A new species of gravel-dwelling loach (Ostariophysi: Nemacheilidae) from the Nepalese Himalayan foothills

Turcinoemacheilus himalaya, new species, is described from the Koshi and Gandaki River basins of Nepal. The new species is distinguished from its hypothesised congener, Turcinoemacheilus kosswigi, from the Euphrates, Tigris and Karoun basins of the Middle East, by the presence of small scales on the posterior half of its body (v. absence of all scales), its shorter caudal peduncle (caudal peduncle length 12-15% standard length, L(S) v. 16-23), its shorter snout (snout length 28-36% head length, L(H) v. 40-49) and by features of its colour pattern, including the presence of small irregularly shaped dark grey markings over the lateral body surface. Turcinoemacheilus himalaya is known to date only from Nepal.     

Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes)

Yang, L., Mayden, R. L., Sado, T., He, S., Saitoh, K. & Miya, M. (2010). Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes). —Zoologica Scripta, 39, 527–550. Carps (e.g. Koi) of the genus Cyprinus and Crucian carps (e.g. Goldfish) of the genus Carassius are among the most popular freshwater fishes around the world. However, their phylogenetic positions within the subfamily Cyprininae, relationships with their allies (e.g. Procypris, Carassioides), and the monophyly of the group formed by them and their allies, which is referred as the tribe Cyprinini sensu stricto, are far from clear. Historically, the Cyprinini was defined by different people according to whether a cyprinine fish possessed a spinous anal‐fin ray (or anal spine), the spine was serrated or not, and occasionally, the number of branched dorsal‐fin rays. Some definitions were established without providing any diagnostic characters. In this study, we investigated the monophyly of the tribe Cyprinini sensu stricto, based on four different historical definitions, and explored the phylogenetic relationships of these members in the subfamily Cyprininae. Using five mitochondrial genes as markers, both maximum‐likelihood and Bayesian trees were constructed using the optimal partitioning strategy. Both analyses successfully resolved a monophyletic Cyprininae and recovered seven major clades from this subfamily. The diagnosis limiting the tribe Cyprinini sensu stricto to four genera, Cyprinus, Carassius, Carassioides and Procypris, received most support. We propose that only those cyprinines that possess a serrated anal spine and have no <10 branched dorsal‐fin rays should be considered members of this tribe. Cyprinini is sister to the Sinocyclocheilus clade, a group traditionally considered a barbin, and together they form the ‘Cyprinini‐Sinocyclocheilus’ clade. Procypris forms the basal clade of the Cyprinini, whereas species of Carassius and Carassioides locate at the top.     

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.     

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]     

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.     

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 relationships of the enigmatic ornate shiner,Cyprinella ornata,a species endemic to Mexico (Teleostei: Cyprinidae)

The systematics and taxonomy of North Americancyprinid fishes has historically been said tobe in a chaotic state of affairs. Much of theconfusion as to relationships of species restsin the lack of explicit phylogenetic hypothesesof species and reliance upon degree ofdistinctiveness of taxa or their overallsimilarity for generic placement. Some specieshave had more turbulent or variable taxonomichistories than others. The ornate shiner, Cyprinella ornata, is one of those species,having been placed in the genera Notropis,Codoma, and Cyprinella within the last20 years and found in current texts in any ofthese three genera. Most of the confusionregarding placement of this species has beenrelated to lack of explicit phylogenetichypotheses to formulate its classification, butto a certain degree some researchers haveignored phylogenetic studies and preferred torely upon its morphological distinctiveness orreproductive behavioral traits of questionablehomology to place it in a monotypic genus andalign it with the genera Pimephales andOpsopoeodus.I present a phylogenetic analysis based oncomplete Cytochrome b sequences fromornate shiners, other species of Cyprinella, purported relatives, and severalother species of the Shiner Clade to determinethe phylogenetic affinities of this enigmaticspecies. Molecular analysis reveals the ornateshiner to be more closely related to species ofCyprinella than to a Pimephalesplus Opsopoeodus clade as previouslydiscussed in one morphological analysis, or asargued by Page and Johnston (1990), Johnstonand Page (1992) and Page and Ceas (1989) basedon observations of spawning behaviors andhypotheses of homology between crevice-spawningand egg-clumping behaviors. This molecularanalysis is more consistent with earliermorphological phylogenetic hypotheses of Mayden(1989) wherein these two clades are notconsidered to be closely related and the ornateshiner is a member of the genus Cyprinella.     

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 major clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial SSU and LSU rDNA sequences

Suckers (Family Catostomidae) are holarctic in distribution and include 76 recent species in 14 genera, with 13 genera and 75 species occurring in North and Central America and Siberia. Although this group constitutes a significant component of many aquatic ecosystems, most historic systematic effort has been either alpha- or limited beta-level studies focusing on the two largest tribes within the family, the Catostomini and the Moxostomatini. A recent phylogenetic study based on morphological, biochemical, and early life history characters has advanced current understanding of relationships among catostomid fishes. To further examine phylogenetic relationships among basal lineages of catostomids, we sequenced the entire mitochondrial (mt) SSU and LSU rRNA genes from genera representing all subfamilies and tribes within Catostomidae. Phylogenetic analysis of gene sequences yielded monophyletic Catostomidae, Ictiobinae, and Catostominae and para- or polyphyletic Cycleptinae, with Myxocyprinus as the basal-most taxon and Cycleptus as either the next most-basal taxon or the taxon basal to the Catostominae. Relationships within the Catostominae were generally consistent with those proposed in the above-noted recent phylogenetic study although Thoburnia and Hypentelium were either a clade sister to or a grade group relative to Moxostoma and Scartomyzon. In all trees, Scartomyzon was paraphyletic and embedded within Moxostoma. Phylogenetic affinities of Erimyzon and Minytrema varied depending on data set and character weighting scheme employed. To better reflect phylogenetic relationships resolved in this extensive analysis, we propose the following changes to the classification of catostomids: formation of the new subfamily Myxocyprininae, containing Myxocyprinus from China; restriction of the Cycleptinae to the two species of Cycleptus from North America; restriction of the tribe Moxostomatini to Moxostoma and Scartomyzon; Erimyzon and Minytrema are incertae sedis within Catostominae; and resurrection of the tribe Thoburniini, containing Thoburnia and expanded to include Hypentelium.     

Geographic independence and phylogenetic diversity of red shiner introductions

Identifying areas at risk of invasion can be difficult when the distribution of a non-native species encompasses geographically disjunct regions. Understanding genealogical relationships among native and non-native populations can clarify the origins of fragmented distributions, which in turn can clarify how fast and far a non-native species may spread. We evaluated genetic variation across the native and invasive ranges of red shiner (Cyprinella lutrensis), a minnow known to displace and hybridize with native species, to reconstruct invasion pathways across the United States (USA). Examination of mitochondrial cytochrome-b variation found that native range populations of red shiner fall into four highly divergent lineages that likely warrant species recognition. Introduced red shiner populations in the eastern and western USA are derived from only two of these lineages. Western USA populations originate from the mid-western and western genetic lineages, whereas eastern introductions derive only from the mid-western lineage. Western USA invasive populations exhibit fewer, but more diverse haplotypes compared to eastern USA invasive populations. We also recovered an undescribed, divergent lineage of Cyprinella that has been cryptically introduced into the western USA, which raises the possibility that hybridization has proceeded following secondary contact between previously allopatric lineages. Approximate Bayesian Computation modeling suggests that the disjunct distribution of red shiner across North America is an agglomeration of independent regional invasions with distinct origins, rather than stepwise advance of an invasion front or secondary introductions across regions. Thus localized control may be effective in managing non-native red shiner, including further spread to areas of conservation concern.