Fish Skin Mucus Extracts: An Underexplored Source of Antimicrobial Agents

The slow discovery of new antibiotics combined with the alarming emergence of antibiotic-resistant bacteria underscores the need for alternative treatments. In this regard, fish skin mucus has been demonstrated to contain a diverse array of bioactive molecules with antimicrobial properties, including peptides, proteins, and other metabolites. This review aims to provide an overview of the antimicrobial molecules found in fish skin mucus and its reported in vitro antimicrobial capacity against bacteria, fungi, and viruses. Additionally, the different methods of mucus extraction, which can be grouped as aqueous, organic, and acidic extractions, are presented. Finally, omic techniques (genomics, transcriptomics, proteomics, metabolomics, and multiomics) are described as key tools for the identification and isolation of new antimicrobial compounds. Overall, this study provides valuable insight into the potential of fish skin mucus as a promising source for the discovery of new antimicrobial agents.

Evolution of modular and pleiotropic enhancers

Cis-regulatory elements (CREs), or enhancers, are segments of noncoding DNA that regulate the spatial and temporal expression of nearby genes. Sometimes, genes are expressed in more than one tissue, and this can be driven by two main types of CREs: tissue-specific "modular" CREs, where different CREs drive expression of the gene in the different tissues, or by "pleiotropic" CREs, where the same CRE drives expression in the different tissues. In this perspective, we will discuss some of the ways (i) modular and pleiotropic CREs might originate; (ii) propose that modular CREs might derive from pleiotropic CREs via a process of duplication, degeneration, and complementation (the CRE-DDC model); and (iii) propose that hotspot loci of evolution are associated with the origin of modular CREs belonging to any gene in a regulatory network.

Molecular Characterization of TGF-Beta Gene Family in Buffalo to Identify Gene Duplication and Functional Mutations

The TGF-β superfamily is ubiquitously distributed from invertebrates to vertebrates with diverse cellular functioning such as cell adhesion, motility, proliferation, apoptosis, and differentiation. The present study aimed to characterize the TGF-β gene superfamily in buffalo through evolutionary, structural, and single nucleotide polymorphism (SNPs) analyses to find the functional effect of SNPs in selected genes. We detected 32 TGF-β genes in buffalo genome and all TGF-β proteins exhibited basic nature except INHA, INHBC, MSTN, BMP10, and GDF2, which showed acidic properties. According to aliphatic index, TGF-β proteins were thermostable but unstable in nature. Except for GDF1 and AMH, TGF-β proteins depicted hydrophilic nature. Moreover, all the detected buffalo TGF-β genes showed evolutionary conserved nature. We also identified eight segmental and one tandem duplication event TGF-β gene family in buffalo, and the ratio of Ka/Ks demonstrated that all the duplicated gene pairs were under selective pressure. Comparative amino acid analysis demonstrated higher variation in buffalo TGF-β gene family, as a total of 160 amino acid variations in all the buffalo TGF-β proteins were detected. Mutation analysis revealed that 13 mutations had an overall damaging effect that might have functional consequences on buffalo growth, folliculogenesis, or embryogenesis.

Evolutionary Growth of Genome Representations on Artificial Cellular Organisms with Indirect Encodings

Evolutionary design targets systems of continuously increasing complexity. Thus, indirect developmental mappings are often a necessity. Varying the amount of genotype information changes the cardinality of the mapping, which in turn affects the developmental process. An open question is how to find the genotype size and representation in which a developmental solution would fit. A restricted pool of genes may not be large enough to encode a solution or may need complex heuristics to find a realistic size. On the other hand, using the whole set of possible regulatory combinations may be intractable. In nature, the genomes of biological organisms are not fixed in size; they slowly evolve and acquire new genes by random gene duplications. Such incremental growth of genome information can be beneficial also in the artificial domain. For an evolutionary and developmental (evo-devo) system based on cellular automata, we investigate an incremental evolutionary growth of genomes without any a priori knowledge on the necessary genotype size. Evolution starts with simple solutions in a low-dimensional space and incrementally increases the genotype complexity by means of gene duplication, allowing the evolution of scalable genomes that are able to adapt genetic information content while compactness and efficiency are retained. The results are consistent when the target phenotypic complexity, the geometry size, and the number of cell states are scaled up.

Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution

BACKGROUND

Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history.

RESULTS

Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently.

CONCLUSION

Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life.

Fourfold paralogy regions on human HOX-bearing chromosomes: role of ancient segmental duplications in the evolution of vertebrate genome

BACKGROUND

Susumu Ohno's idea that modern vertebrates are degenerate polyploids (concept referred as 2R hypothesis) has been the subject of intense debate for past four decades. It was proposed that intra-genomic synteny regions (paralogons) in human genome are remains of ancient polyploidization events that occurred early in the vertebrate history. The quadruplicated paralogon centered on human HOX clusters is taken as evidence that human HOX-bearing chromosomes were structured by two rounds of whole genome duplication (WGD) events.

RESULTS

Evolutionary history of human HOX-bearing chromosomes (chromosomes 2/7/12/17) was evaluated by the phylogenetic analysis of multigene families with triplicated or quadruplicated distribution on these chromosomes. Topology comparison approach categorized the members of 44 families into four distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated simultaneously, whereas genes of two distinct co-duplicated groups do not share their evolutionary history and have not duplicated in concert with each other.

CONCLUSION

The recovery of co-duplicated groups suggests that "ancient segmental duplications and rearrangements" is the most rational model of evolutionary events that have generated the triplicated and quadruplicated paralogy regions seen on the human HOX-bearing chromosomes.

An enhanced hypercube-based encoding for evolving the placement, density, and connectivity of neurons

Intelligence in nature is the product of living brains, which are themselves the product of natural evolution. Although researchers in the field of neuroevolution (NE) attempt to recapitulate this process, artificial neural networks (ANNs) so far evolved through NE algorithms do not match the distinctive capabilities of biological brains. The recently introduced hypercube-based neuroevolution of augmenting topologies (HyperNEAT) approach narrowed this gap by demonstrating that the pattern of weights across the connectivity of an ANN can be generated as a function of its geometry, thereby allowing large ANNs to be evolved for high-dimensional problems. Yet the positions and number of the neurons connected through this approach must be decided a priori by the user and, unlike in living brains, cannot change during evolution. Evolvable-substrate HyperNEAT (ES-HyperNEAT), introduced in this article, addresses this limitation by automatically deducing the node geometry from implicit information in the pattern of weights encoded by HyperNEAT, thereby avoiding the need to evolve explicit placement. This approach not only can evolve the location of every neuron in the network, but also can represent regions of varying density, which means resolution can increase holistically over evolution. ES-HyperNEAT is demonstrated through multi-task, maze navigation, and modular retina domains, revealing that the ANNs generated by this new approach assume natural properties such as neural topography and geometric regularity. Also importantly, ES-HyperNEAT's compact indirect encoding can be seeded to begin with a bias toward a desired class of ANN topographies, which facilitates the evolutionary search. The main conclusion is that ES-HyperNEAT significantly expands the scope of neural structures that evolution can discover.

Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20 provides no evidence in favor of the vertebrate octoploidy hypothesis

Fourfold paralogy regions in the human genome have been considered historical remnants of whole-genome duplication events predicted to have occurred early in vertebrate evolution. Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the prediction that the ancestral vertebrate genome was shaped by two rapid rounds of whole-genome duplication within a period of 10 million years. Both the map self-comparison approach and a phylogenetic analysis revealed that gene families identified as tetralogous on human chromosomes 1/2/8/20 arose by small-scale duplication events that occurred at widely different time points in animal evolution. Furthermore, the data discount the likelihood that tree topologies of the form ((A,B)(C,D)) are best explained by the octoploidy hypothesis. We instead propose that such symmetrical tree patterns are also consistent with local duplications and rearrangement events.

Picbreeder: a case study in collaborative evolutionary exploration of design space

For domains in which fitness is subjective or difficult to express formally, interactive evolutionary computation (IEC) is a natural choice. It is possible that a collaborative process combining feedback from multiple users can improve the quality and quantity of generated artifacts. Picbreeder, a large-scale online experiment in collaborative interactive evolution (CIE), explores this potential. Picbreeder is an online community in which users can evolve and share images, and most importantly, continue evolving others' images. Through this process of branching from other images, and through continually increasing image complexity made possible by the underlying neuroevolution of augmenting topologies (NEAT) algorithm, evolved images proliferate unlike in any other current IEC system. This paper discusses not only the strengths of the Picbreeder approach, but its challenges and shortcomings as well, in the hope that lessons learned will inform the design of future CIE systems.

Abandoning objectives: evolution through the search for novelty alone

In evolutionary computation, the fitness function normally measures progress toward an objective in the search space, effectively acting as an objective function. Through deception, such objective functions may actually prevent the objective from being reached. While methods exist to mitigate deception, they leave the underlying pathology untreated: Objective functions themselves may actively misdirect search toward dead ends. This paper proposes an approach to circumventing deception that also yields a new perspective on open-ended evolution. Instead of either explicitly seeking an objective or modeling natural evolution to capture open-endedness, the idea is to simply search for behavioral novelty. Even in an objective-based problem, such novelty search ignores the objective. Because many points in the search space collapse to a single behavior, the search for novelty is often feasible. Furthermore, because there are only so many simple behaviors, the search for novelty leads to increasing complexity. By decoupling open-ended search from artificial life worlds, the search for novelty is applicable to real world problems. Counterintuitively, in the maze navigation and biped walking tasks in this paper, novelty search significantly outperforms objective-based search, suggesting the strange conclusion that some problems are best solved by methods that ignore the objective. The main lesson is the inherent limitation of the objective-based paradigm and the unexploited opportunity to guide search through other means.

Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX-cluster paralogons

BACKGROUND

Vertebrate genomes contain extensive intra-genomic conserved synteny, which is the presence of similar set of genes on two or more chromosomes (paralogons). The existence of these paralogons has led to the proposal that vertebrate genome was structured by one or more rounds of ancient whole genome duplications (2R hypothesis).

RESULTS

The 2R hypothesis was tested by phylogenetic analysis of gene families residing on human HOX-bearing chromosomes (HOX-cluster paralogons). These results revealed that, based on their duplication history, 23 gene families with representation on three or four of the human HOX-bearing chromosomes can be partitioned into four discrete co-duplicated groups. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups do not share their evolutionary history and are not duplicated simultaneously. These co-duplicated groups are large constituting members from 3 to 8 gene families and suggest that human HOX-cluster paralogons were shaped by ancient segmental duplications (SDs) and rearrangement events that occurred at least as early as before the divergence of bony fishes and tetrapods.

CONCLUSIONS

Based on the recovery of ancient SD events in this analysis and given the widespread evidence in favor of the fact that recent SD events played a pivotal role in changing genome architecture of primates and other recently diverged animals, it is concluded that a more realistic model of ancient vertebrate genome evolutionary history can be deduced by tracing the evolutionary trajectory of the genomes of recently diverged vertebrate species.

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

BACKGROUND

Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes.

RESULTS

Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance.

CONCLUSIONS

Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.

Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans

Differences between yeast and worm duplicates result from differences in mechanisms of duplication and effective population size.

Background

The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication can be generalized across diverse lineages or are species-specific. Here we present results from an analysis comprising 68 duplication events in the Saccharomyces cerevisiae genome. We partition the yeast duplicates into ohnologs (generated by a whole-genome duplication) and non-ohnologs (from small-scale duplication events) to determine whether their disparate origins commit them to divergent evolutionary trajectories and genomic attributes.

Results

We conclude that, for the most part, ohnologs tend to appear remarkably similar to non-ohnologs in their structural attributes (specifically the relative composition frequencies of complete, partial and chimeric duplicates), the discernible length of the duplicated region (duplication span) as well as genomic location. Furthermore, we find notable differences in the features of S. cerevisiae gene duplicates relative to those of another eukaryote, Caenorhabditis elegans, with respect to chromosomal location, extent of duplication and the relative frequencies of complete, partial and chimeric duplications.

Conclusions

We conclude that the variation between yeast and worm duplicates can be attributed to differing mechanisms of duplication in conjunction with the varying efficacy of natural selection in these two genomes as dictated by their disparate effective population sizes.

A hypercube-based encoding for evolving large-scale neural networks

Research in neuroevolution-that is, evolving artificial neural networks (ANNs) through evolutionary algorithms-is inspired by the evolution of biological brains, which can contain trillions of connections. Yet while neuroevolution has produced successful results, the scale of natural brains remains far beyond reach. This article presents a method called hypercube-based NeuroEvolution of Augmenting Topologies (HyperNEAT) that aims to narrow this gap. HyperNEAT employs an indirect encoding called connective compositional pattern-producing networks (CPPNs) that can produce connectivity patterns with symmetries and repeating motifs by interpreting spatial patterns generated within a hypercube as connectivity patterns in a lower-dimensional space. This approach can exploit the geometry of the task by mapping its regularities onto the topology of the network, thereby shifting problem difficulty away from dimensionality to the underlying problem structure. Furthermore, connective CPPNs can represent the same connectivity pattern at any resolution, allowing ANNs to scale to new numbers of inputs and outputs without further evolution. HyperNEAT is demonstrated through visual discrimination and food-gathering tasks, including successful visual discrimination networks containing over eight million connections. The main conclusion is that the ability to explore the space of regular connectivity patterns opens up a new class of complex high-dimensional tasks to neuroevolution.

Are we degenerate tetraploids? More genomes, new facts

Background

Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been associated with two genome duplications (2R hypothesis) at the origin of vertebrates. However, in spite of extensive debate the validity of the 2R hypothesis remains controversial. The paucity of sequence data in early years of genomic era was an intrinsic obstacle in tracking the genome evolutionary history of chordates.

Hypothesis

In this article I review the 2R hypothesis by taking into account the recent availability of genomic sequence data for an expanding range of animals. I argue here that genetic architecture of lower metazoans and representatives of major vertebrate and invertebrate lineages provides no support for the hypothesis relating the origin of vertebrates with widespread gene or genome duplications.

Conclusion

It appears that much of the genomic complexity of modern vertebrates is very ancient likely predating the origin of chordates or even the Bilaterian-Nonbilaterian divergence. The origin and evolution of vertebrates is partly accompanied by an increase in gene number. However, neither can we take this subtle increase in gene number as an only causative factor for evolution of phenotypic complexity in modern vertebrates nor we can take it as a reflection of polyplodization events early in their history.

Reviewers

This article was reviewed by Eugene Koonin, Joshua Cherry (nominated by David Lipman), and Jerzy Jurka.

Genome duplication and the origin of the vertebrate skeleton

During vertebrate embryonic development, tissue patterning and differentiation are regulated by members of multigene families. Evolutionary expansion of these families is thought to have played a role in the evolution of anatomical complexity, including the origins of new cell and tissue types. A defining feature of vertebrates is an endoskeleton, the primary components of which are cartilage and bone. The molecular control of skeletal patterning has been the subject of intensive investigation for over two decades. More recently, comparative studies of organisms at key phylogenetic positions have highlighted the importance of gene duplication in the evolutionary diversification of connective tissues. Understanding the natural histories of gene families involved in skeletogenesis is therefore central to the issue of vertebrate skeletal evolution.

Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs

It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. To test this hypothesis, we examined the sizes of 14 introns in a nonflying relative of birds, the American alligator (Alligator mississippiensis), and in 19 flighted and flightless birds in 12 taxonomic orders. Our results indicate that a substantial fraction (66%) of the reduction in intron size as well as in genome size had already occurred in nonflying archosaurs. Using phylogenetically independent contrasts, we found that the proposed inverse correlation of genome size and basal metabolic rate (BMR) is significant among amniotes and archosaurs, whereas intron and genome size variation within birds showed no significant correlation with BMR. We show statistically that the distribution of genome sizes in birds and mammals is underdispersed compared with the Brownian motion model and consistent with strong stabilizing selection; that genome size differences between vertebrate clades are overdispersed and punctuational; and that evolution of BMR and avian intron size is consistent with Brownian motion. These results suggest that the contrast between genome size/BMR and intron size/BMR correlations may be a consequence of different intensities of selection for these traits and that we should not expect changes in intron size to be significantly associated with metabolically costly behaviors such as flight.

An insight into the phylogenetic history of HOX linked gene families in vertebrates

Background

The human chromosomes 2q, 7, 12q and 17q show extensive intra-genomic homology, containing duplicate, triplicate and quadruplicate paralogous regions centered on the HOX gene clusters. The fact that two or more representatives of different gene families are linked with HOX clusters is taken as evidence that these paralogous gene sets might have arisen from a single chromosomal segment through block or whole chromosome duplication events. This would imply that the constituent genes including the HOX clusters reflect the architecture of a single ancestral block (before vertebrate origin) where all of these genes were linked in a single copy.

Results

In the present study we have employed the currently available set of protein data for a wide variety of vertebrate and invertebrate genomes to analyze the phylogenetic history of 11 multigene families with three or more of their representatives linked to human HOX clusters. A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1), and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2) gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups may not share their evolutionary history and may not have duplicated simultaneously.

Conclusion

We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters) which occurred at different time points during chordate evolution. Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q) is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

Changes in gene expression as biochemical adaptations to environmental change: a tribute to Peter Hochachka

Changes in gene expression are likely to play a critical role in both acclimation and adaptation to a changing environment. There is a rapidly growing body of literature implicating quantitative changes in gene expression during acclimation to environmental change, but less is known about the role of qualitative changes in gene expression, such as switching between alternative isoforms. Alternative isoforms can arise via gene duplication, alternative splicing, or alternative promoter usage. Organisms that have undergone recent genome duplication events may make use of environment-specific isoforms coded by multiple genes, but their role in other organisms is less well known. However, recent data suggest that isoforms arising from alternative splicing may be an under-appreciated source of physiological variation. The role of changes in gene expression during evolutionary adaptation has received comparatively limited attention, but novel approaches to addressing the adaptive significance of changes in gene expression have been applied to a few cases of differences in gene expression among taxa. Recent advances in genomics, including microarray technology, knock-out and knock-down approaches, and the wealth of data coming from large-scale sequencing projects have provided (and will continue to provide at ever increasing rates) new insights into these classic questions in comparative biochemistry.

Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid

Most eukaryotes have undergone genome doubling at least once during their evolutionary history. Hybridization followed by genome doubling (allopolyploidization) is a prominent mode of speciation in plants, leading to phenotypic novelty and changes in genome structure and gene expression. Molecular events that take place immediately after polyploid formation can be studied using newly synthesized allopolyploids. Here we studied the extent of gene silencing in a newly created and genomically stable allotetraploid cotton, of genotype AAGG, using an AFLP-cDNA display screen. Over 2000 transcripts were screened and approximately 5% of the duplicated genes in the allotetraploid were inferred to have been silenced or downregulated. Sequencing of 24 AFLP-cDNA fragments revealed genes with a variety of functions. Analysis by RT-PCR showed silencing or a strong expression bias toward one copy for 9 of 13 genes examined. Comparisons of expression patterns among eight organs in the allopolyploid showed that silencing and preferential expression are organ specific. Examination of silencing patterns in two other synthetic polyploids, of genotype AADD, showed that the same gene can be silenced independently in different genotypes. These results provide a detailed portrayal of gene silencing events that can occur following allopolyploidization and suggest epigenetic causal factors.

Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution

The widely accepted notion that two whole-genome duplications occurred during early vertebrate evolution (the 2R hypothesis) stems from the fact that vertebrates often possess several genes corresponding to a single invertebrate homolog. However the number of genes predicted by the Human Genome Project is less than twice as many as in the Drosophila melanogaster or Caenorhabditis elegans genomes. This ratio could be explained by two rounds of genome duplication followed by extensive gene loss, by a single genome duplication, by sequential local duplications, or by a combination of any of the above. The traditional method used to distinguish between these possibilities is to reconstruct the phylogenetic relationships of vertebrate genes to their invertebrate orthologs; ratios of invertebrate-to-vertebrate counterparts are then used to infer the number of gene duplication events. The lancelet, amphioxus, is the closest living invertebrate relative of the vertebrates, and unlike protostomes such as flies or nematodes, is therefore the most appropriate outgroup for understanding the genomic composition of the last common ancestor of all vertebrates. We analyzed the relationships of all available amphioxus genes to their vertebrate homologs. In most cases, one to three vertebrate genes are orthologous to each amphioxus gene (median number=2). Clearly this result, and those of previous studies using this approach, cannot distinguish between alternative scenarios of chordate genome expansion. We conclude that phylogenetic analyses alone will never be sufficient to determine whether genome duplication(s) occurred during early chordate evolution, and argue that a "phylogenomic" approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed.

A taxonomy for artificial embryogeny

A major challenge for evolutionary computation is to evolve phenotypes such as neural networks, sensory systems, or motor controllers at the same level of complexity as found in biological organisms. In order to meet this challenge, many researchers are proposing indirect encodings, that is, evolutionary mechanisms where the same genes are used multiple times in the process of building a phenotype. Such gene reuse allows compact representations of very complex phenotypes. Development is a natural choice for implementing indirect encodings, if only because nature itself uses this very process. Motivated by the development of embryos in nature, we define artificial embryogeny (AE) as the subdiscipline of evolutionary computation (EC) in which phenotypes undergo a developmental phase. An increasing number of AE systems are currently being developed, and a need has arisen for a principled approach to comparing and contrasting, and ultimately building, such systems. Thus, in this paper, we develop a principled taxonomy for AE. This taxonomy provides a unified context for long-term research in AE, so that implementation decisions can be compared and contrasted along known dimensions in the design space of embryogenic systems. It also allows predicting how the settings of various AE parameters affect the capacity to efficiently evolve complex phenotypes.

Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution

It has been proposed that two events of duplication of the entire genome occurred early in vertebrate history (2R hypothesis). Several phylogenetic studies with a few gene families (mostly Hox genes and proteins from the MHC) have tried to confirm these polyploidization events. However, data from a single locus cannot explain the evolutionary history of a complete genome. To study this 2R hypothesis, we have taken advantage of the phylogenetic position of the lamprey to study the history of gene duplications in vertebrates. We selected most gene families that contain several paralogous genes in vertebrates and for which lamprey genes and an out-group are known in databases. In addition, we isolated members of the nuclear receptor superfamily in lamprey. Hagfish genes were also analyzed and found to confirm the lamprey gene analysis. Consistent with the 2R hypothesis, the phylogenetic analysis of 33 selected gene families, dispersed through the whole genome, revealed that one period of gene duplication arose before the lamprey-gnathostome split and this was followed by a second period of gene duplication after the lamprey-gnathostome split. Nevertheless, our analysis suggests that numerous gene losses and other gene-genome duplications occurred during the evolution of the vertebrate genomes. Thus, the complexity of all the paralogy groups present in vertebrates should be explained by the contribution of genome duplications (2R hypothesis), extra gene duplications, and gene losses.

Comprehensive analysis of blood coagulation pathways in teleostei: evolution of coagulation factor genes and identification of zebrafish factor VIIi

It is not clear how the complex mammalian coagulation pathways evolved from an entirely dissimilar invertebrate coagulation cascade. Comprehensive analysis of pro-coagulant factors and their regulators is lacking in early vertebrates to discern the mechanism of evolution of these genes from the invertebrates. To elucidate the coagulation pathways found in early vertebrates, zebrafish cDNAs/gene orthologues for major coagulant, anticoagulant, and fibrinolytic proteins were identified and characterized by homology to mammalian sequences. We found that zebrafish carry all hemostatic genes present in mammals, providing evidence that the coagulation system of teleosts is nearly identical to mammals. Zebrafish factor VII and X genes were identified and analyzed to reveal a novel factor VII-like gene flanked by the factor VII and factor X genes. This gene encodes a protein homologous to factor VII, but lacks critical residues for factor VII activity. Expression of the factor VII-like protein (named factor VIIi) demonstrated that it functions as an inhibitor of blood coagulation in biochemical assays using zebrafish or human plasmas. Analysis of intergenic DNA between the zebrafish VII/VIIi/X gene cluster and a Drosophila trypsin gene cluster revealed significant homology, and based upon these data, we propose a model for a rapid evolution of coagulation factors from the invertebrates.

Pattern and timing of gene duplication in animal genomes

Duplication of genes, giving rise to multigene families, has been a characteristic feature of the evolution of eukaryotic genomes. In the case of vertebrates, it has been proposed that an increase in gene number resulted from two rounds of duplication of the entire genome by polyploidization (the 2R hypothesis). In the most extensive test to date of this hypothesis, we compared gene numbers in homologous families and conducted phylogenetic analyses of gene families with two to eight members in the complete genomes of Caenorhabditis elegans and Drosophila melanogaster and the available portion of the human genome. Although the human genome showed a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the 2R hypothesis. A substantial majority (70.9%) of human four-member families and four-member clusters in larger families showed topologies inconsistent with two rounds of polyploidization in vertebrates.

Coparalogy: physical and functional clusterings in the human genome

Two rounds of large-scale duplications are thought to have occurred in early vertebrate ancestry; this is now known as the "2R hypothesis." They have led to the constitution of subfamilies of paralogous genes. Chromosomal regions that contain present-day paralogs (paralogous regions or paralogons) have been identified in mammals. We show that sets of paralogons (PGs) can be assembled in a tentative "human genome paralogy map" that includes all autosomes and X. A total of 14 PGs, containing more than 1600 genes, were assembled in this paralogy map. Genes that belong to the same PG are coparalogs. We show that identification of coparalogy can be used (i) to broaden data on gene mapping, (ii) to identify physical gene clusters that derive from early cis-duplications, and (iii) to speculate on coevolution and coregulation of genes sharing a common structure or function (functional clusters). Thus, coparalogy analyses should parallel phylogenetic analyses and can help draw hypotheses on gene and genome evolution.

Genome duplication, divergent resolution and speciation

What are the evolutionary consequences of gene duplication? One answer is speciation, according to a model initially called Reciprocal Silencing and recently expanded and renamed Divergent Resolution. This model shows how the loss of different copies of a duplicated gene in allopatric populations (divergent resolution) can promote speciation by genetically isolating these populations should they become reunited. Genome duplication events produce thousands of duplicated genes. Therefore, lineages with a history of genome duplication might have been especially prone to speciation via divergent resolution.

Simulation of the evolution of genomic complexity

A general evolutionary trend is the generation of organisms of increasing complexity, notwithstanding that reduction and simplification phenomena do occur in the evolutionary process. This paper proposes an evolutionary model incorporating the mechanisms of gene amplification and deletion. The evolutionary process leading to genomic complexity and the coexistence of simpler organisms with complicated ones were both simulated using the proposed model. The model was also used to investigate the influence of various factors on the evolution of complexity. The simulations indicated that the evolution of complexity is largely influenced by adaptation to complicated environments. Nevertheless, complex organisms require relatively more resources for survival and replication, which limits the on going tendency towards complexity. Moreover, the analysis showed that if the environment varies rapidly and the profit obtained from complexity is greater than the resources consumed, selection will tend to favor complexity. However, high living cost will tend to limit the trend of complexity and if the environment is relatively stable, reduction and simplification will become the dominant trends.

Yesterday's polyploids and the mystery of diploidization

Thirty years after Susumu Ohno proposed that vertebrate genomes are degenerate polyploids, the extent to which genome duplication contributed to the evolution of the vertebrate genome, if at all, is still uncertain. Sequence-level studies on model organisms whose genomes show clearer evidence of ancient polyploidy are invaluable because they indicate what the evolutionary products of genome duplication can look like. The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one.

Polyploid incidence and evolution

Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immediate shifts in morphology, breeding system, and ecological tolerances. Theoretical models support the potential for increased adaptability in polyploid lineages. The evidence suggests that polyploidization can produce shifts in genetic systems and phenotypes that have the potential to result in increased evolutionary diversification, yet conclusive evidence that polyploidy has changed rates and patterns of diversification remains elusive.

Homeobox gene clusters and the human paralogy map

Homeobox genes encode important developmental control proteins. In vertebrates, those encoding the proteins of the HOX class and their most closely related families, including paraHOX and metaHOX classes, are clustered in paralogous regions (or paralogons). We show that the majority of the other homeobox genes (we called contraHOX) can also be clustered and belong to paralogons in humans. This suggests that they duplicated during vertebrate evolution along the same processes as the HOX genes. We tentatively assembled several paralogons in superparalogons. One of the superparalogons contains the contraHOX genes. These observations were extended to hundreds of genes, and allowed to describe a primary human genome paralogy map.

The Origin of Interspecific Genomic Incompatibility via Gene Duplication

One of the great unsolved mysteries of evolutionary biology concerns the genetic mechanisms underlying the origin of genomic incompatibilities between species. Two prevailing thoughts are that such incompatibilities often result from epistatically interacting genes that act as loss-of-function alleles in hybrid backgrounds or from chromosomal rearrangements that result in mis-segregation during meiosis in hybrids. However, it is unclear how genes that cause a radical breakdown in hybrids arise without reducing fitness within species, and numerous cases of speciation appear to be unassociated with obvious chromosomal rearrangements. Here we suggest that duplicate genes, and more generally any kind of genomic redundancies, provide a powerful substrate for the origin of genomic incompatibilities in isolated populations. The divergent resolution of genomic redundancies, such that one population loses function from one copy while the second population loses function from a second copy at a different chromosomal location, leads to chromosomal repatterning such that gametes produced by hybrid individuals can be completely lacking in functional genes for a duplicate pair. Under this model, incompatibility factors accumulate with essentially no loss of fitness within populations as postulated under the Bateson-Dobzhansky-Muller (BDM) model of speciation and despite the fact that they arise from degenerative mutations. However, unlike the situation often envisioned under the BDM model, no change in the mode of gene action in hybrid backgrounds need be invoked. The plausibility of this model derives from a number of recent observations, including the fact that most genomes harbor substantial numbers of gene duplicates whose turnover is common and ongoing process and the fact that many genes have complex regulatory regions that facilitate their divergent resolution in sister taxa.

The evolutionary fate and consequences of duplicate genes

Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

Phylogenetic analysis of T-Box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome

The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

Co-option of male courtship signals from aggressive display in bowerbirds

The pre-existing trait hypothesis suggests that females evolve a mating preference for an already existing male trait. This hypothesis poses a simple resolution to Darwin's long-standing question of how elaborate, male display traits evolve. The frequently observed convergence of aggressive and courtship displays across a wide array of species provides the only current support for this hypothesis. Here we provide much more detailed supporting evidence from bowerbird skrraa calls used in aggression and courtship. Consistent with the pre-existing trait hypothesis we show that (i) putatively co-opted skrraa calls used in courtship and aggression are homologous, (ii) skrraa calls were used in aggression in bowerbirds before being used in courtship, (iii) historically, intense, aggressive-like courtship calls were present near the time of co-option, and (iv) bower types contemporaneous with co-option emphasize design features that provide females protection from the adverse effects of intense courtship displays. These results, plus evidence for a female preference for males with intense aggressive-like courtship skrraa calls, suggest that aggressive skrraa calls have been co-opted for use in male courtship display

Choosing among alternative trees of multigene families

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.