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Javier Quilez
Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC)
Ciencies Experimetals i de la Salut
Spain

Analysis of genomic structural diversity and uncharacterized novel sequences in wolves and dogs

talk 

Author(s): Quilez, J, Lorente-Galdos, B, Twigg, D, Sirakov, S, Ramirez, O, Olalde, I, Berglund, J, Bustamante, CD, Freeman, AH, Webster, M, Novembre, J, Boyko, A, Wayne, R, Vila, C, Kidd, JM, Marques-Bonet, T

Summary:

The domestic dog has been widely recognized as an important organism for studying the relationship between selection, genome variation, and phenotypic diversity. Both dogs and wolves have been extensively surveyed using mtDNA, microsatellites, SNPs inferred from genotyping platforms or pooled sequencing or from a handful of individuals with low genomic coverage. Although structural variation, including variation in multicopy gene families, has been recognized as one of the major contributions to differential phenotypes, extensive characterization of this kind of variation in canines is still lacking. We set out to explore the full spectrum of copy-number and structural genome diversity via next-generation sequencing of a diverse panel of high coverage full genome sequencing of 29 canid genomes. The set includes unrelated specimens from all major populations including 14 wolves, 4 coyotes, 10 dog breeds and one basal dog lineage (Basenji). Validations and genotyping by arrayCGH have been performed in a total set of 20 wolves and 7 dogs. Our analyses have found over 170 Mbps of structural variants in the dog and wolves genomes affecting the complete gene structure on ~250 genes. As expected from their demographic histories, the amount of segregating structural variants is lower in dogs than in wolves. We have also identified specific gene expansions and contractions accounting for 150 coding sequences and we can now date the origin of gene duplications. Finally, we also explored the contribution of dog and wolf novel sequences that encompass 4 million assembled sequences that are not present in the dog genome assembly. The study of those specific expansions will help us to improve our understanding on the biology of these newly expanded gene families and their role in rapid phenotypic changes.

Marc Robinson-Rechavi
University of Lausanne
Department of Ecology and Evolution
Switzerland

Bgee, a database for the study of gene expression evolution

poster 

Author(s): Robinson-Rechavi, M, Team, B, Bastian, FB

Summary:

Gene expression patterns (where and when genes are expressed) are a key feature in understanding gene function and evolution. To apply compare results between different model organisms and human, or to study gene expression evolution, a comparative approach must be used, but no tools allow to easily compare gene expression across species. We have thus developed Bgee (Base for Gene Expression Evolution), a database designed to automatically compare expression patterns between animals. This is achieved by i) the aggregation and curation of expression data from different types and sources, to map them to formal representations of anatomies and developments of different species; Bgee release 12 contains curated and quality controlled data for Affymetrix chips EST libraries, and RNA-seq libraries annotated by our curators, as well as in situ hybridizations. ii) the analysis of these data by dedicated statistical tests to define high confidence gene expression patterns. iii) the definition of comparison criteria between anatomies of different species; Bgee curators have designed relationships between more than 5000 species-specific terms, which map to more than 1000 homologous organ groups; the latter are organized in multi-species ontologies (the HOG and vHOG ontologies). Bgee is available at: http://bgee.unil.ch/

Jesper Bechsgaard
Aarhus University
Bioscience
Denmark

Consequence of the evolution of social behavior in spiders on the intensity of selection

poster 

Author(s): Bechsgaard, JS, Settepani, V, Bilde, T

Summary:

The evolution of social behavior in spiders has profound influence at most aspects the biology of the species. Especially, the selection intensity is predicted to be highly decreased due to low effective population sizes caused by common characteristics of severe inbreeding, female biased sex ratio, reproductive skew and strong meta-population dynamics. In the Stegodyphus genus three species have independently evolved social behavior. We compare historical selection intensities (dN/dS - interspecific) and current selection intensities (πN/πS - intraspecific) among the three social species and their three solitary sister species to test the prediction of decreased selection intensities in social species. We have sampled 10 individuals from each of 5 populations in all 6 species, and sequenced ~1% of each genome (~30mb and ~300kb protein coding) using double digest RAD sequencing. We have recently sequenced the genome of one of the social species, which facilities the analyses. We find that effective population sizes are highly decreased in the three social species revealed by very low diversity. We do not detect decreased historical selection intensities in the social species; however, current selection intensities are suggested to be highly reduced. These results suggest that social behavior evolved recently. The results are backed up by simulation studies of relation among πN/πS and dN/dS.

Laurent Excoffier
Institute of Ecology and Evolution, University of Berne
Switzerland

Detection of polygenic selection at different evolutionary levels

talk 

Author(s): Excoffier, L, Daub, J

Summary:

Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of individually ´significant´ genes with strong effects. However, a collection of small effect mutations could have a large effect on a given biological pathway that includes many genes, and such a polygenic mode of adaptation has not been systematically investigated in humans or other mammals. We therefore propose to evidence polygenic selection by detecting signals of adaptation at the pathway or gene set level instead of analyzing single independent genes. Using a gene-set enrichment test, we identify genome-wide signals of recent adaptation among human populations as well as more ancient signals of adaptation in the human lineage and in primates.

Nadja Kryuchkova
University of Lausanne
Department of Ecology and Evolution
Switzerland

Determinants of protein evolutionary rates in light of ENCODE functional genomics

talk 

Author(s): Kryuchkova, N, Robinson-Rechavi, M

Summary:

The aim is to understand how the complex anatomy and developmental processes of animal influence the evolution of protein-coding genes.

The influence of different parameters, from gene size to expression levels, on the evolution of proteins has been previously studied in yeast, Drosophila and mammals. Here we investigate these relations further, especially taking in account gene expression and chromatin organization in different organs and different developmental stages. For expression we used a microarray experiment over zebrafish development as well as the RNA-seq data from ENCODE for 22 different tissues of mouse. We also used chromatin accessibility in mouse tissues, and we use ENCODE data to define which transcript is used as reference to compute gene length, intron number, etc. We find strong differences between tissues or developmental stages in impact of expression on evolutionary rate. Over all tissues, an interesting result is that evolutionary rate is better correlated with maximal expression in one tissue then with average expression value over all tissues.

Michael Whitlock
University of British Columbia
Department of Zoology
Canada

Equilibrium and non-equilibrium demographic history and the distribution of FST: deviations from the island model can strongly affect the conclusions of QST and FST outlier tests

talk 

Author(s): Whitlock, M, Lotterhos, K

Summary:

Local adaptation predicts that selected alleles and traits will differ in frequencies among populations, as each population adapts to its own optimum. Recently, our field has made increasing use of several methods designed to look for loci or traits that have greater divergence among populations than expected by genetic drift alone. Statistical conclusions from QST approaches (in the case of traits) or FST genome scans (for selected loci) depend on the demographic properties assumed by their null models. Typically an island model or a Dirichlet distribution is assumed. We explored through simulation a number of demographic models that differ increasingly from the island model, including several realistic scenarios out of equilibrium. For both QST and FST, the distribution of differentiation measures sometimes is well described by the island model, but often the differences are profound. We show that the differences can cause a great excess of false positives in QST or FST outlier approaches, and we make several suggestions about how to identify and ameliorate these problems in real biological settings.

Linda Dib
Univeristé de Lausanne, Faculté de biologie et de médecine
Department of Ecology and Evolution
Switzerland

Evolution of correlated sites in the melanocortin system

talk 

Author(s): Dib, LR, Salamin, N

Summary:

Ten years ago it has been demonstrated that evolutionarily co-evolving residues in a protein mediate allosteric communication involved in cellular signaling. Recently, it has been observed that co-evolving positions can also explain folding, and key mutations implied in genetic diseases. Although predictions and biological evidence showed that some positions are correlated in the DNA and protein sequences, the evolutionary models used in phylogeny assume that these positions are evolving in an independent fashion. Here we propose a new model that considers co-evolving positions. The model is based on a 16X16 instantaneous rate matrix and three parameters: s, d, w. where s is the rate associated with a transition from a co-evolving combination to a non-co-evolving one, d is the rate of a transition from one non-co-evolving combination to a co-evolving one, w is the rate attributed to a single mutation occurring between two non-co-evolving combinations. To evaluate the new model, we use likelihood ratio test (LRT) between two models: the null model where independent evolution is assumed for each position (i.e. s=d=w) and the dependent model in which co-evolution is assumed. The results show that the null model has a weaker likelihood when two positions are co-evolving, whereas in the case of independent positions, the dependent and the null models have similar likelihoods. In the past decade several methods have been developed to identify co-evolving positions using probabilistic or combinatorial approaches. These models give a score of correlation but they do not distinguish within co-evolving positions, combinations of nucleotides that are indeed co-evolving across the phylogeny. This likelihood-based framework represents a step forward in reconstructing the evolution of co-evolving patterns based on a phylogeny with potential applications in evolutionary studies and mutagenesis experiments.

Sara Rocha
CIBIO/UP
Portugal

Evolution of heme-copper oxidases superfamily: reconciling gene duplications, losses and transfers to understand the origin of aerobic respiration

poster 

Author(s): Rocha, S, Fonseca, M, Posada, D, Pereira, M

Summary:

To understand the origin and evolution of heme-copper oxydases, the terminal enzymes of aerobic respiratory chains, is fundamental to clarify the emergence of this important cellular process and how biological activity has shaped the history of our planet. Prior gene-phylogeny analyses were unable to clarify if they predate oxygenic photosynthesis already reducing oxygen, if they predate oxygenic photosynthesis but without reducing oxygen or if they postdate oxygenic photosynthesis. Using an enlarged sampling of 2723 genomes from 1485 prokaryotes (all available prokaryote genomes at November 2011) we characterized the distribution and number of the different types of HCO’s across Archaean and Bacterial phylums. We further used a time-calibrated tree-of-life against which we reconciled the inferred HCO gene phylogeny, under duplication, loss and transfers models, to test hypotheses about possible evolutionary scenarios for this family. All different HCO clades seem to make equally parsimonious roots of the gene-tree and multiple hypotheses remain open as possible evolutionary scenarios, but overall, results point to an early origin and diversification of this gene-family, prior to the origin of photosynthetic algae, and also with high amounts of duplications and lateral gene transfers. Although difficult and computationally intensive, only the simultaneous consideration of different evolutionary phenomena acting at different evolutionary scales, such as duplications, losses, lateral gene transfers and incomplete lineage sorting may properly elucidate deep and shallow patterns of diversification and co-evolution.

Eduardo Tarazona-Santos
Universidade Federal de Minas Gerais
Departamento de Biologia Geral
Brazil

Evolutionary dynamics of the human nadph oxidase genes CYBB, CYBA, NCF2 and NCF4: functional implications

poster 

Author(s): Tarazona-Santos, E, Machado, M, Magalhães, WCS, Redondo, RAF, Yeager, M, Chanock, SJ

Summary:

The phagocyte NADPH oxidase catalyzes the reduction of oxygen to reactive species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox and p67-phox (encoded by NCF4, NCF1 and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. By means of evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggest that this region may have a function probaby in host-pathogen interaction. Based on a resequence analysis of ~35kb of CYBB, CYBA, NCF2 and NCF4 in 102 ethnically diverse individuals, we show that the pattern of diversity of CYBA is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations also shows a suggestive pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of a pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial non-phagocyte NADPH oxidases, which are relevant in the pathogenesis of cardiovascular diseases and other complex diseases.

Joao Alves
IPATIMUP // IGC
Portugal

Evolutionary history of the 17q21 human polymorphic inversion

poster 

Author(s): Alves, JMF, Lopes, A, Heutink, P, Chikhi, L, Amorim, A

Summary:

With the aid of novel and powerful molecular biology techniques the study of the structural plasticity of the genome has gained momentum, and one particular subtype of chromosomal rearrangement – inversions – was recently found to be far more common than predicted from classical cytogenetics. Moreover, large inversions have been identified at high frequency in some human populations.

One particularly large inversion (900 kb) described in humans and several Great Apes, namely 17q21, has been shown to exhibit ‘frozen’ haplotypes (H1 and H2) which were originally identified by specific mutations and by their opposite orientations. The fact that they accumulate mutations independently is not necessarily surprising since recombination is expected to be limited between inverted regions. However, three surprising results were also found (i) age estimates of the inverted-associated haplotype (H2) are in the order of magnitude of millions of years, and (ii) the frequency of the inverted haplotypes vary between 5 and 35% in Europe only, (iii) cases were found in which the inversion status was in contradiction with the molecular haplotype, i.e. some H2 haplotypes (as defined by specific mutations) were in the same orientation as H1.

These results suggest that (i) the inversion might be recurrent despite its size, or (ii) the polymorphism was kept during a large evolutionary timescale and resisted various speciation processes since it is observed in other Apes.

In order to clarify the complex history of 17q21 human polymorphic inversion we are merging NGS data from 14 populations with cytogenetic (e.g. Fluorescent in situ hybridization) and molecular techniques. Furthermore, we will apply population genetics approaches to compare different evolutionary models.

Contacts

Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028
email: mail@eseb2013.com

Address

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
Portugal

Website

Computational Biology & Population Genomics Group 
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