Differential genome duplication and fish diversity

The duplication of genes and entire genomes arebelieved to be important mechanisms underlyingmorphological variation and functionalinnovation in the evolution of life andespecially for the broad diversity observed inthe speciation of fishes. How did these fishspecies and their genetic diversity arise? Theoccurrence of three rounds of genomeduplication during vertebrate evolution mightexplain why many gene families are typicallyabout half the size in land vertebrates as theyare in fishes. However, mechanisms of geneticdiversity in fish lineages need to be furtherexplained. Here we propose that differentialgenome duplication of from two to six roundsoccurred in different fish lines, offering newopportunities during the radiation of fishlineages. This model provides a fundamentalbasis for the understanding of theirspeciation, diversity and evolution.

     

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)

An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic studies suggest that, during the evolution of vertebrates, the entire genome was duplicated in two rounds (2R) of duplication. Later, approximately 350 mya, in the stem lineage of ray-finned (actinopterygian) fishes, but not in that of the land vertebrates, a third genome duplication occurred-the fish-specific genome duplication (FSGD or 3R), leading, at least initially, to up to eight copies of the ancestral deuterostome genome. Therefore, the sarcopterygian (lobe-finned fishes and tetrapods) genome possessed originally only half as many genes compared to the derived fishes, just like the most-basal and species-poor lineages of extant fishes that diverged from the fish stem lineage before the 3R duplication. Most duplicated genes were secondarily lost, yet some evolved new functions. The genomic complexity of the teleosts might be the reason for their evolutionary success and astounding biological diversity.     

鱼类特异的基因组复制

辐鳍鱼类是脊椎动物中种类最多、分布最广的类群,其基因组大小不等。过去的观点认为,在脊椎动物进化历程中曾发生了两次基因组复制。近期的系统基因组学研究资料进一步提出,在大约350百万年,辐鳍鱼还发生了第三次基因组复制,即鱼类特异的基因组复制(fish-specificgenomeduplication,FSGD),且发生的时间正处在“物种极度丰富”的硬骨鱼谱系(真骨总目)和“物种贫乏”的谱系(辐鳍鱼纲基部的类群)出现分歧的时间点,表明FSGD与硬骨鱼物种和生物多样性的增加有关。进一步开展鱼类比较基因组学和功能基因组学研究将进一步验证FSGD这一假说。     

Hox gene duplication in fish

The study of Hox gene clusters continues to serve as a paradigm for those interested in vertebrate genome evolution. Recent exciting discoveries about Hox gene composition in fishes challenges conventional views about vertebrate Hox gene evolution, and has initiated lively debates concerning the evolutionary events making the divergence of the major vertebrate lineages. Comparative analyses indicate that Hox cluster duplications occurred in early vertebrate evolution, and again within the order Cypriniformes of teleost fish. Loss of Hox genes was more widespread than duplication during fish evolution.     

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.     

Are all fishes ancient polyploids?

Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.     

南极鱼类多样性和适应性进化研究进展

南极地区是地球上唯一未被人类活动大量影响的地区, 其极端寒冷的环境为南极生物的进化提供了“温床”。过去三千万年间, 南极鱼亚目鱼类在南极海洋逐渐变冷的过程中快速进化, 从一个温暖海域的底栖祖先分化成南极海域最为多样化的鱼类类群。由于其在南极圈内和南极圈外的各种温度区间都有分布, 因而成为研究鱼类适应性进化和耐寒机制的良好生物模型。本文综述了有关南极海域鱼类区系组成与物种多样性现状, 南极鱼亚目鱼类适应低温的一系列特化的生物学性状及其关键的遗传进化机制。现有研究表明: 南极鱼类在几千万年零度以下低温环境的进化中发生了大量基因的大规模扩增和基因表达的改变, 如铁调素、卵壳蛋白和逆转座子等118个基因发生了显著的扩增。另外, 有些从南极鱼中获得的抗寒基因已经用于提高动植物低温抗性的研究并取得了良好的效果。在今后的几年中, 将会有多个南极鱼物种的全基因组得到破译, 在低温适应相关基因的功能和进化方面的研究也会更加深入, 这些研究将深入揭示低温压力下基因组的进化规律以及鱼类低温适应的分子机制。     

The evolution of teleost pigmentation and the fish‐specific genome duplication

Teleost fishes have evolved a unique complexity and diversity of pigmentation and colour patterning that is unmatched among vertebrates. Teleost colouration is mediated by five different major types of neural‐crest derived pigment cells, while tetrapods have a smaller repertoire of such chromatophores. The genetic basis of teleost colouration has been mainly uncovered by the cloning of pigmentation genes in mutants of zebrafish Danio rerio and medaka Oryzias latipes. Many of these teleost pigmentation genes were already known as key players in mammalian pigmentation, suggesting partial conservation of the corresponding developmental programme among vertebrates. Strikingly, teleost fishes have additional copies of many pigmentation genes compared with tetrapods, mainly as a result of a whole‐genome duplication that occurred 320–350 million years ago at the base of the teleost lineage, the so‐called fish‐specific genome duplication. Furthermore, teleosts have retained several duplicated pigmentation genes from earlier rounds of genome duplication in the vertebrate lineage, which were lost in other vertebrate groups. It was hypothesized that divergent evolution of such duplicated genes may have played an important role in pigmentation diversity and complexity in teleost fishes, which therefore not only provide important insights into the evolution of the vertebrate pigmentary system but also allow us to study the significance of genome duplications for vertebrate biodiversity.     

Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity.     

Opsin gene duplication and divergence in ray-finned fish

Opsin gene sequences were first reported in the 1980s. The goal of that research was to test the hypothesis that human opsins were members of a single gene family and that variation in human color vision was mediated by mutations in these genes. While the new data supported both hypotheses, the greatest contribution of this work was, arguably, that it provided the data necessary for PCR-based surveys in a diversity of other species. Such studies, and recent whole genome sequencing projects, have uncovered exceptionally large opsin gene repertoires in ray-finned fishes (taxon, Actinopterygii). Guppies and zebrafish, for example, have 10 visual opsin genes each. Here we review the duplication and divergence events that have generated these gene collections. Phylogenetic analyses revealed that large opsin gene repertories in fish have been generated by gene duplication and divergence events that span the age of the ray-finned fishes. Data from whole genome sequencing projects and from large-insert clones show that tandem duplication is the primary mode of opsin gene family expansion in fishes. In some instances gene conversion between tandem duplicates has obscured evolutionary relationships among genes and generated unique key-site haplotypes. We mapped amino acid substitutions at so-called key-sites onto phylogenies and this exposed many examples of convergence. We found that dN/dS values were higher on the branches of our trees that followed gene duplication than on branches that followed speciation events, suggesting that duplication relaxes constraints on opsin sequence evolution. Though the focus of the review is opsin sequence evolution, we also note that there are few clear connections between opsin gene repertoires and variation in spectral environment, morphological traits, or life history traits.     

Circular DNA intermediate in the duplication of Nile tilapia vasa genes

vasa is a highly conserved RNA helicase involved in animal germ cell development. Among vertebrate species, it is typically present as a single copy per genome. Here we report the isolation and sequencing of BAC clones for Nile tilapia vasa genes. Contrary to a previous report that Nile tilapia have a single copy of the vasa gene, we find evidence for at least three vasa gene loci. The vasa gene locus was duplicated from the original site and integrated into two distant novel sites. For one of these insertions we find evidence that the duplication was mediated by a circular DNA intermediate. This mechanism of gene duplication may explain the origin of isolated gene duplicates during the evolution of fish genomes. These data provide a foundation for studying the role of multiple vasa genes in the development of tilapia gonads, and will contribute to investigations of the molecular mechanisms of sex determination and evolution in cichlid fishes.     

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes

With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.     

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Background  

Based on the observation of an increased number of paralogous genes in teleost fishes compared with other vertebrates and on the conserved synteny between duplicated copies, it has been shown that a whole genome duplication (WGD) occurred during the evolution of Actinopterygian fish. Comparative phylogenetic dating of this duplication event suggests that it occurred early on, specifically in teleosts. It has been proposed that this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish, notably by allowing the sub- or neo-functionalization of many duplicated genes.     

Duplication of phospholipase C-delta gene family in fish genomes

Fishes possess more genes than other vertebrates, possibly because of a genome duplication event during the evolution of the teleost (ray-finned) fish lineage. To further explore this idea, we cloned five genes encoding phosphoinositide-specific phospholipase C-delta (PLC-delta), designated respectively PoPLC-deltas, from olive flounder (Paralichthys olivaceus), and we performed phylogenetic analysis and sequence comparison to compare our putative gene products (PoPLC-deltas) with the sequences of known human PLC isoforms. The deduced amino acid sequences shared high sequence identity with human PLC-delta1, -delta3, and -delta4 isozymes and exhibited similar primary structures. In phylogenetic analysis of PoPLC-deltas with PLC-deltas of five teleost fishes (zebrafish, stickleback, medaka, Tetraodon, and Takifugu), three tetrapods (human, chicken, and frog), and two tunicates (sea squirt and pacific sea squirt), whose putative sequences of PLC-delta are available in Ensembl genome browser, the result also indicated that the two paralogous genes corresponding to each PLC-delta isoform originated from fish-specific genome duplication prior to the divergence of teleost fish. Our analyses suggest that an ancestral PLC-delta gene underwent three rounds of genome duplication during the evolution of vertebrates, leading to the six genes of three PLC-delta isoforms in teleost fish.     

Neuropeptide Y family of peptides: structure, anatomical expression, function, and molecular evolution.

Evolutionary relationships between neuroendocrine peptides are often difficult to resolve across divergent phyla due to independent duplication events in different lineages. Thanks to peptide purification and molecular cloning in many different species, the situation is beginning to clear for the neuropeptide Y (NPY) family, which also includes peptide YY (PYY), the tetrapod pancreatic polypeptide (PP) and the fish pancreatic peptide Y (PY). It has long been assumed that the first duplication to occur in vertebrate evolution generated NPY and PYY, as both of these are found in all gnathostomes as well as lamprey. Evidence from other gene families show that this duplication was probably a chromosome duplication event. The origin of a second PYY peptide found in lamprey remains to be explained. Our recent cloning of NPY, PYY and PY in the sea bass proves that fish PY is a separate gene product. We favour the hypothesis that PY is a duplicate of the PYY gene and that it may have occurred late in fish evolution, as PY has so far only been found in acanthomorph fishes. Thus, this duplication seems to be independent of the one that generate PP from PYY in tetrapods, although both tetrapod PP and fish PY are expressed in the pancreas. Studies in the sea bass and other fish show that PY, in contrast to PP, is expressed in the nervous system. We review the literature on the distribution and functional aspects of the various NPY-family peptides in vertebrates.     

Evolution of Duplicated <Emphasis Type="BoldItalic">reggie</Emphasis> Genes in Zebrafish and Goldfish

Invertebrates, tetrapod vertebrates, and fish might be expected to differ in their number of gene copies, possibly due the occurrence of genome duplication events during animal evolution. Reggie (flotillin) genes code for membrane-associated proteins involved in growth signaling in developing and regenerating axons. Until now, there appeared to be only two reggie genes in fruitflies, mammals, and fish. The aim of this research was to search for additional copies of reggie genes in fishes, since a genome duplication might have increased the gene copy number in this group. We report the presence of up to four distinct reggie genes (two reggie-1 and two reggie-2 genes) in the genomes of zebrafish and goldfish. Phylogenetic analyses show that the zebrafish and goldfish sequence pairs are orthologous, and that the additional copies could have arisen through a genome duplication in a common ancestor of bony fish. The presence of novel reggie mRNAs in fish embryos indicates that the newly discovered gene copies are transcribed and possibly expressed in the developing and regenerating nervous system. The intron/exon boundaries of the new fish genes characterized here correspond with those of human genes, both in location and phase. An evolutionary scenario for the evolution of reggie intron-exon structure, where loss of introns appears to be a distinctive trait in invertebrate reggie genes, is presented. Received: 24 January 2001 / Accepted: 27 July 2001     

A comparative view on sex determination in medaka

In fish, an amazing variety of sex determination mechanisms are known, ranging from hermaphroditism to gonochorism and from environmental to genetic sex determination. This makes fish especially suited for studying sex determination from the evolutionary point of view. In several fish groups, different sex determination mechanisms are found in closely related species, and evolution of this process is still ongoing in recent organisms. The medaka (Oryzias latipes) has an XY-XX genetic sex determination system. The Y-chromosome in this species is at an early stage of evolution. The molecular differences between X and Y are only very subtle and the Y-specific segment is very small. The sex-determining region has accumulated duplicated sequences from elsewhere in the genome, leading to recombinational isolation. The region contains a candidate for the male sex-determining gene named dmrt1bY. This gene arose through duplication of an autosomal chromosome fragment of linkage group 9. While all other genes degenerated, dmrt1bY is the only functional gene in the Y-specific region. The duplication leading to dmrt1bY occurred recently during evolution of the genus Oryzias. This suggests that different genes might be the master sex-determining gene in other fish.     

A review of the influence of biogeography,riverine linkages,and marine connectivity on fish assemblages in evolving lagoons and lakes of coastal southern Africa

The Holocene evolution of eight South African coastal lakes and lagoons is examined and related to changes in fish composition over that period. Historical and current connectivity with riverine and marine environments are the primary determinants of present‐day fish assemblages in these systems. A small and remarkably consistent group of relict estuarine species have persisted in these coastal lakes and lagoons. The loss or reduction of connectivity with the sea has impacted on the diversity of marine fishes in all eight study systems, with no marine fishes occurring in those water bodies where connectivity has been completely broken (e.g. Sibaya, Groenvlei). In systems that have retained tenuous linkages with the sea (e.g., Verlorenvlei, Wilderness lakes), elements of the marine fish assemblage have persisted, especially the presence of facultative catadromous species. Freshwater fish diversity in coastal lakes and lagoons is a function of historical and present biogeography and salinity. From a freshwater biogeography perspective, the inflowing rivers of the four temperate systems reviewed here contain three or fewer native freshwater fishes, while the subtropical lakes that are fed by river systems contain up to 40 freshwater fish species. Thus, the significantly higher fish species diversity in subtropical versus temperate coastal lakes and lagoons comes as no surprise. Fish species diversity has been increased further in some systems (e.g., Groenvlei) by alien fish introductions. However, the impacts of fish introductions and translocations have not been studied in the coastal lakes and lagoons of South Africa. In these closed systems, it is probable that predation impacts on small estuarine fishes are significant. The recent alien fish introductions is an example of the growing threats to these systems during the Anthropocene, a period when human activities have had significant negative impacts and show potential to match the changes recorded during the entire Holocene.     

马鞍列岛岩礁生境鱼类群落生态学.Ⅰ.种类组成和多样性

为了解潮下带岩礁生境的鱼类区系特征,于2009年对马鞍列岛岩礁生境进行了12个月的多网目组合刺网采样,从分类学和生态型组成等方面,结合多样性和相对重要性指数,对该生境的鱼类组成和多样性特征进行了分析。全年共采集鱼类87种,隶属2纲14目50科73属。其中鲈形目鱼类51种,占58.6%;趋礁性鱼类49种,占56.3%;放流鱼类7种,占8%。所有鱼类个体中,幼鱼的总比例为67.4%。暖水种、暖温种和冷温种分别为50、36和1种;底层、近底层和中上层鱼类各为19、46和22种,其中褐菖鲉(Sebasti scus marmoratus)、黄姑鱼(Nibea albiflora)和赤鼻棱鳀(Thryssa kammalensis)分别为各水层的绝对优势种;定居种、季节性洄游种和偶见种各为32、55和11种。岩礁生境鱼类多样性呈现明显的季节变化特征,2月份最低,9月份最高。研究结果表明,马鞍列岛岩礁生境是以趋礁鱼类为特征群体、暖水性和暖温性鱼类共同主导、各个类型的幼鱼在夏秋季集群出现、同时也分布了一定量放流种的高鱼类多样性栖息地,它为各种鱼类提供了优良的摄食、避敌和繁殖场所,是近岸海洋生态系统中相当重要的生境。然而相比过去,该生境的鱼类多样性已经大大降低,因此需对其保护工作予以更多关注。