Impact of gene gains,losses and duplication modes on the origin and diversification of vertebrates

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators.     

Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae

Whole-genome duplications(WGDs) are an important contributor to phenotypic innovations in evolutionary history. The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates. In this study, the evolutionary changes of hemoglobin(Hb) repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish, including eight diploid and four tetraploid species. Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes. Data were integrated with the expression profiles of the genes during ontogeny. Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family; each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications. This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.     

Orthologs, paralogs and genome comparisons

During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.     

Evolutionary Dynamics of Recently Duplicated Genes: Selective Constraints on Diverging Paralogs in the <Emphasis Type="Italic">Drosophila pseudoobscura</Emphasis> Genome

Duplicated genes produce genetic variation that can influence the evolution of genomes and phenotypes. In most cases, for a duplicated gene to contribute to evolutionary novelty it must survive the early stages of divergence from its paralog without becoming a pseudogene. I examined the evolutionary dynamics of recently duplicated genes in the Drosophila pseudoobscura genome to understand the factors affecting these early stages of evolution. Paralogs located in closer proximity have higher sequence identity. This suggests that gene conversion occurs more often between duplications in close proximity or that there is more genetic independence between distant paralogs. Partially duplicated genes have a higher likelihood of pseudogenization than completely duplicated genes, but no single factor significantly contributes to the selective constraints on a completely duplicated gene. However, DNA-based duplications and duplications within chromosome arms tend to produce longer duplication tracts than retroposed and inter-arm duplications, and longer duplication tracts are more likely to contain a completely duplicated gene. Therefore, the relative position of paralogs and the mechanism of duplication indirectly affect whether a duplicated gene is retained or pseudogenized. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Selection on coding regions determined Hox7 genes evolution

The important role of Hox genes in determining the regionalization of the body plan of the vertebrates makes them invaluable candidates for evolutionary analyses regarding functional and morphological innovation. Gene duplication and gene loss led to a variable number of Hox genes in different vertebrate lineages. The evolutionary forces determining the conservation or loss of Hox genes are poorly understood. In this study, we show that variable selective pressures acted on Hox7 genes in different evolutionary lineages, with episodes of positive selection occurring after gene duplications. Tests for functional divergence in paralogs detected significant differentiation in a region known to modulate HOX7 protein activity. Our results show that both positive and negative selection on coding regions are influencing Hox7 genes evolution.     

核糖核酸酶基因超家族分子进化

核糖核酸酶基因(Ribonuclease A, RNASE A)超家族是进化生物学中研究新基因起源及新功能演变的重要模式系统之一。RNASE A超家族中的很多成员表现出基因复制的进化模式, 而且在适应性(正)选择的驱动下, 发生了功能分化。文章综述了RNASE A超家族成员在不同动物类群中进化模式的研究进展, 包括近年来越来越多在基因组水平上开展的相关研究, 显示该基因超家族可能具有比人们以往认识的更为复杂的基因进化模式。随着越来越多动物基因组数据的产生, 对更多动物代表类群进行RNASE A超家族研究, 将有望揭示新的进化机制和功能分化, 为系统认识动物适应进化的遗传机制奠定基础。     

The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome

The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with < or =10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.     

Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae)

Accumulating evidence for alternative gene orders demonstrates that vertebrate mitochondrial genomes are more evolutionarily dynamic than previously thought. Several lineages of parthenogenetic lizards contain large, tandem duplications that include rRNA, tRNA, and protein-coding genes, as well as the control region. Such duplications are hypothesized as intermediate stages in gene rearrangement, but the early stages of their evolution have not been previously studied. To better understand the evolutionary dynamics of duplicated segments of mitochondrial DNA, we sequenced 10 mitochondrial genomes from recently formed ( approximately 300,000 years ago) hybrid parthenogenetic geckos of the Heteronotia binoei complex and 1 from a sexual form. These genomes included some with an arrangement typical of vertebrates and others with tandem duplications varying in size from 5.7 to 9.4 kb, each with different gene contents and duplication endpoints. These results, together with phylogenetic analyses, indicate independent and frequent origins of the duplications. Small, direct repeats at the duplication endpoints imply slipped-strand error as a mechanism generating the duplications as opposed to a false initiation/termination of DNA replication mechanism that has been invoked to explain duplications in other lizard mitochondrial systems. Despite their recent origin, there is evidence for nonfunctionalization of genes due primarily to deletions, and the observed pattern of gene disruption supports the duplication-deletion model for rearrangement of mtDNA gene order. Conversely, the accumulation of mutations between these recent duplicates provides no evidence for gene conversion, as has been reported in some other systems. These results demonstrate that, despite their long-term stasis in gene content and arrangement in some lineages, vertebrate mitochondrial genomes can be evolutionary dynamic even at short timescales.     

Gene duplication: past, present and future

Gene duplication is of central interest to evolutionary developmental biology, having been implicated in evolutionary increases in complexity. These ideas stem principally from the Lewis model for the evolution of the BX-C and Ohno's proposal for genome duplications during chordate evolution. Here I revisit these models and show how recent data have confirmed their essential features, but forced some important revisions. These include revised dates for homeotic gene duplications and for widespread gene duplication in vertebrate evolution. I also outline the major unresolved questions in the study of gene duplication, and its relevance to evolution and development.     

Transmembrane electron transport and the neutral theory of evolution

Based on the concept of "pairs of basic functional states" the evolution of the first chemiosmotic mechanism of energy conversion is discussed in terms of point mutations, gene duplications and of the neutral theory of evolution. A model for estimating the overall probability of the evolutionary step in question is presented, both for the "selectionist" and "neutralist" position. It is concluded that, concerning the present stage of knowledge, the evolution of transmembrane electron transport is an unsolved problem in evolutionary biology.     

Molecular evolution of growth hormone gene family in old world monkeys and hominoids

Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25–50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events.     

Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes

Current models for the evolution of plant disease resistance (R) genes are based on mechanisms such as unequal crossing-over, gene conversion and point mutations as sources for genetic variability and the generation of new specificities. Size variation in leucine-rich repeat (LRR) domains was previously mainly attributed to unequal crossing-over or template slippage between LRR units. Our analysis of 112 R genes and R gene analogs (RGAs) from 16 different gene lineages from monocots and dicots showed that individual LRR units are mostly too divergent to allow unequal crossing-over. We found that illegitimate recombination (IR) is the major mechanism that generates quasi-random duplications within the LRR domain. These initial duplications are required as seeds for subsequent unequal crossing-over events which cause the observed rapid increase or decrease in LRR repeat numbers. Ten of the 16 gene lineages studied contained such duplications, and in four of them the duplications served as a template for subsequent repeat amplification. Our analysis of Pm3-like genes from rice and three wheat species showed that such events can be traced back more than 50 million years. Thus, IR represents a major new evolutionary mechanism that is essential for the generation of molecular diversity in evolution of RGAs.     

The evolutionary dynamics of plant duplicate genes

Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution.     

Gene duplications and the early evolution of neural crest development

Neural crest cells are an important cell type present in all vertebrates, and elaboration of the neural crest is thought to have been a key factor in their evolutionary success. Genomic comparisons suggest there were two major genome duplications in early vertebrate evolution, raising the possibility that evolution of neural crest was facilitated by gene duplications. Here, we review the process of early neural crest formation and its underlying gene regulatory network (GRN) as well as the evolution of important neural crest derivatives. In this context, we assess the likelihood that gene and genome duplications capacitated neural crest evolution, particularly in light of novel data arising from invertebrate chordates.     

Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos

The acquisition of key innovations and the invasion of new areas constitute two major processes that facilitate ecological opportunity and subsequent evolutionary diversification. Using a major lizard radiation as a model, the Australasian diplodactyloid geckos, we explored the effects of two key innovations (adhesive toepads and a snake‐like phenotype) and the invasion of new environments (island colonization) in promoting the evolution of phenotypic and species diversity. We found no evidence that toepads had significantly increased evolutionary diversification, which challenges the common assumption that the evolution of toepads has been responsible for the extensive radiation of geckos. In contrast, a snakelike phenotype was associated with increased rates of body size evolution and, to a lesser extent, species diversification. However, the clearest impact on evolutionary diversification has been the colonization of New Zealand and New Caledonia, which were associated with increased rates of both body size evolution and species diversification. This highlights that colonizing new environments can drive adaptive diversification in conjunction or independently of the evolution of a key innovation. Studies wishing to confirm the putative link between a key innovation and subsequent evolutionary diversification must therefore show that it has been the acquisition of an innovation specifically, not the colonization of new areas more generally, that has prompted diversification.     

Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints

Various characteristics of complex gene regulatory networks (GRNs) have been discovered during the last decade, e.g., redundancy, exponential indegree distributions, scale-free outdegree distributions, mutational robustness, and evolvability. Although progress has been made in this field, it is not well understood whether these characteristics are the direct products of selection or those of other evolutionary forces such as mutational biases and biophysical constraints. To elucidate the causal factors that promoted the evolution of complex GRNs, we examined the effect of fluctuating environmental selection and some intrinsic constraining factors on GRN evolution by using an individual-based model. We found that the evolution of complex GRNs is remarkably promoted by fixation of beneficial gene duplications under unpredictably fluctuating environmental conditions and that some internal factors inherent in organisms, such as mutational bias, gene expression costs, and constraints on expression dynamics, are also important for the evolution of GRNs. The results indicate that various biological properties observed in GRNs could evolve as a result of not only adaptation to unpredictable environmental changes but also non-adaptive processes owing to the properties of the organisms themselves. Our study emphasizes that evolutionary models considering such intrinsic constraining factors should be used as null models to analyze the effect of selection on GRN evolution.     

Transgenic Arabidopsis expressing osmolyte glycine betaine synthesizing enzymes from halophilic methanogen promote tolerance to drought and salt stress

Gene duplication events exert key functions on gene innovations during the evolution of the eukaryotic genomes. A large portion of the total gene content in plants arose from tandem duplications events, which often result in paralog genes with high sequence identity. Ubiquitin ligases or E3 enzymes are components of the ubiquitin proteasome system that function during the transfer of the ubiquitin molecule to the substrate. In plants, several E3s have expanded in their genomes as multigene families. To gain insight into the consequences of gene duplications on the expansion and diversification of E3s, we examined the evolutionary basis of a cluster of six genes, duplC-ATLs, which arose from segmental and tandem duplication events in Brassicaceae. The assessment of the expression suggested two patterns that are supported by lineage. While retention of expression domains was observed, an apparent absence or reduction of expression was also inferred. We found that two duplC-ATL genes underwent pseudogenization and that, in one case, gene expression is probably regained. Our findings provide insights into the evolution of gene families in plants, defining key events on the expansion of the Arabidopsis Tóxicos en Levadura family of E3 ligases.     

Protein robustness promotes evolutionary innovations on large evolutionary time-scales

Recent laboratory experiments suggest that a molecule's ability to evolve neutrally is important for its ability to generate evolutionary innovations. In contrast to laboratory experiments, life unfolds on time-scales of billions of years. Here, we ask whether a molecule's ability to evolve neutrally-a measure of its robustness-facilitates evolutionary innovation also on these large time-scales. To this end, we use protein designability, the number of sequences that can adopt a given protein structure, as an estimate of the structure's ability to evolve neutrally. Based on two complementary measures of functional diversity-catalytic diversity and molecular functional diversity in gene ontology-we show that more robust proteins have a greater capacity to produce functional innovations. Significant associations among structural designability, folding rate and intrinsic disorder also exist, underlining the complex relationship of the structural factors that affect protein evolution.