New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi)

We provide 15 new primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes in an attempt to resolve relationships of this diverse group of freshwater fishes with extensive taxonomic sampling. Sequences from this region have the following desirable characteristics for phylogenetic analyses, some of which are lacking from the more commonly used cyt b and 12S/16S rRNA genes: they are (1) easy to align, (2) relatively long (ca. 3.4 kb), and (3) contain more phylogenetically informative variation at 1st and 2nd codon positions. Moreover, the ND4/ND5 gene region is easy to amplify and sequence when employing the protocol suggested herein.     

Gill‐filament ossifications: a possible morphological synapomorphy uniting the families Balitoridae and Cobitidae (Ostariophysi: Cypriniformes)

Ossifications associated with the gill filaments of members of the Balitoridae and Cobitidae are described for the first time. Although gill‐filament ossifications are common in teleosts, similar ossifications were not observed in other members of the order Cypriniformes. Their presence is interpreted as a shared and derived character uniting the families Balitoridae and Cobitidae as a monophyletic group.     

Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences

Family Catostomidae is a diverse group of benthic freshwater fishes that are distributed across North America and in parts of East Asia. In this study, the phylogenetic relationships of Catostomidae is examined using 3436 nucleotides of mitochondrial ND4 and ND5 protein coding genes and intervening tRNAs. All 13 genera and 60 species of catostomids were sampled to represent diversity of the family. Catostomidae and its four subfamilies were found to be monophyletic; however, relationships of the subfamilies are not strongly supported with bootstrapping. The analysis provides strong support for recognizing four tribes in subfamily Catostominae.     

Phylogenetic interrelationships of ginglymodian fishes (Actinopterygii: Neopterygii)

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.     

The ontogeny and homology of the Weberian apparatus in the zebrafish Danio rerio (Ostariophysi: Cypriniformes)

The ontogeny of the Weberian apparatus was examined in the zebrafish, Danio rerio , using both cleared and stained specimens and histology. Over 300 individuals from four independent zebrafish lineages, ranging in size from 3 to 28 mm TL, were examined for this study. Results provide a basic understanding of the development of the Weberian apparatus in the wild-type zebrafish. Our results, in conjunction with those already published, point to substantial variation in the development of the Weberian apparatus among otophysans and new interpretations of the homology of certain ossicles (e.g. tripus and claustrum). Hypotheses of homology among various Weberian ossicles are considered and represent an important step in understanding the evolution of sound transmission in ostariophysan fishes.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 241–254.     

Phylogenetic relationships of fossil and Recent gonorynchiform fishes (Teleostei: Ostariophysi)

This paper represents the first cladistic analysis of the interrelationships of all nominal fossil and living gonorynchiform genera. Gonorynchiformes is the basal group of the superorder Ostariophysi, and is confirmed as monophyletic on the basis of 12 synapomorphies. The Gonorynchiformes is be subdivided into two monophyletic suborders, Chanoidei and Gonorynchoidei. The Chanoidei includes the family Chanidae, which in turn includes the Recent Chanos plus five fossil genera, grouped in two subfamilies: Chaninae (( Chanos +† Tharrhiai) + † Parachanos +† Dastilbe ) and † Rubiesichthyinae († Rubiesichthys +† Gordichthys ). † Aethalionopsis is the sister-group to the Chanidae. Gonorynchoidei includes two families Gonorynchidae and Kneriidae. Gonorynchidae is formed by ( Gonorynchus, † Notogoneus ) and four fossil taxa of uncertain definition and interrelationships: †Charitosomus, † Charitopsis, † Ramallichthys, and †fudeichthys. The last four genera were previously included in the families †Charitosomidae and †Judeichthyidae, which could not be supported as monophyletic in this analysis. Kneriidae consists of two subfamilies Phractolaeminae with one genus Phractolaemus, and Kneriinae which includes (( Kneria + Parakneria ) + ( Grasseichthys + Cromeria )), the latter two being paedomorphic forms. The Phractolaeminae and the Kneriinae are freshwater African taxa with no known fossil record. The order Gonorynchiformes is represented herein by 18 genera, extending back to the Early Cretaceous. More work is required to clarify the interrelationships of the Gonorynchidae and the paedomorphic characters that apparently played an important role in the evolution of this morphologically diverse group of fishes.     

Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study

After the completion of several entire genome projects and a remarkable increase in public genetic databases in the recent years the results of post-genomic analyses can facilitate a better understanding of the genomic evolution underlying the diversity of organisms and the complexity of gene function. This influx of genomic information and resources is also beneficial to the discipline of systematic biology. In this paper, we describe a set of 6 previous and 22 new PCR/sequencing primers for RAG1, Rhodopsin and four novel nuclear markers from IRBP, EGR1, EGR2B and EGR3 that we developed through an approach making use of public genetic/genomic data mining for one of the ongoing tree of life projects aimed at understanding the evolutionary relationships of the planet's largest clade of freshwater fishes — the Cypriniformes. The primers and laboratory protocols presented here were successfully tested in 33 species comprising all cypriniform family and subfamily groups. Phylogenetic performance of each gene, as well as their implications in the investigation of the evolution of cypriniform fishes were assessed and discussed.     

Phylogenetic relationships of Mexican minnows of the genus Notropis (Actinopterygii, Cyprinidae)

We conducted phylogenetic analyses based on complete mitochondrial cytochrome b gene sequences among southern and central Mexican cyprinid species, included in the genera Notropis and Hybopsis. In addition 15 northern species of the genera Notropis and Hybopsis were included in the analyses in order to place the Mexican species into a larger phylogenetic framework. The phylogenetic relationships supported the existence of five major clades: (1) including species of the subgenus Alburnops of the genus Notropis plus N. shumardi; (2) species of the subgenus Notropis; (3) species of the genus Hybopsis; (4) species of the N. texanus + N. volucellus species group of the genus Notropis; (5) Mexican endemic species of the genus Notropis plus the genus Yuriria. Previous phylogenetic inferences based on morphological characters resolved the Mexican minnows analysed as N. sallaei, N. calientis, N. boucardi and Y. alta, non‐monophyletic. According to our cytochrome b evidence all Mexican minnows of the genera Notropis and Yuriria formed a monophyletic group with respect to the northern species of the genera Notropis and Hybopsis. Within the Mexican clade, three well‐supported clades were identified: the first included the closely related species N. moralesi and N. boucardi, which occur in three independent drainages of south Mexico; the second consisted of two different lineages, N. imeldae and an undescribed species of Notropis, inhabiting two independent drainages of south Mexico; the third comprised two central Mexican Notropis species (N. calientis and N. sallaei) and the Y. alta populations. Based on this study and pending a more extensive taxonomic revision of the genus Notropis, we adopt the conservative criterion of considering all Notropis species from southern and central Mexico examined, including Y. alta, as belonging to the genus Notropis. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 323–337.     

Microanatomy of the paired‐fin pads of ostariophysan fishes (Teleostei: Ostariophysi)

Members of the teleost superorder Ostariophysi dominate freshwater habitats on all continents except Antarctica and Australia. Obligate benthic and rheophilic taxa from four different orders of the Ostariophysi (Gonorynchiformes, Cypriniformes, Characiformes, and Siluriformes) frequently exhibit thickened pads of skin along the ventral surface of the anteriormost ray or rays of horizontally orientated paired (pectoral and pelvic) fins. Such paired‐fin pads, though convergent, are externally homogenous across ostariophysan groups (particularly nonsiluriform taxa) and have been considered previously to be the result of epidermal modification. Histological examination of the pectoral and/or pelvic fins of 44 species of ostariophysans (including members of the Gonorynchiforms, Cypriniformes, Characiformes, and Siluriformes) revealed a tremendous and previously unrecognized diversity in the cellular arrangement of the skin layers (epidermis and subdermis) contributing to the paired‐fin pads. Three types of paired‐fin pads (Types 1–3) are identified in nonsiluriform ostariophysan fishes, based on differences in the cellular arrangement of the epidermis and subdermis. The paired‐fin pads of siluriforms may or may not exhibit a deep series of ridges and grooves across the surface. Two distinct patterns of unculus producing cells are identified in the epidermis of the paired‐fin pads of siluriforms, one of which is characterized by distinct bands of keratinization throughout the epidermis and is described in Amphilius platychir (Amphiliidae) for the first time. General histological comparisons between the paired fins of benthic and rheophilic ostariophysan and nonostariophysan percomorph fishes are provided, and the possible function(s) of the paired‐fin pads of ostariophysan fish are discussed. J. Morphol. 2012. © 2012 Wiley Periodicals, Inc.     

A Y‐chromosomal comparison of the Madjars (Kazakhstan) and the Magyars (Hungary)

The Madjars are a previously unstudied population from Kazakhstan who practice a form of local exogamy in which wives are brought in from neighboring tribes, but husbands are not, so the paternal lineages remain genetically isolated within the population. Their name bears a striking resemblance to the Magyars who have inhabited Hungary for over a millennium, but whose previous history is poorly understood. We have now carried out a genetic analysis of the population structure and relationships of the Madjars, and in particular have sought to test whether or not they show a genetic link with the Magyars. We concentrated on paternal lineages because of their isolation within the Madjars and sampled males representing all extant male lineages unrelated for more than eight generations (n = 45) in the Torgay area of Kazakhstan. The Madjars show evidence of extensive genetic drift, with 24/45 carrying the same 12‐STR haplotype within haplogroup G. Genetic distances based on haplogroup frequencies were used to compare the Madjars with 37 other populations and showed that they were closest to the Hungarian population rather than their geographical neighbors. Although this finding could result from chance, it is striking and suggests that there could have been genetic contact between the ancestors of the Madjars and Magyars, and thus that modern Hungarians may trace their ancestry to Central Asia, instead of the Eastern Uralic region as previously thought. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Phylogenetic relationships and intraspecific variations of loaches of the genus Lefua (Balitoridae,Cypriniformes)

Three nominal species are known in East Asian balitorid loaches of the genus Lefua, i.e. L. echigonia, L. nikkonis, and L. costata. Lefua echigonia, with large morphological variations was recently separated into two groups, L. echigonia including the holotype and L. sp., based on morphological and ecological traits. We performed protein and DNA analyses to elucidate phylogenetic relationships among loaches of the genus Lefua and to settle the taxonomic status of L. sp. We also investigated intraspecific variations in L. echigonia s. str. to shed light on the process of formation of freshwater fish fauna in Japan. Protein analyses using two-dimensional gel electrophoresis showed that genetic distances between L. sp. and L. echigonia s. str. and between L. sp. and L. nikkonis were as large as that between L. echigonia s. str. and L. nikkonis. DNA analyses of the mitochondrial D-loop region showed that L. sp. and L. echigonia s. str. were monophyletic, respectively, while neither L. nikkonis nor L. costata was monophyletic and these species formed together a clade. The results supported the specific status of L. sp. and proposed reevaluation of the taxonomic status of L. nikkonis and L. costata. DNA analyses also showed that L. sp. was more closely related to L. echigonia s. str. than to the L. nikkonis-L. costata complex, and four local populations were distinguished in L. echigonia s. str. Distribution patterns of the four local populations of L. echigonia s. str. in Japan were approximately congruent with those of the medaka, Oryzias latipes, suggesting that differentiation in the two distantly related fishes have a common historical background.     

Major issues in the origins of ray‐finned fish (Actinopterygii) biodiversity

Ray‐finned fishes (Actinopterygii) dominate modern aquatic ecosystems and are represented by over 32000 extant species. The vast majority of living actinopterygians are teleosts; their success is often attributed to a genome duplication event or morphological novelties. The remainder are ‘living fossils’ belonging to a few depauperate lineages with long‐retained ecomorphologies: Polypteriformes (bichirs), Holostei (bowfin and gar) and Chondrostei (paddlefish and sturgeon). Despite over a century of systematic work, the circumstances surrounding the origins of these clades, as well as their basic interrelationships and diagnoses, have been largely mired in uncertainty. Here, I review the systematics and characteristics of these major ray‐finned fish clades, and the early fossil record of Actinopterygii, in order to gauge the sources of doubt. Recent relaxed molecular clock studies have pushed the origins of actinopterygian crown clades to the mid‐late Palaeozoic [Silurian–Carboniferous; 420 to 298 million years ago (Ma)], despite a diagnostic body fossil record extending only to the later Mesozoic (251 to 66 Ma). This disjunct, recently termed the ‘Teleost Gap’ (although it affects all crown lineages), is based partly on calibrations from potential Palaeozoic stem‐taxa and thus has been attributed to poor fossil sampling. Actinopterygian fossils of appropriate ages are usually abundant and well preserved, yet long‐term neglect of this record in both taxonomic and systematic studies has exacerbated the gaps and obscured potential synapomorphies. At the moment, it is possible that later Palaeozoic‐age teleost, holostean, chondrostean and/or polypteriform crown taxa sit unrecognized in museum drawers. However, it is equally likely that the ‘Teleost Gap’ is an artifact of incorrect attributions to extant lineages, overwriting both a post‐Palaeozoic crown actinopterygian radiation and the ecomorphological diversity of stem‐taxa.     

Comparative ultrastructure of Langerhans‐like cells in spleens of ray‐finned fishes (Actinopterygii)

We studied the morphology and occurrence of splenic Langerhans‐like (LL) cells in species representing 11 orders of ray‐finned fishes, Actinopterygii. LL cells were frequent in spleen tissue of species among Cypriniformes, Esociformes, Salmoniformes, and Pleuronectiformes. These cells contained granules which resembled Birbeck granules known to occur in mammalian Langerhans cells. The ultrastructure of LL cells in Northern pike, Esox lucius, and in Atlantic halibut, Hippoglossus hippoglossus were similar to those reported in salmonids. LL cells found in cyprinids shared some characteristics with the LL cells in other Actinopterygii species, although unique structures distinguished them from the latter. They contained dense bodies within the Birbeck‐like (BL) granules, a characteristic that was never observed in species outside the Cypriniformes. Two types of BL granules were characterized in cyprinid LL cells. The ultrastructure of BL granules across the species is discussed. LL cells in all Actinopterygii species demonstrated close contacts with nearby cells, characterized by adherens‐like junctions. Additionally, multivesicular bodies were present within the cytoplasm and large aggregates of exosomes were observed closely associated with the plasma membrane suggesting their release from the cells. These structures are discussed in relation to mammalian dendritic cells. Macrophages found in European perch, Perca fluviatilis, blue gourami, Trichogaster trichopterus, and Atlantic halibut, Hippoglossus hippoglossus contained lysosomes and residual bodies with structures resembling Birbeck granules. These granules and cells were clearly distinct from LL cells. J. Morphol. 2010. © 2010 Wiley‐Liss, Inc.     

Genus-level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro-evolutionary scenarios

We used the supertree approach of matrix representation with parsimony to reconstruct to date the most exhaustive (genus‐level) phylogeny of Cyprinidae. The supertree of Cyprinidae, representing 397 taxa (237 nominal genera) and 990 pseudocharacters, was well resolved (96%) through extended consensus majority rule, although 36 nodes (9.4%) were unsupported. The proportion of shared taxa among source trees was very low after calculation of the taxonomic coverage index (TCI = 0.059), which is proposed here as a more accurate alternative to the usual ratios calculated from the number of pseudo‐characters or source trees per taxon. We define a new index for the calculation of partitioned qualitative clade support, the partitioned rQS (_prQS), which offers a straightforward visualization of the relative supports of source tree partitions at supertree nodes.The use of _prQS showed that the molecular source tree partition contributed to most node supports within the supertree of Cyprinidae (73%, contra 21% for the morphological partition) and evidenced a fair proportion of conflict at nodes between the two partitions (21%), notably reflecting (i) the greater number and resolution of molecular source trees, and (ii) potential morphological convergences. Most of the higher‐level relationships within Cyprinidae were supported by both morphological and molecular source tree partitions. Our supertree showed a well‐supported dichotomy between a clade consisting of a ‘barbine’ + ‘rasborine’ lineage, sister group to (Barbinae [paraphyletic], (Cyprininae, Labeoninae)), and a clade consisting of other rasborines (large polytomy) and the two monophyletic groups ((Tincinae, Tanichthys), (Ecocarpia, (Acheilognathinae, (Gobioninae, Leuciscinae)))) and (Squaliobarbinae, (Xenocyprinae, Cultrinae)). Through the non‐monophyly of almost all the traditional subfamilies of Cyprinidae and 34 genera, our supertree exemplified the taxonomic chaos that reigns in the classification of the family. It also highlighted that further efforts should aim at increasing taxonomic sampling and generating alternative phylogenetic signals, notably for the still poorly apprehended Tincinae, Squaliobarbinae, Acheilognathinae, Gobioninae, and Rasborinae, the latter representing a key taxon for the understanding of early cyprinid evolution. Our supertree also proved useful for testing macro‐evolutionary scenarios at a wide taxonomic scale. Ancestral reconstructions using linear parsimony confirmed that the Oriental tropical region was the centre of origin of Cyprinidae, and identified three Oriental‐to‐Palaearctic, two Palaearctic‐to‐Nearctic, and one Oriental‐to‐Afrotropical major migration events. On the other hand, we almost completely rejected the hypothesis of presence of barbels as a plesiomorphic condition within Cyprinidae (although ambiguous for maxillary barbels of the Barbinae‐Cyprininae type). The supertree of Cyprinidae serves as a basis to discuss the applications and bias of the newly proposed _prQS, to provide future guidelines for a better achievement of cyprinid phylogeny, and to elaborate further on inter‐continental migrations and the adaptive value of barbels.     

Rho‐kinase inhibitor Y‐27632 facilitates the proliferation,migration and pluripotency of human periodontal ligament stem cells

The selective in vitro expansion and differentiation of multipotent stem cells are critical steps in cell‐based regenerative therapies, while technical challenges have limited cell yield and thus affected the success of these potential treatments. The Rho GTPases and downstream Rho kinases are central regulators of cytoskeletal dynamics during cell cycle and determine the balance between stem cells self‐renewal, lineage commitment and apoptosis. Trans‐4‐[(1R)‐aminoethyl]‐N‐(4‐pyridinyl)cylohexanecarboxamidedihydrochloride (Y‐27632), Rho‐associated kinase (ROCK) inhibitor, involves various cellular functions that include actin cytoskeleton organization, cell adhesion, cell motility and anti‐apoptosis. Here, human periodontal ligament stem cells (PDLSCs) were isolated by limiting dilution method. Cell counting kit‐8 (CCK8), 5‐ethynyl‐2′‐deoxyuridine (EdU) labelling assay, cell apoptosis assay, cell migration assay, wound‐healing assay, alkaline phosphatase (ALP) activity assay, Alizarin Red S staining, Oil Red O staining, quantitative real‐time polymerase chain reaction (qRT‐PCR) were used to determine the effects of Y‐27632 on the proliferation, apoptosis, migration, stemness, osteogenic and adipogenic differentiation of PDLSCs. Afterwards, Western blot analysis was performed to elucidate the mechanism of cell proliferation. The results indicated that Y‐27632 significantly promoted cell proliferation, chemotaxis, wound healing, fat droplets formation and pluripotency, while inhibited ALP activity and mineral deposition. Furthermore, Y‐27632 induced PDLSCs proliferation through extracellular‐signal‐regulated kinase (ERK) signalling cascade. Therefore, control of Rho‐kinase activity may enhance the efficiency of stem cell‐based treatments for periodontal diseases and the strategy may have the potential to promote periodontal tissue regeneration by facilitating the chemotaxis of PDLSCs to the injured site, and then enhancing the proliferation of these cells and maintaining their pluripotency.