Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics

Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.     

鱼类肌间骨发育分子调控机制及遗传选育研究进展

鱼类的肌间骨(Intermuscular bones, IBs),又称肌间小骨,是分布于鱼体两侧肌隔中及连接在椎体上的小骨,仅存在于低等真骨鱼类中。随着鱼类的系统演化,肌间骨的数目和形态也发生着由无到多再到无、由简单到复杂再到简单的变化。中国的大宗淡水鱼类都存在一定数目的肌间骨,严重影响了其食用和加工价值。鉴于鱼类肌间骨重要的系统进化科学研究价值及产业意义,近年来国内外水产研究者围绕鱼类肌间骨分子调控机制和遗传育种开展了系列研究,文章对此进行了系统的阐述,并对其发展前景进行了分析,可为肌间骨发生发育分子机制及少/无肌间骨鱼类新品种的遗传选育研究提供基础资料。     

Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences

The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA).     

Microstructure,mineral and mechanical properties of teleost intermuscular bones

There is an increasing interest in understanding teleost bone biomechanics in several scientific communities, for instance as interesting biomaterials with specific structure-function relationships. Intermuscular bones of teleost fish have previously been described to play a role in the mechanical force transmission between muscle and bone, but their biomechanical properties are not yet fully described. Here, we have investigated intermuscular bones (IBs) of the North Atlantic Herring with regard to their structure and micro-architecture, mineral-related properties, and micro-mechanical tensile properties. A total of 115 IBs from 18 fish were investigated. One cohort of IBs, containing 20 bones from 2 smaller fish and 23 bones of 3 larger fish, was used for mechanical testing, wide-angle X-ray scattering, and scanning electron microscopy. Another cohort, containing 36 bones from 7 smaller fish and 36 bones from 6 larger fish, was used for microCT. Results show some astonishing properties of the IBs: (i) IBs present higher ductility, lower Young's modulus but similar strength and TMD (Tissue Mineral Density) compared to mammalian bone, and (ii) IBs from small fish were 49% higher in Young’s modulus than fish bones from larger fish while their TMD was not statistically different and crystal length was 8% higher in large fish bones. Our results revealed that teleost IB presents a hybrid nature of soft and hard tissue that differs from other bone types, which might be associated with their evolution from mineralized tendons. This study provides new data regarding teleost fish bone biomechanical and micro-structural properties.     

The evolution of pharyngeal bones and teeth in Gobioninae fishes (Teleostei: Cyprinidae) analyzed with phylogenetic comparative methods

The subfamily Gobioninae is a subgroup in the specious fish family Cyprinidae, which bears high diversity in morphological and ecological dimensions and has its most components distributed in East Asia. In this study, the pharyngeal bones and teeth of 39 species belonging to 19 genera of the Gobioninae were examined, with the phylogenetic comparative method (PCM) and correlation methods employed to analyze the character evolution. Three characters on pharyngeal bones (shape of the pharyngeal bones, extension for attachment of the pharyngo-cleithralis internus posterior (PCIP) muscle, and teeth-bearing area) and six characters of pharyngeal teeth (shape of the five teeth in the main row, number of rows of the teeth) were identified and compared. When the character states were mapped on a molecular phylogenetic tree, it was found that, to adapt to different masticatory operations, different Gobioninae species have various morphological types of pharyngeal bones and teeth: some have intermediate pharyngeal bones bearing multiple rows of diverse teeth (conical, coarsely compressed, and compressed), others have broad pharyngeal bones bearing a single row of molar teeth, and still others have narrow pharyngeal bones bearing a single row of extremely compressed teeth. Tests on the phylogenetic signal and evolutionary associations revealed that evolution of the examined characters was all phylogenetically constrained and correlated. Owing to the homoplasy in evolution, it was suggested that the conventional method of using pharyngeal bones and teeth for phylogenetic reconstruction of cyprinid fishes should not be encouraged.     

中国鲤形目鱼类的中轴骨骼数及其生态适应性

为探讨中国鲤形目鱼类中轴骨骼数及其与系统发育和生态习性的相关性,采用X光透视照相法对157种鲤科(Cyprinidae)、鳅科(Cobitidae)、平鳍鳅科(Balitoridae)鱼类的脊椎骨数、肋骨数、尾椎数进行了比较分析。结果显示,中国鲤形目鱼类的脊椎骨数在30-52枚之间,均值39.45?4.44;肋骨数在8-28对之间,均值15.27?3.08;尾椎数在14-34枚之间,均值21.08?2.89。依据脊椎骨数、肋骨数、尾椎数对鲤科各亚科进行聚类,显示鲤科12个亚科分为2大类：雅罗鱼类,包括雅罗鱼亚科、鲌亚科、鲴亚科、裂腹鱼亚科等4亚科;鲃类,包括鲢亚科、鮈亚科、鱼丹亚科、鲃亚科、野鲮亚科、鳅鮀亚科、鲤亚科、鱊亚科等8亚科。单因素方差分析显示,鲤科肉食性鱼类的肋骨数与脊椎骨数的比值显著少于植食性鱼类(P＜0.05),而脊椎骨数、尾椎数则显著多于植食性鱼类(P＜0.05)。中上层鱼类的脊椎骨数、尾椎数显著多于下层鱼类(P＜0.05)。极小型鱼类的脊椎骨数、肋骨数,以及肋骨数与脊椎骨数之比显著少于大型鱼类(P＜0.05)。表明鲤科鱼类的中轴骨骼数与其系统发育和生态习性及体型具有明显的相关性。     

S7核糖体蛋白基因序列变异与(鱼丹)亚科鱼类的单系性研究

使用分子生物学的方法对Dan亚科鱼类的单系性进行了探讨。通过PCR方法,获得了13种鲤科鱼类S7核糖体蛋白基因第1内含子序列,其中包括6种Dan亚科鱼类。使用MEGA软件中的Neighbor-Joining法和Most-Parsimony法分别构建分支系统图。研究结果显示目前所确认的Dan亚科鱼类实际上没有形成单系类群。其中Dan属、波鱼属和低线Lie属位于系统树基部,显示出原始性,而由细鲫属、马口鱼属和Lie属构成的类群相对于Dan亚科中的原始种类起源较晚,可能和较晚起源的东亚鲤科类群之间有更为密切的关系。     

Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids

The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates. Received: 2 February 1999 / Accepted: 16 March 1999     

On the karyosystematics of cyprinid fishes and a summary of fish chromosome studies in China

To date, the chromosomes of 210 species of fresh-water fishes have been studied in China. They are principally cyprinids. Based upon the karyotypic data so far obtained mainly by the authors' laboratory, a report is here submitted on the karyosystematics of Chinese cyprinid fishes.The primitive karyotype of cyprinid fishes may be inferred as being 2n=50. During phyletic evolution the cyprinid fishes probably have been differentiated into two large branches, one of which with the Leuciscinae as a basic group and another branch with the Barbinae as a basic group. As to the modes of their chromosome evolution, Robertsonian translocation seems to be prominent in the first branch, whereas polyploidization appears to be prominent in the second branch. Based on the chromosome studies in cyprinid fishes, some tentative ideas about the classification of the subfamilies in Cyprinidae are presented.A table containing the karyotypes of Chinese fresh-water fishes is attached.This work was partially supported by the Science Fund of the Chinese Academy of Science.     

Phylogenetic relationships of Iberian cyprinids: systematic and biogeographical implications.

The phylogenetic relationships among all Iberian endemic cyprinids were inferred using the complete nucleotide sequence of the cytochrome b gene. The inferred molecular phylogeny included representatives from Central European, Asian and North African species, and is highly congruent with previous phylogenies based on osteological characters. Iberian cyprinids were grouped into only five, very speciose lineages (with the exception of the monotypic Anaecypris): Barbus, Luciobarbus, Chondrostoma, Leuciscus and Anaecypris. The existence of such a relatively small number of Iberian cyprinid lineages can be explained by the historical isolation of the Iberian Peninsula. North African and Asian barbels are the sister group of Iberian Luciobarbus, supporting a south-eastern route of colonization of the Iberian Peninsula for this subgenus. With leuciscins, Anaecypris hispanica was considered a relict species as it could not be related to any other Iberian cyprinid. The phylogenetic relationships among the main lineages of Iberian cyprinids based on cytochrome b sequence data supported the traditional division of the Cyprinidae into two subfamilies: Cyprininae and Leuciscinae.     

Asymmetry of the behavioral response in roach Rutilus rutilus (L.) (Teleostei: Cyprinidae) to a new object

The young roach Rutilus rutilus (L.) (Cyprinidae) displays lateralized behavior when facing a barrier through which a simulated bigger fish was visible. The asymmetry consists in a significant tendency to detour a barrier rightwards in the presence of a dummy fish. However, asymmetry is insignificant without the model. A comparison with the available literature shows that the roach has the same direction of this lateral bias as some other shoaling cyprinid fishes, which also preferentially turn to the right in the presence of a dummy fish. This seems to be a characteristic of cyprinids, as opposed to species of some other families displaying a leftward bias or a lack of asymmetry. The results of the study testify to the hypothesis that behavioral lateralization is associated with the taxonomic status of fishes. Currently, it is unclear whether the asymmetry found in roach in a detour test is due to the preferential use of the lateral fields of the right and left eyes as in some other fishes, or if it is a result of motor lateralization, which becomes evident in the presence of an unfamiliar and potentially dangerous object.     

广西南宁渐新世基于咽齿的鲤亚科一新属

记述了产自广西南宁盆地渐新世早—中期的鲤科鲤亚科一新属种——伍氏南宁鲤(+Nanningocyprinus wui gen.et sp.nov).化石材料包括一些咽喉骨和咽齿.这些咽喉骨和咽齿的以下特征组合明显不同于其他鲤科鱼类:齿式-3·2·1,主行第一枚咽齿大小是第二枚的3～4倍,第二枚咽齿及第二行第一枚咽齿咀嚼面上各仅有一条沟纹,咽骨前角很发育.该属种的发现进一步证明鲤亚科是鲤科中较早的分支,中国南方很有可能是鲤亚科的起源和分化中心.     

Evolution of miniaturization and the phylogenetic position of <Emphasis Type="Italic">Paedocypris</Emphasis>, comprising the world's smallest vertebrate

Background  

Paedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic position among the subfamilies of this largest teleost family, with over 2400 species, does not exist. Here we present a phylogenetic analyses of 227 cypriniform taxa, including 213 cyprinids, based upon complete mitochondrial DNA cytochrome b nucleotide sequences in order to determine the phylogenetic position of Paedocypris and to study the evolution of miniaturization among cyprinids.     

Isolation and characterization of major histocompatibility class IIβ genes in an endangered North American cyprinid fish, the Rio Grande silvery minnow (Hybognathus amarus)

The major histocompatibility complex (MHC) is a critical component of the adaptive immune response in vertebrates. Due to the role that MHC plays in immunity, absence of variation within these genes may cause species to be vulnerable to emerging diseases. The freshwater fish family Cyprinidae comprises the most diverse and species-rich group of freshwater fish in the world, but some are imperiled. Despite considerable species richness and the long evolutionary history of the family, there are very few reports of MHC sequences (apart from a few model species), and no sequences are reported from endemic North American cyprinids (subfamily Leuciscinae). Here we isolate and characterize the MH Class II beta genes from complementary DNA and genomic DNA of the non-model, endangered Rio Grande silvery minnow (Hybognathus amarus), a North American cyprinid. Phylogenetic reconstruction revealed two groups of divergent MH alleles that are paralogous to previously described loci found in deeply divergent cyprinid taxa including common carp, zebrafish, African large barb and bream. Both groups of alleles were under the influence of diversifying selection yet not all individuals had alleles belonging to both allelic groups. We concluded that the general organization and pattern of variation of MH class II genes in Rio Grande silvery minnow is similar to that identified in other cyprinid fishes studied to date, despite distant evolutionary relationships and evidence of a severe genetic bottleneck.     

鲤咽齿个体发生及其与近缘种间关系的比较研究

鲤具鲤科咽齿个体发生的共同性征,又呈现其种的独特性状.主要特性;(1)主列齿相连3齿胚几乎同时出现、同时脱落,形成3个相连齿种同时置换的特殊模式;(2)主列齿发生中曾出现4枚齿,替换3代后A_4齿退化消失,最终齿式1.1.3-3.1.1,成为迄今3列咽齿的鱼类中齿数最少的种类.鲤与其近缘种间系统关系比较结果;依最近缘属顺次排列为中鲤、原鲤、肥鲤;而最近缘的亚科为肥亚科.       

Lower sensitivity of cyprinid fishes to three acetylcholinesterase inhibitor pesticides: an evaluation based on no-effect concentrations

Researchers have suggested that cyprinid fishes are less sensitive to chemical stress than comparable fish families, yet few empirically based evaluations of this hypothesis have been conducted. In this study, we developed a generalized linear mixed model in which the no-effect concentrations (NECs; threshold concentration below which no effect on survival is predicted during prolonged exposure) of 29 fish species from 13 families exposed to an acetylcholinesterase inhibitor pesticide (carbaryl, chlorpyrifos, or malathion) were used as the response variable. The corresponding specific somatic maintenance (SSM) rates, as a size-independent proxy for fish metabolism and a categorical variable regarding whether the species is a cyprinid, were used as the predictor variables. We included SSM rates in the analysis because previous work demonstrated that they are negatively correlated with NECs. Our results indicate that the NECs for cyprinid fishes were significantly higher than those for other fishes, suggesting that cyprinids are indeed less sensitive to the three studied pesticides. Although the SSM rates were negatively related with the NECs, the actual relationship between the two was not clear, implying that the importance of SSM rates may depend on the taxonomic group tested.     

Variation in abundance and survival of fish larvae in shallow eutrophic lake Tjeukemeer

Synopsis Variations in abundance and survival of larvae of the major fish species, bream, roach, pikeperch, perch and smelt were studied in shallow eutrophic lake Tjeukemeer (1986–1988). Except for smelt, the size of the spawning stock and the abundance of larvae were not related. Both the timing of appearance of larvae and their growth rate were determined by water temperature as was shown by a growth model developed earlier for Tjeukemeer fishes. In cyprinids and percids the survival of the larvae was hypothesized to be negatively related to the duration of the earliest stages. Except in cyprinids, the abundance of 0+ juvenile fish could be explained by the number of larvae. In cyprinids 0+ juvenile abundance at the end of the year was not related to the number of larvae in May and June. The cyprinid juvenile survival rates are hypothesized to be related to the size of the main cyprinid predator, 0+ pikeperch.     

Can host body size explain the parasite species richness in tropical freshwater fishes?

Summary The variability of monogenean gill ectoparasite species richness in 19 West African cyprinid species was analyzed using the following seven predictor variables: host size, number of drainage basins, number of sympatric cyprinid species, host diversity, association with mainland forest, host ecology, and monogenean biological labelling. The size of the host species accounted for 77% of the variation in the number of parasite species per host, and host ecology an additional 8%. Together the effects of host size and host ecology accounted for 85% of the variation in monogenean species richness. This study shows that the deciding factors for explaining monogenean species richness in West African cyprinid fishes are host species size and host ecology. These results were compared with main factors responsible for parasite species richness in fish communities. Other possible explanations of monogenean community structure in west African cyprinids are discussed.     

Toothless predators: feeding performance and techniques among the piscivores within Lake Tana's endemic barbus species flock (Pisces:Cyprinidae)

With more than 2000 fish species the Cyprinidae is the largest family of vertebrates. Lake Tana, a large lake (3050 km²) situated in the NW‐ highlands of Ethiopia, harbours, as far as we know the only remaining intact species flock of large (max. 100 cm FL) cyprinid fishes (15 Barbus spp.). One of the most intriguing aspects of this endemic Barbus species flock is the large number of piscivores (8). Cyprinid fishes seem not well designed for piscivory, they lack teeth in the oral jaw, have a small slit‐shaped pharyngeal cavity and all lack a stomach with low pH for digesting large prey. Many barbs are benthivorous species, like the ancestral barb in Lake Tana's isolated system. Why then is piscivory, which is rare among cyprinids, so common in Lake Tana Barbus? The aim of present study was to compare the performance and techniques of these piscivorous Barbus with known piscivores from other fish families. We studied prey handling times over prey size, prey capture using high‐speed movies, and assessed the effect of prey size on performance and prey selection in the field. Performances were explained by functional morphology of their feeding system. Overall, Lake Tana's piscivorous Barbus perform relatively 'poor', compared to piscivores from other fish families. For example, Lake Tana's piscivores are only able to handle prey fish smaller than 16% of their own body length. However, Lake Tana lacks potential piscivorous competitors, rendering the piscivorous Barbus by far the 'best' and apparently highly successful. They have adapted to all available macro‐habitats (littoral, offshore pelagic and offshore benthic), using different techniques (ambush, pursuit and cruising), a unique scenario for barbs.     

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.