Department of Ecology and Evolution
Bgee, a database for the study of gene expression evolution
Author(s): Robinson-Rechavi, M, Team, B, Bastian, FB
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/
Consequence of the evolution of social behavior in spiders on the intensity of selection
Author(s): Bechsgaard, JS, Settepani, V, Bilde, T
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.
Evolution of heme-copper oxidases superfamily: reconciling gene duplications, losses and transfers to understand the origin of aerobic respiration
Author(s): Rocha, S, Fonseca, M, Posada, D, Pereira, M
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.
Departamento de Biologia Geral
Evolutionary dynamics of the human nadph oxidase genes CYBB, CYBA, NCF2 and NCF4: functional implications
Author(s): Tarazona-Santos, E, Machado, M, Magalhães, WCS, Redondo, RAF, Yeager, M, Chanock, SJ
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.
Evolutionary history of the 17q21 human polymorphic inversion
Author(s): Alves, JMF, Lopes, A, Heutink, P, Chikhi, L, Amorim, A
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.
Institute of Integrative Biology
Evolutionary inferences using nucleotide polymorphism and divergence data in the tomato clade
Author(s): Paris, M, Jean-Claude, W, Ana, F, Thomas, S
The recent revolution in sequencing technology offers great prospects to answer some key questions in evolutionary biology, such as determining the main forces shaping patterns of nucleotide polymorphism within and between species. Due to their relatively recent divergence, differences in mating system, and the genomic resources available, wild tomatoes (Solanum section Lycopersicon) are ideally suited for the study of polymorphism and divergence at a genome-wide scale. Of particular interest is the relative importance of various evolutionary and ecological processes that have shaped these patterns, such as differences in mating system, demographic/speciation history, recombination, and natural selection. We have sequenced 104 transcriptomes of species-wide samples from seven green-fruited species. Based on ~1 million SNPs, we have characterized patterns of genome-wide nucleotide polymorphism and divergence between these species, which reflect varying proportions of ancestral polymorphism between them. Population-genetic analyses will assess the role of evolutionary forces and life history traits on these patterns. For example, levels of synonymous and nonsynonymous polymorphism and divergence will be used to disentangle the importance of purifying and positive selection in the context of varying effective population size, mating system, and recombinational landscape.
Department of Ecology and Environmental Science
Genome-wide patterns of genetic variation in European aspen (Populus tremula)
Author(s): Wang, J, Ingvarsson, PK
The recent advancement of next-generation sequencing (NGS) technology is now widely applied as a cost-effective approach to large-scale re-sequencing of many individuals from species where draft de novo genome assemblies are available. This advance offers unprecedented power to characterize genetic variation at the whole-genome level and provides important insights into the evolutionary forces that shape and maintain this variation. However, the utility of such NGS data rely crucially on the accuracy and quality of variant and genotype calling. Here, we provide a workflow for variant calling and genotype inference using a data set of whole-genome re-sequencing data of a number of European aspen (Populus tremula) individuals each sequenced to a depth of about 20 × coverage. We also estimate levels of nucleotide polymorphism and population differentiation of P. tremula using data from the first 500 scaffolds of twelve individuals sampled from four natural populations in Sweden. Compared to previous studies that were based on a small number of genes, we found higher genome-wide estimates of nucleotide diversity (π=0.00996) and lower genetic differentiation across populations (mean FST=0.00263).
Courant Research Center Geobiology
Genomic basis and possible evolutionary consequences of ectosymbiotic lifestyle in a sulfide-rich environment
Author(s): Cerveau, N, Bauermeister, J, Dattagupta, S
Ectosymbioses between invertebrates and chemosynthetic microbes are common and ecologically important in sulfidic marine environments such as hydrothermal vents, cold seeps, and organic-rich coastal sediments. In these habitats, invertebrates have developed stable ectosymbiotic associations with epsilon and gamma-proteobacteria. It has long been documented that Thiothrix, gamma-proteobacteria belonging to the Thiotrichaceae family, are ectosymbionts of a marine amphipod. Nevertheless, the associations between gammaridean amphipods of the genus Niphargus and sulfur oxidizing Thiothrix bacteria, discovered recently in the Frasassi caves of central Italy, were the first reported examples of chemosynthetic ectosymbioses from a freshwater habitat. The Frasassi caves are underground ecosystem solely sustained by chemoautotrophy. Mats of filamentous sulfur-oxidizing gamma- and epsilonproteobacteria cover the sulfidic cave water bodies. The Niphargus amphipods directly interact with these mats, but have established ectosymbioses with Thiothrix clades, which are furthermore distinct from Thiothrix of the free-living communities. With the advent of the next-generation sequencing technology, comparative genomics have been exhaustively used to study endosymbioses, but have so far never been applied to ectosymbioses. Our aim is to compare the genomes of Thiothrix ectosymbionts of Niphargus with those of free-living Thiothrix present in Frasassi microbial mats to uncover the genomic basis and possible evolutionary consequences of an ectosymbiotic lifestyle. Recent studies revealed that Niphargus-Thiothrix ectosymbioses are not restricted to Frasassi, but occur in subterranean environments across Europe, including Movile cave in Romania and Melissotrypa cave in Greece. These newly discovered associations, which involve different host species and Thiothrix ectosymbiont clades, may serve as natural biological replicates for our comparative genomic studies.
Department of Cell and Molecular Biology
Insights from single cell genomics and metagenomics into microdiversification processes in freshwater bacteria of the SAR11 clade
Author(s): Zaremba-Niedzwiedzka, K, Viklund, J, Zhao, W, McMahon, KD, Ast, J, Bertilsson, S, Stepanauskas, R, Andersson, SGE
The SAR11 clade include oceanic and freshwater alphaproteobacteria. SAR11 is one of the most abundant bacteria in the upper surface waters of the oceans. The freshwater group, referred to as LD12, is uncultivated. Comparison of closely related groups that inhabit very different environments give a unique opportunity to investigate mechanisms and forces that shape their evolution. Here, we analyzed single amplified genomes from ten LD12 cells. Phylogenetic analysis of concatenated pan-orthologous proteins confirmed presence of a monophyletic LD12 cluster within the broader SAR11 clade. Most of the single gene trees agreed in topology, with a few clear examples of incongruence due to recombination events. Oceanic SAR11 strains have among the highest estimated ratio of recombination to mutation in bacteria, but little is known about the LD12 clade. Our study indicated substantially lower recombination frequencies for LD12. Based on sequence shared between the nine most complete single cell genomes, calculated recombination to mutation ratio placed the LD12 at the opposite extreme of the scale compared to the marine sequences. Pairwise comparisons of substitution frequencies showed the presence of microclusters. The LD12 single cells also displayed conservation of gene order structure. The recruitments of metagenomic reads from six lakes in Sweden and the US were used to investigate phylogenetic representation of the single cells and estimate the population mutation and recombination rates. Clustering of metagenomic reads showed no relationship with the trophic status of these lakes, but indicated both geographic and seasonal variability. Some microclusters were present in several lakes and we hypothesize that periodic selection for adaptation to different ecological niches leads to variation in abundances depending on the lake and conditions.
Department of Genetic Research
Inter- and intraspecific genetic divergence in genus Apodemus (Rodentia, Muridae): a framework for NGS
Author(s): Jovanovic, VM, Adnađević, T, Blagojević, J, Stamenković, G, Vujošević, M
The genus Apodemus includes more than 20 species of field and forest mice, with some of them sharing similar morphologies and living in sympatry. Interspecific divergences were previously investigated by means of morphological, biochemical, karyological, and analyses of nuclear and mitochondrial gene sequences. The aim of this research was to describe the divergence among and within several Apodemus clades by comparing the structure of six microsatellite loci. Furthermore, the evolutionary distances among these clades were measured in the data sample of 1483 partial and complete cytochrome b sequences (GenBank accessions). Both microsatellite allelic diversity and polymorphism in presence and length data add to already established line of evidence on interspecific differences among Apodemus species. We strengthened the distinct position of subgenus Sylvaemus, and emphasized intraspecific diversity in A. sylvaticus. This intraspecific divergence in the presence of microsatellite loci was compared to divergences at the karyological level. Bearing in mind that a good phylogenetic framework contributes to the phylogenomic research, we pinpoint the optimal choice of sample size for next generation sequencing (NGS) and the populations of interest.