 Myr (Upper Jurassic), Thiollierepycnodus belongs to the stratigraphically oldest Pycnodontidae, still possessing some primitive features such as four incisiform teeth in the dentary, a crown of bifurcated anterior dentary teeth, reduced scale bars posterior to the dorsal fin origin, but the area of pterygiophores without scales and nine to 10 postanal ventral keel scales and approximately 10 complete scale rows posterior to the cloaca. A phylogenetic analysis leads to the placement of this taxon in Proscinetinae. This and the introduction of two additional taxa from the Cretaceous of Lebanon in the phylogeny are further steps to enlighten the broader evolutionary patterns of Pycnodontidae. [ABSTRACT FROM AUTHOR]

The extinct ray-finned fish taxon Robustichthys luopingensis from Luoping, eastern Yunnan, China represents the largest holostean known in the Middle Triassic. Despite its potential significance for investigating the holostean phylogeny and reconstructing the Triassic marine ecosystems, Robustichthys has so far not been described in detail and its phylogenetic position within the Holostei was controversy. This study provides a redescription and revision of Robustichthys based upon a comparative study of eight type specimens and nine new specimens. Newly recognized information includes a toothed parasphenoid, a pair of premaxillae not pierced by the olfactory nerve, a splint-like quadratojugal, a hatchet-shaped hyomandibula, an hourglass-shaped symplectic, anterior and posterior ceratohyals, a complete series of branchiostegal rays, and sclerotic bones. A revised reconstruction of Robustichthys is presented. Results of a cladistic analysis confirmed Robustichthys as an ionoscopiform within the Halecomorphi; the previous placements of Robustichthys as a basal ginglymodian and Ionoscopidae as a basal amiiform clade are not supported. The sister group relationship between Sinamiinae (Sinamia and Ikechaoamia) and Amiinae (Amia and Cyclurus) within the Amiidae is newly recognized. This revised topology provides new insights into the evolution and historical paleoecology of halecomorph fishes. [ABSTRACT FROM AUTHOR]

The Eocene whiptail stingrays of the family Dasyatidae from the Bolca Lagerstätte, NE Italy, are revised herein in detail. The analysis of the anatomical and morphometric features allows us to identify the species "Dasyatis" zigni (Molin, 1861) as a junior synonym of "D." muricatus (Volta, 1796), and to assign it to the new genus Tethytrygon gen. n. This new taxon exhibits a unique combination of features (e.g., rhombic disc wider than long, elongated tail folds fail to reach the tip of the tail, thorns absent, single serrated tail sting, "caniniform" teeth on upper jaw, tooth crown ornamentation absent, 175–179 vertebrae, 108–117 pectoral radials, 24–27 pelvic radials and other features of clasper anatomy) that clearly support its attribution to the subfamily Neotrygoninae of the stingray family Dasyatidae. The morphological and phylogenetic affinities of Tethytrygon gen. n. with the living neotrygonines (Neotrygon and Taeniura) suggest a close association of this taxon with the tropical shallow‐water habitats hypothesized for the Bolca palaeoenvironment during the early Eocene. Moreover, the analysis of the fossil occurrences of the neotrygonines provides new insights into the role of the Tethys for the origin and evolutionary history of certain whiptail stingrays. [ABSTRACT FROM AUTHOR]

A new specimen of coelacanth based on a new specimen from the Meride Limestone Formation of the UNESCO World Heritage area of Monte San Giorgio is described. It represents the first occurrence of an actinistian in this formation. The newly discovered specimen shares many characters with the poorly known Heptanema paradoxum Bellotti, 1857 from the Ladinian Perledo Formation of Northern Italy. A comparison with the holotype and only existing specimen of H. paradoxum supports the assignment of the new specimen to the genus Heptanema. Some anatomical differences between the two specimens are most probably due to different ontogenetic stages, while few may support the erection of a new species; since the specimen is a juvenile it is preferred not to erect a new species, but to classify the specimen as Heptanema sp. New available data from both the holotype of H. paradoxum and form the new specimen allows an attempt to assess the phylogenetic relationships of Heptanema. [ABSTRACT FROM AUTHOR]

The previously alleged ‘semionotid’ fish Asialepidotus shingyiensis from the Middle Triassic (Ladinian) marine deposits of Guizhou and Yunnan, China has recently been identified as a halecomorph, but its phylogenetic relationships with other halecomorphs remain controversial. This taxon was successively placed in different halecomorph orders: Amiiformes, Parasemionotiformes and ‘Panxianichthyiformes’. Here, a detailed redescription of Asialepidotus is presented based upon a comparative study of the original material with 50 new specimens. Newly recognized anatomical information includes a V-shaped rostral, paired vomers, a toothed parasphenoid, a dermosphenotic with a canal-bearing innerorbital flange, a splint-like quadratojugal, a branch of the infraorbital sensory canal in the maxilla, and many elements in the hyoid and branchial apparatuses and the lower jaw. Results of a cladistic analysis incorporating these new data indicate that the ‘Panxianichthyiformes’ is a poorly defined, paraphylectic grade; Asialepidotus is not sister to Panxianichthys as previously suggested; instead, it is more derived than Panxianichthys and consists of the sister taxon of the clade Robustichthys plus Jurassic–Cretaceous ionoscopiforms. This phylogenetic reassessment of Asialepidotus extends the stratigraphic range of the Ionoscopiformes in China by ~4 Myr and supports the hypothesis that the early ionoscopiform diversification was already established by the Middle Triassic. [ABSTRACT FROM AUTHOR]

A new pycnodont fish from the early-mid Cenomanian, Late Cretaceous, of the ‘Ein Yabrud quarry near the village of Beit Eil in Israel is the first pycnodont fish to be described from this locality. Due to the locality where it was found, Scalacurvithys naishi gen. et sp. nov. is considered an inhabitant of reefal waters interspersed with lagoons in the eastern Tethys Sea. Scalacurvichthys naishi is notable for its protruding, hook-shaped first dorsal ridge scale above a large triangular dermatocranium, a deeply sloped and antero-posteriorly shortened skull and bifurcated cloacal scales. The bifurcating scales are a new character previously unknown in pycnodontomorph fishes but have been discovered in two more taxa, which indicates a new type of character that will be useful for future phylogenetic analyses of pycnodontomorph fishes. The new taxon is a member of Pycnodontidae and we conducted a phylogenetic analysis to establish its relationships to other pycnodont fishes. Our results reveal that Scalacurvichthys naishi is a well-resolved member of the subfamily Pycnodontinae.http://zoobank.org/urn:lsid:zoobank.org:pub:04383E2A-551A-4F57-8996-68E06EFA52E0 [ABSTRACT FROM AUTHOR]

The Permo-Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern extinction risk, but this is not so commonly the case for mass extinctions in deep time. Here, we explore the evolution of non-teleostean Actinopterygii (bony fishes) from the Devonian to the present day, and we concentrate on the Permo-Triassic mass extinction. We apply a variety of time-scaling metrics to date the phylogeny, and show that diversity peaked in the latest Permian and declined severely during the Early Triassic. In line with previous evidence, we find the phylogenetic signal of extinction increases across the mass extinction boundary: extinction of species in the earliest Triassic is more clustered across phylogeny compared to the more randomly distributed extinction signal in the late Permian. However, body length plays no role in differential survival or extinction of taxa across the boundary. In the case of fishes, size did not determine which species survived and which went extinct, but phylogenetic signal indicates that the mass extinction was not a random field of bullets. [ABSTRACT FROM AUTHOR]

Background: The RAS signaling pathway is a pivotal developmental pathway that controls many fundamental biological processes including cell proliferation, differentiation, movement and apoptosis. Drosophila Seven-INAbsentia (SINA) is a ubiquitin E3 ligase that is the most downstream signaling "gatekeeper" whose biological activity is essential for proper RAS signal transduction. Vertebrate SINA homologs (SIAHs) share a high degree of amino acid identity with that of Drosophila SINA. SINA/SIAH is the most conserved signaling component in the canonical EGFR/RAS/RAF/MAPK signal transduction pathway. Results: Vertebrate SIAH1, 2, and 3 are the three orthologs to invertebrate SINA protein. SINA and SIAH1 orthologs are found in all major taxa of metazoans. These proteins have four conserved functional domains, known as RING (Really Interesting New Gene), SZF (SIAH-type zinc finger), SBS (substrate binding site) and DIMER (Dimerization). In addition to the siah1 gene, most vertebrates encode two additional siah genes (siah2 and siah3) in their genomes. Vertebrate SIAH2 has a highly divergent and extended N-terminal sequence, while its RING, SZF, SBS and DIMER domains maintain high amino acid identity/similarity to that of SIAH1. But unlike vertebrate SIAH1 and SIAH2, SIAH3 lacks a functional RING domain, suggesting that SIAH3 may be an inactive E3 ligase. The SIAH3 subtree exhibits a high degree of amino acid divergence when compared to the SIAH1 and SIAH2 subtrees. We find that SIAH1 and SIAH2 are expressed in all human epithelial cell lines examined thus far, while SIAH3 is only expressed in a limited subset of cancer cell lines. Conclusion: Through phylogenetic analyses of metazoan SINA and SIAH E3 ligases, we identified many invariant and divergent amino acid residues, as well as the evolutionarily conserved functional motifs in this medically relevant gene family. Our phylomedicinal study of this unique metazoan SINA/SIAH protein family has provided invaluable evolution-based support towards future effort to design logical, potent, and durable anti-SIAH-based anticancer strategies against oncogenic K-RAS-driven metastatic human cancers. Thus, this method of evolutionary study should be of interest in cancer biology. [ABSTRACT FROM AUTHOR]

This study evaluates the phylogeny of ray-finned fishes (Actinopterygii) combining most available information (44 markers from nuclear and mitochondrial DNA and 274 morphological characters). The molecular partition of the dataset was produced through a pipeline (GB-to-TNT) that allows the fast building of large matrices from GenBank format. The analysed dataset has 8104 species, including representatives of all orders and 95% of the 475 families of Actinopterygii, making it the most diverse phylogenetic dataset analysed to date for this clade of fishes. Analysed morphological characters are features historically considered diagnostic for families or orders, which can be unequivocally coded from the literature. Analyses are by parsimony under several weighting schemes. General results agree with previous classifications, especially for groups with better gene sampling and those long thought (from morphological evidence) to be monophyletic. Many clades have low support and some orders are not recovered as monophyletic. Additional data and synthetic studies of homology are needed to obtain synapomorphies and diagnoses for most clades. [ABSTRACT FROM AUTHOR]

ABSTRACT Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic- Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early- Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene- Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous- Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints. [ABSTRACT FROM AUTHOR]

Since Darwin, biologists have been struck by the extraordinary diversity of teleost fishes, particularly in contrast to their closest "living fossil" holostean relatives. Hypothesized drivers of teleost success include innovations in jaw mechanics, reproductive biology and, particularly at present, genomic architecture, yet all scenarios presuppose enhanced phenotypic diversification in teleosts. We test this key assumption by quantifying evolutionary rate and capacity for innovation in size and shape for the first 160 million y (Permian-Early Cretaceous) of evolution in neopterygian fishes (the more extensive clade containing teleosts and holosteans). We find that early teleosts do not show enhanced phenotypic evolution relative to holosteans. Instead, holostean rates and innovation often match or can even exceed those of stem-, crown-, and total-group teleosts, belying the living fossil reputation of their extant representatives. In addition, we find some evidence for heterogeneity within the teleost lineage. Although stem teleosts excel at discovering new body shapes, early crown-group taxa commonly display higher rates of shape evolution. However, the latter reflects low rates of shape evolution in stem teleosts relative to all other neopterygian taxa, rather than an exceptional feature of early crown teleosts. These results complement those emerging from studies of both extant teleosts as a whole and their sublineages, which generally fail to detect an association between genome duplication and significant shifts in rates of lineage diversification. [ABSTRACT FROM AUTHOR]

Biochemical thought posits that rate-limiting steps (defined here as points of flux control) are strongly selected as points of pathway regulation and control and are thus expected to be evolutionarily conserved. Conversely, population genetic thought based upon the concepts of mutation-selection-drift balance at the pathway level might suggest variation in flux controlling steps over evolutionary time. Glycolysis, as one of the most conserved and best characterized pathways, was studied to evaluate its evolutionary conservation. The flux controlling step in glycolysis was found to vary over the tree of life. Further, phylogenetic analysis suggested at least 60 events of gene duplication and additional events of putative positive selection that might alter pathway kinetic properties. Together, these results suggest that even with presumed largely negative selection on pathway output on glycolysis, the co-evolutionary process under the hood is dynamic. [ABSTRACT FROM AUTHOR]

Bony fishes are the principal group of backboned animals in contemporary aquatic settings. Extant species are the focus of a vigorous program of macroevolutionary research, but paleontology offers important perspectives. Multiple fossil records bear on the evolution of bony fishes, each with its own strengths and weaknesses. Understanding of the interrelationships among living bony fishes has improved substantially in recent years, but confidence in the phylogenetic placement of fossils is highly variable. This reflects limitations in current understanding of both fossil anatomy and hard-tissue characters for extant clades. Patterns of taxonomic and morphological diversity over bony fish history remain incompletely known, with most studies restricted to particular clades or specific intervals of time. The wealth of anatomical data recorded by the fossil record could make an important addition to a growing body of work examining phenotypic evolution across living species, but incorporating this information requires the placement of fossils within phylogenetic trees. [ABSTRACT FROM AUTHOR]

Background: Teleosts constitute more than 99 % of living actinopterygian fishes and fossil teleosts have been studied for about two centuries. However, a general consensus on the definition of Teleostei and the relationships among the major teleostean clades has not been achieved. Our current ideas on the origin and early diversification of teleosts are mainly based on well-known Mesozoic marine taxa, whereas the taxonomy and phylogenetic relationships of many Jurassic continental teleosts are still poorly understood despite their importance to shed light on the early evolutionary history of this group. Here, we explore the phylogenetic relationships of the Late Jurassic (Oxfordian - Tithonian) freshwater †Luisiella feruglioi from Patagonia, in a comprehensive parsimony analysis after a thorough revision of characters from previous phylogenetic studies on Mesozoic teleosts. Results: We retrieved †Luisiella feruglioi as the sister taxon of the Late Jurassic †Cavenderichthys talbragarensis, both taxa in turn forming a monophyletic group with the Early Cretaceous †Leptolepis koonwarri. This new so far exclusively Gondwanan freshwater teleost clade, named †Luisiellidae fam. nov. herein, is placed outside crown Teleostei, as a member of the stem-group immediately above the level of †Leptolepis coryphaenoides. In addition, we did not retrieve the Late Jurassic †Varasichthyidae as a member of †Crossognathiformes. The position of †Crossognathiformes within Teleocephala is confirmed whereas †Varasichthyidae is placed on the stem. Conclusions: The general morphology of luisiellids is that of basal, stem Teleocephala; however, most of their synapomorphies have evolved independently in teleocephalans. Similarly, the resemblance between varasichthyids and crossognathiforms might be due to parallel evolution. In accordance to most teleostean phylogenies, our analysis shows that a major morphological change occurred along the stem line and are currently recorded at the level of †Leptolepis coryphaenoides. A stem-based total clade Teleostei has been accepted for this work. [ABSTRACT FROM AUTHOR]

High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes--generically known as restriction site associated DNA sequencing (RAD-seq)--is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting " neutral" elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/ PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods. [ABSTRACT FROM AUTHOR]

The fossil record represents an important test to molecular divergence estimates, with known occurrences representing minimum divergence times for sister taxa. As such, accurately placing fossils in phylogenies is integral to understanding the patterns and processes that shape the tree of life. The chelicerate order Xiphosura comprises classic archetypes of morphological stasis, with the earliest known Ordovician representatives exhibiting all key morphological characteristics of the group. Molecular studies on the four extant species consistently retrieve a basal split between Limulinae and Tachypleinae, but conflict regarding the relationships of the three Asian species. Molecular divergence estimates using either no or a single fossil calibration point infer a Cretaceous or Palaeogene origin for Limulidae and a Palaeogene or Neogene origin for Tachypleinae and Tachypleus. Here, we present male and female specimens of Tachypleus syriacus (=' Mesolimulus' syriacus) from the Cretaceous of Lebanon, revealing an anterior scalloped carapace margin in males-a derived condition of sexual dimorphism shared with Tachypleus tridentatus. Morphological phylogenetic analysis of total group Limulidae retrieves a monophyletic Tachypleus with a minimum divergence time during the Cretaceous, while crown-group Tachypleinae and Limulidae are both present during the Triassic, showing that molecular clock analyses have significantly underestimated the divergence times for these taxa. [ABSTRACT FROM AUTHOR]

The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. [ABSTRACT FROM AUTHOR]

This review summarizes the achievements and novel perspectives that our fish mitochondrial genome (mitogenome) project has brought to molecular phylogenetics and evolution of fishes during the last 15 years (1999-2014). To date, we have assembled ≈1,340 whole mitogenome sequences from fishes, publishing 83 mitogenomic papers on all major fish lineages (except agnathans). Those papers have been cited 5,303 times in total as of 30 September 2014 and have been featured in many textbooks and scientific articles as well as various media. These results have not only had a significant impact on the scientific community, but also attracted considerable attention from the general public. The success of the project largely owes to our own development of a novel, PCR-based approach for sequencing whole mitogenomes (ca. 16,500 bp), which opened a new avenue toward addressing higher-level relationships of fishes based on longer DNA sequences from a number of taxa. Shortly after the development of the method, we explicitly demonstrated the phylogenetic utility of mitogenomic data and actually resolved a long-standing issue in basal teleostean relationships. On the basis of those encouraging results from the initial studies, we published a series of four mitogenomic papers in 2003, which together encompass the whole of actinopterygian diversity and provided a 'big picture' phylogenetic framework for the group. Those four studies offered a useful phylogenetic basis for subsequent studies (i.e., with a different choice of outgroups and targeted taxa) and have facilitated massive sequencing efforts for a wide variety of fishes from chondrichthyians to higher teleosts living in diverse habitats from freshwaters to the deep sea. We highlight some of the 83 mitogenomic papers by subject and briefly refer to the phylogenetic and evolutionary significances of those studies. Finally, we argue that intensive taxonomic sampling from an interface between species and populations together with the massive character sampling from mitogenome sequences using next-generation sequencing (NGS) technologies would enable simultaneous attempts to delimit species boundaries and to reconstruct evolutionary relationships at much finer scale, eventually unraveling the fish part of the Tree of Life in a bottom-up manner with more accurate estimations of species diversity. [ABSTRACT FROM AUTHOR]