Phylogenetic Relationships of the Creek Chubs and the Spine-Fins: an Enigmatic Group of North American Cyprinid Fishes (Actinopterygii: Cyprinidae)

Phylogenetic analyses based on the complete nucleotide sequence of the mitochondrial 12S ribosomal RNA gene were performed for representatives of major North American cyprinid clades. These analyses resolved four monophyletic groups: (1) Western Clade, represented by Acrocheilus and Gila , (2) Creek Chub Clade, represented by Couesius, Hemitremia, Semotilus , and Margariscus , (3) Open Posterior Myodome Clade, represented by Campostoma, Phenacobius, Cyprinella, Notropis, Platygobio , and Rhinichthys , and (4) Plagopterin Clade, represented by Snyderichthys, Lepidomeda , and Meda . The overall results of these analyses refute previous hypotheses of relationships of North American Cyprinidae based on morphological data. Our analyses support recognition of Snyderichthys , formerly considered a subgenus of Gila, and indicate that the Plagopterin Clade is sister to the Creek Chub Clade. Furthermore, this analysis indicates that hypotheses of relationship between plagopterins and other Western taxa are unsupported and the Open Posterior Myodome Clade is a monophyletic group.     

Hormonally regulated programmed cell death in barley aleurone cells

Cell death was studied in barley (cv Himalaya) aleurone cells treated with abscisic acid and gibberellin. Aleurone protoplasts incubated in abscisic acid remained viable in culture for at least 3 weeks, but exposure to gibberellin initiated a series of events that resulted in death. Between 4 and 8 days after incubation in gibberellin, >70% of all protoplasts died. Death, which occurred after cells became highly vacuolated, was manifest by an abrupt loss of plasma membrane integrity followed by rapid shrinkage of the cell corpse. Hydrolysis of DNA began before death and occurred as protoplasts ceased production of alpha-amylase. DNA degradation did not result in the accumulation of discrete low molecular weight fragments. DNA degradation and cell death were prevented by LY83583, an inhibitor of gibberellin signaling in barley aleurone. We conclude that cell death in aleurone cells is hormonally regulated and is the final step of a developmental program that promotes successful seedling establishment.     

Expression of the alpha 1-proteinase inhibitor gene family during evolution of the genus Mus

alpha 1-Proteinase inhibitors (alpha 1-PIs) are members of the serpin superfamily of proteinase inhibitors, and are important in the maintenance of homeostasis in a wide variety of animal taxa. Previous studies have shown that in mice (genus Mus), evolution of alpha 1-PIs is characterized by gene amplification, region-specific concerted evolution, and rapid accumulation of amino acid substitutions. The latter occurs primarily in the reactive center, which is the region of the alpha 1-PI molecule that determines the inhibitor's specificity for target proteinases. The P1 residue within the reactive center, which is methionine in so-called orthodox alpha 1-PIs and an amino acid other than methionine in unorthodox alpha 1-PIs, is a primary determinant of inhibitor specificity. In the present study, we find that the expression of mRNAs encoding unorthodox alpha 1-PIs is polymorphic within Mus species, i.e., among individuals or inbred strains. This is in striking contrast to mRNAs that encode orthodox alpha 1-PIs, whose concentrations are relatively invariant. The intraspecies variations in mRNA expression represent polymorphisms in the structure of the alpha 1- PI gene family. The results, taken together with previously described aspects of alpha 1-PI evolution, indicate that the dissimilar levels of polymorphism exhibited by orthodox and unorthodox alpha 1-PIs, which likely have distinct physiological functions, may reflect different levels of selective constraint. The significance of this finding to the evolution of gene families is discussed.      

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.     

Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes)

Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (～ 71132 base pairs) for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.     

Balitora eddsi,a new species of hillstream loach (Ostariophysi: Balitoridae) from Nepal

A new species of hillstream loach Balitora eddsi is described from the Karnali River drainage in south‐western Nepal. The new species is distinguished from all its congeners by possessing the following combination of characters: six to seven unbranched pectoral‐fin rays, pelvic‐fin length 12–14% standard length (L_S), dorsal surface without circular or irregular shaped dark blotches, snout pointed, median lobe between anterior rostral barbels pointed posteriorly, dorsal‐fin origin posterior to pelvic‐fin origin, lateral line scales 66–67, caudal peduncle length 22–23·2% L_S, caudal peduncle depth 4·1–4·2 times its length.     

Mitogenomic Evolution and Interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The First Evidence Toward Resolution of Higher-Level Relationships of the World’s Largest Freshwater Fish Clade Based on 59 Whole Mitogenome Sequences

Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world’s largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon–position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely “noise” from the data set and avoids the apparent lack of signal by retaining all available positions in the data set. [Reviewing Editor: Rafael Zardoya]     

Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico

Most of the recognized species of the genus Dionda inhabit drainages of the Gulf of Mexico from central Mexico to central Texas, USA, and have been considered a monophyletic group based on morphological, osteological, and allozyme investigations. Phylogenetic relationships of 15 species of Dionda and 34 species from closely related genera were inferred from one mitochondrial (cytb) and three nuclear gene sequences (S7, Rhodopsin, Rag1) totaling 4487 nucleotides. Separate analyses of all four genes yield congruent phylogenies; however the 15 putative species of Dionda evaluated were never recovered as a monophyletic group when species from nine related genera were included in the analyses. Among the ingroup taxa, one well-supported and highly divergent clade is consistently recognized and consists of six recognized and three undescribed northern species currently recognized in the genus Dionda. These nine species inhabit present or past tributaries of the Rio Grande basin of northern Mexico and southern USA, and were recovered as a basal clade in all analyses. Another large, also strongly supported clade, consisting of seven genera, include five southern recognized species currently in the genus Dionda, forming the sister group to the Codoma clade. These five species comprise the "Southern Dionda clade" and inhabit headwaters of the Pánuco-Tamesí drainage and some adjacent coastal rivers in the Tampico Embayment. The consistent and repeated identification of eight different clades recovered in most of the separate gene analyses strongly supports a division of the non-natural genus Dionda. A new genus, Tampichthys, is proposed for the clade of species endemic to east-central Mexico and formerly in Dionda. Tampichthys and the putative monotypic genus Codoma are more related to Mexican species of the genera Cyprinella and Notropis than to other species referred to Dionda sensu stricto.     

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.