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Kohtaro Tanaka
Instituto Gulbenkian de Ciência

cis-regulatory evolution and functional diversification of gene duplicates in Diptera


Author(s): Tanaka, K, Hazbun, A, Vreede, B, Diekmann, Y, Roch, F, Sucena, É


Gene duplication plays a major role in evolution of novel gene functions as it provides a material basis for variation and selection. We are interested in elucidating how cis-regulatory changes contribute to functional diversification ensuing gene duplication. To address this question we are studying the Three-Finger-Domain Protein/Ly6 gene family in insects. Members of this family encode different GPI-anchored membrane proteins and are fully conserved across drosophilids. Our analyses of the sequenced insect genomes indicate that a subset of these genes is unique to higher dipterans. We are focusing our attention on seven paralogues of Drosophila, which our phylogenetic analysis showed to derive from sequential duplications of a single orthologue. In order to determine how their expression domains diversified, we have characterized the embryonic expression patterns of the Drosophila paralogues and their unduplicated orthologues in other insects representing different phylogenetic positions and stages of duplication (the Mediterranean fruit fly, Ceratitis capitata, the scuttle fly, Megaselia abdita, the mosquito, Anopheles, the butterfly, Bicyclus anynana and the red flour beetle, Tribolium castaneum). We found that the original expression domain of the unduplicated orthologue localized predominantly to the developing nervous system, which, upon subsequent duplications, expanded to a wide array of tissues. While a subset of the duplicates retained the tissue-specificity of the unduplicated orthologues, the others acquired novel tissue-specific expression suggesting neofunctionalization. We are currently identifying the cis-regulatory elements of the duplicates and the unduplicated orthologues to elucidate the cis-regulatory mechanisms underlying the evolution of divergent expression patterns.

Lene Martinsen
Harvard University/Oslo University
Department of Organismic and Evolutionary Biology
United States

Are there patterns in the formation and expression of novel genes?


Author(s): Martinsen, L, Ponce, R


Observed differences between species are often due to differences at genomic level. In particular, the analysis of newly evolved genes provides information that helps us to understand the evolution of novel functions. Here, we examine the mechanisms involved in the formation of novel genes (less than 50 MYA) and we characterize the expression patterns of these genes. This illustrates the variety of mechanisms implicated in the formation of new genes, as well as the preferential location of expression of novel functions. We further analyze the Sdic gene family and use it to investigate in greater detail the formation and expression of novel genes. The Sdic gene family, a young gene family in Drosophila melanogaster, represents an interesting window into the evolution of novel genes, as it evolved after the split of D. melanogaster and D. simulans i.e. less than 2 million years ago. This gene family originated from a formation of a chimera of two unrelated genes, that was followed by several duplication events, being therefore a candidate for the study of two important mechanisms of gene formation: gene shuffling and duplication. This family is composed by several tandem copies of the gene Sdic, and at least one copy (sdic1) is expressed in testis, incorporated into the sperm tail and encodes a sperm specific intermediate chain. It has recently been showed that although this novel gene is not essential for the development of spermatids and Sdic knock-out males are fertile with no effect on the size or sex ratio of their progeny, Sdic has a role on sperm competition. This effect of Sdic in improving sperm competition suggests that Sdic may have had an important role, contributing to the species barrier between D. melanogaster and D. simulans. The analysis of particular newly evolved genes provides information in finer detail, that we hope can be generalized and will help understand the evolution of new genes and new functions in the genomes.

Raquel Ruivo
CIIMAR, University of Porto

Evolutionary study of RDH10 gene family reveals a novel member retained in ectothermic vertebrates


Author(s): Ruivo, R, Lopes-Marques, M, Santos, MM, Castro, LC


Nuclear receptor-mediated retinoic acid signalling is crucial for organ modelling and maintenance. Active retinoid biosynthesis involves a two-step oxidation cascade: retinol oxidation followed by retinaldehyde dehydrogenase activity, suggested to coordinate retinoic acid supply. Recent studies have highlighted the functional role of a membrane-associated retinol dehydrogenase (RDH10) in the first oxidation step in mammals. This enzyme displays tissue and time-specific expression patterns that correlate with both retinoic acid and retinaldehyde dehydrogenase activities: suggestive of an additional checkpoint for retinoic acid regulation. Here we investigated the evolution of chordate rdh10. While a single copy, rdh10a, is observed in birds and mammals, reptiles, amphibians and teleosts exhibit an additional uncharacterized gene, rdh10b. Both rdh10a and rdh10b have duplicate copies in teleosts. Phylogenetic and paralogy analysis revealed that vertebrate rdh10a and rdh10b resulted from whole genome duplication in stem vertebrate evolution; interestingly, with significant functional divergence amongst paralogues. Following duplication, rdh10b was lost in warm-blooded lineages and retained in cold-blooded animals. Both enzymes exhibit conserved reaction cores and tri-dimensional folding; yet, the membrane-association designs appear different: unlike RDH10A, topology predictions advocate for RDH10B solubility. Also, a unique negatively charged insertion is observed in RDH10A isoforms. Gene expression patterns in teleosts, D. rerio and O. nicotilus, were also examined. While rdh10a is ubiquitously expressed, rdh10b expression is typically restricted to gonads, skin, and brain, and is concomitant with the onset of pigmentation and circulation during teleost embryonic development. Together these results support a functional specialization within the rdh10 family and emphasize a dichotomy among vertebrates according to thermal homeostasis mechanisms.

Antoine Frénoy
Université Paris Descartes
Faculté de Médecine

Genetic architecture promotes the evolution and maintenance of cooperation: the evolutionary constraint of coding overlaps on functionally unrelated genes


Author(s): Frénoy, A, Taddei, F, Misevic, D


When cooperation has a direct cost and an indirect benefit, a selfish behavior is more likely to be selected for than an altruistic one. Kin and group selection do provide evolutionary explanations for the existence of stable populations of cooperators in nature, but we still lack the full understanding of the genomic mechanisms that can prevent cheater invasion. We used Aevol, an agent-based, in silico genomic platform to evolve populations of digital organisms that compete, reproduce, and cooperate by secreting a costly public good. We found that populations of phenotypically equal cooperating individuals often have very different abilities to resist cheater invasion. To understand the underlying mechanisms, we performed bio-inspired genomics analysis by determining and comparing the locations of metabolic and secretion genes, as well as the relevant promoters and terminators. We found that populations of cooperators characterized by the strong association between metabolic and secretion genes (promoter sharing, overlap via frame shift or sense-antisense encoding) were more robust to cheater invasion than ones where such association was weak. We performed mutation analysis of the evolved individuals and determined that the accessibility of mutations decreasing cooperation without decreasing overall fitness was negatively correlated with the amount of operons and overlap between secretion and metabolism. Effectively, cooperation evolved to be protected and robust to mutations through overlapping genetic architecture, especially when cooperation was costly. Due to operon sharing and gene overlap, even when mutations that eliminate cooperation appear, they are likely to be selected against due to their simultaneous and direct negative effect on fitness. Our results uncover an important genetic mechanism for the evolution and maintenance of cooperation, and suggest promising methods for preventing loss of genes introduced into biological synthetic organisms.

Sanne Nygaard
University of Copenhagen

Genomic changes during the evolution of increasing specialization in fungus-farming ants


Author(s): Nygaard, S, Li, C, Schiøtt, M, Zhang, G, Xiao, J, Meng, X, Wang, J, Boomsma, JJ


Ants are an ecologically important group of insects with a vast array of specialized lifestyles and symbioses. One of the most spectacular ant symbioses is fungus farming, found in a single clade of New World (attine) ants, a mutualism to which the ants contribute plant material in exchange for food provided by the fungal crops. Since this mutualism evolved in the Amazon basin from hunter-gatherer like ancestors some 50 mya, it has undergone a series of evolutionary transitions of which the use of specialized rather than generalist fungal strains, active herbivory rather than using dead plant parts, polymorphic rather than monomorphic worker castes, and multiple rather than single mating of queens are the most important. The advent of high-throughput sequencing techniques now allows these questions to also be addressed at the molecular evolutionary level. In a recent study, we showed that the genome sequence of the leafcutter ant Acromyrmex echinatior, a representative of the most highly derived leaf-cutting fungus-farming ants, has characteristic changes in detoxification pathways, loss of function in arginine metabolism pathways, and expansion of specific peptidase gene-families relative to other ant genomes. We have now sequenced and partly analyzed the genomes of five additional fungus-farming ant species, representing all phylogenetic branches of the higher attine ants and a lower attine outgroup, and thus most of the major evolutionary transitions. These comparative genomic analyses allow us to assess rates of gains and losses of genes and variation in lineage-specific selective pressures, differences that we hope to connect to some of the phenotypic adaptations in the respective lineages.

Yukako Katsura
National Institute of Genetics
Division of Evolutionary Genetics

Genomic structures and gene evolution on mammalian X chromosomes


Author(s): Katsura, Y, Satta, Y


Of genomic structures, intrachromosomal segmental duplications (ISDs) are relatively large repeats in neighboring regions on a chromosome. Counting of ISDs on each human chromosome found more ISDs on X than any of the other chromosome. In this study, we show that the concentration of ISDs are not a general characteristic for X chromosomes, or not due to sequence-specificity of the human X chromosome, but are correlated with gene evolution and expression control. ISDs on the X chromosome in four mammalian species with different origins or evolutionary histories (human, mouse, opossum, and platypus) were identified and characterized. The number or the size of ISDs was different among these species; ISDs on human and mouse X chromosomes were much larger in size, in the number, and more structurally complex than those in opossums. Moreover, gene density and the number of different gene families in ISDs-containing regions were larger in the human and mouse, whereas in the opossum, ISD-regions were gene-poor. Interestingly multiple X chromosomes of platypus did not have any ISDs, except for one on the X1 chromosome. These observations indicated that ISDs accumulated on the X chromosome in the eutherian ancestor. In the human, more than 70% of the genes within X chromosomal ISDs were cancer-testis antigen (CTA) genes, and they are highly expressed in testis and cancer cells. The CTAs showed primate or eutherian-lineage specific, suggesting the recent origin and rapid evolution within ISDs. The amplification and complexity of ISDs can be evolutionally maintained by the emergence and functional constraint of CTAs, respectively. In addition, the accumulation of X chromosomal ISDs might be involved in the mechanism for expression control, because the ISD-regions on X chromosomes were low-methylated and genes within the ISDs were expressed specifically in germ cells.

Frédéric Brunet
Ecole Normale Supérieure de Lyon
Institut de Génomique Fonctionnelle de Lyon

Half of the sox genes remained duplicated since the teleost specific whole genome duplication


Author(s): Brunet, FG, Voldoire, E, Volff, J, Galiana, D


Two successive events of whole genome duplications (WGD) occurred at the base of the vertebrate lineage, coined 1R and 2R for Rounds of WGD. An additional third round of WGD (3R) occurred at the base of the teleostean fish. Sox genes encode a family of transcription factors that has experienced a phase of expansion leading to 20 sox genes well described in human and mouse. This gene expansion preceeded the vertebrates lineage and enhanced even more through both the 1R+2R WGDs and tandem duplication occurrences. In fish, additional sox genes have been described with orthologous relationship assessed by phylogenetical analyses. We were interested to know how have evolved such a group of genes since the 3R event. To this end, we carried out a bioinformatic analysis, searching exhaustively the public releases of fish genomes as well as other public databases. We combined both the phylogenetic information and synteny analyses to assess the evolutionary history of fish sox genes. We found evidence that in fish, 10 of the 20 mammalian orthologues of these sox gene family come from and remain duplicated since their 3R origination. This 50% ratio is way above the estimated global average of 12% of genes that remained duplicated since the 3R event, a value in favor of the idea that transcription factors have played a key role in the diversification of the teleost lineage. In addition, we performed expression analyses of these sox genes in three fishes (zebrafish, medaka and platyfish) and observed species specific expression for some of them, in agreement with this hypothesis.

Tiffany Taylor
University of Reading
School of Biological Sciences
United Kingdom

Hotwiring the flagellum: Rapid, repeatable rewiring of a gene regulatory network in Pseudomonas fluorescens


Author(s): Taylor, TB, Mulley, G, Alsohim, A, Silby, MW, Brockhurst, MA, Jackson, RW


Pseudomonas fluorescens, a common microbial inhabitant of the soil and plant commensal, uses flagella for swimming motility and a biosurfactant known as viscosin for sliding motility – both are required to maximise colonisation efficiency in the plant environment. The master regulator gene that differentially regulates flagellum expression is FleQ. Both ΔfleQ mutants and those carrying functional mutations in the viscosin synthase genes maintain partial motility in liquid agar (0.25%) using the other function as a motility mechanism. However, loss of function in both the viscosin synthase and FleQ genes completely abolishes in vitro surface motility. Serendipitously, we observed a SBW25fleQ-viscoin mutant regained motility over agar surfaces after about 72 hours of starvation on agar plates. This heritable motility phenotype was observed with a range of ΔfleQ mutants with independent mutations in viscosin genes following starvation selection. Electron microscopy showed motile evolved mutants were able to express flagella. Further growth analysis revealed major growth defects in minimal medium, and genome sequencing revealed the bacterium had “rewired” its genetic circuitry, co-opting homologous genes from the nitrogen regulation pathway, resulting in restored expression of the flagella at the cost of reduced efficiency in the nitrogen cycle. This work highlights how bacteria can use simple innovations to adapt to potentially catastrophic genome mutations.

Fabian Zimmer
University College London
Department of Genetics, Evolution and Environment
United Kingdom

How important are sex chromosomes in sexual dimorphism?


Author(s): Zimmer, F, Harrison, PW, Mank, JE


There is an extensive body of evolutionary theory predicting that the sex chromosomes should play a large role in encoding sexually dimorphic phenotypes. Although gene expression often follows these theoretical predictions, phenotypic studies have been far less conclusive. Many studies have focused on a gene-by-gene analysis of expression differences between males and females, and although this approach has yielded many new insights, it can fall short in explaining how an expression change in one sex-linked gene can affect the expression pattern of other autosomal genes. To better understand the complex regulatory structure underpinning sexual dimorphism, we employ a network-based approach based on gene co-expression in the chicken, Gallus gallus. We used RNA-seq data from males and females in several tissues and across development to construct a global gene co-expression network. Genes on the Z chromosome are more connected to male-biased autosomal genes. Additionally, male-biased Z-linked genes have a significantly higher connectivity in comparison to unbiased Z-linked genes. Finally, we detected sex-biased sub-networks, revealing that sex-biased genes on the sex-chromosomes are tightly connected with sex-biased genes on the autosomes. Taken together, these analyses suggest that the Z chromosome plays a large regulatory role in male-biased expression, and therefore male-specific phenotypes. Our analysis also shows the potential of network approaches that integrate large-scale transcriptomic datasets in a systems biology framework for revealing the influence of the sex chromosomes on general sex-specific gene expression patterns.

Heli Havukainen
Norwegian University of Life Sciences
Department of Chemistry, Biotechnology and Food Science

Multifunctional vitellogenin – Can the evolution of a pleiotropic gene be linked to the domain architecture of its protein product?


Author(s): Havukainen, H, Amdam, GV


How do single proteins perform a broad range of tasks, and how can evolution act on pleiotropic genes/proteins? Vitellogenin is a multitask protein mostly associated with its egg-yolk function. It transports lipids to the egg and provides a source of amino acids for the embryo, and this function is conserved across several taxa. However, in the honey bee workers, vitellogenin is also a central life-history regulator that supports immune cell viability, protects against oxidative stress, and suppresses risky foraging behavior. It is expressed in queens, workers and males. In fish, this egg-yolk protein has bactericidal effects and is overexpressed in infected females and males. The key to this multifunctionality may lie in the evolution and diversity of specific structural domains. Typical structural elements of vitellogenins are, among others, N-sheet, alpha-helical and the vertebrate phosvitin domain. The latter has been pinpointed as the bactericidal actor in fish. In the honeybee, it is known that different vitellogenin domains are evolving under differing selection pressure, the putative receptor-binding N-sheet being more conserved than the other parts of the sequence. Furthermore, honeybee vitellogenin is a structurally adjustable protein that can shed the N-sheet domain. We have identified the alpha-helical domain as a membrane-binding region. Using the methods of cell and molecular biology, we show that the membrane-binding can be linked to vitellogenin’s antioxidative and putative anti-inflammatory functions in the honey bee. Thus, research on protein domains can facilitate understanding the evolution of pleiotropic genes such as vitellogenin.


Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028


XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon


Computational Biology & Population Genomics Group