David Brawand
University of Lausanne
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Publication
Featured researches published by David Brawand.
Nature | 2011
David Brawand; Magali Soumillon; Anamaria Necsulea; Philippe Julien; Gábor Csárdi; Patrick Harrigan; Manuela Weier; Angélica Liechti; Ayinuer Aximu-Petri; Martin Kircher; Frank W. Albert; Ulrich Zeller; Philipp Khaitovich; Frank Grützner; Sven Bergmann; Rasmus Nielsen; Svante Pääbo; Henrik Kaessmann
Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.
Nature | 2014
David Brawand; Catherine E. Wagner; Yang I. Li; Milan Malinsky; Irene Keller; Shaohua Fan; Oleg Simakov; Alvin Yu Jin Ng; Zhi Wei Lim; Etienne Bezault; Jason Turner-Maier; Jeremy A. Johnson; Rosa M. Alcazar; Hyun Ji Noh; Pamela Russell; Bronwen Aken; Jessica Alföldi; Chris T. Amemiya; Naoual Azzouzi; Jean-François Baroiller; Frédérique Barloy-Hubler; Aaron M. Berlin; Ryan F. Bloomquist; Karen L. Carleton; Matthew A. Conte; Helena D'Cotta; Orly Eshel; Leslie Gaffney; Francis Galibert; Hugo F. Gante
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
PLOS Genetics | 2010
Vincent Croset; Raphael Rytz; Scott F. Cummins; Aidan Budd; David Brawand; Henrik Kaessmann; Toby J. Gibson; Richard Benton
Ionotropic glutamate receptors (iGluRs) are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which are best characterized for their roles in synaptic communication in vertebrate nervous systems. A variant subfamily of iGluRs, the Ionotropic Receptors (IRs), was recently identified as a new class of olfactory receptors in the fruit fly, Drosophila melanogaster, hinting at a broader function of this ion channel family in detection of environmental, as well as intercellular, chemical signals. Here, we investigate the origin and evolution of IRs by comprehensive evolutionary genomics and in situ expression analysis. In marked contrast to the insect-specific Odorant Receptor family, we show that IRs are expressed in olfactory organs across Protostomia—a major branch of the animal kingdom that encompasses arthropods, nematodes, and molluscs—indicating that they represent an ancestral protostome chemosensory receptor family. Two subfamilies of IRs are distinguished: conserved “antennal IRs,” which likely define the first olfactory receptor family of insects, and species-specific “divergent IRs,” which are expressed in peripheral and internal gustatory neurons, implicating this family in taste and food assessment. Comparative analysis of drosophilid IRs reveals the selective forces that have shaped the repertoires in flies with distinct chemosensory preferences. Examination of IR gene structure and genomic distribution suggests both non-allelic homologous recombination and retroposition contributed to the expansion of this multigene family. Together, these findings lay a foundation for functional analysis of these receptors in both neurobiological and evolutionary studies. Furthermore, this work identifies novel targets for manipulating chemosensory-driven behaviours of agricultural pests and disease vectors.
Cell Reports | 2013
Magali Soumillon; Anamaria Necsulea; Manuela Weier; David Brawand; Xiaolan Zhang; Hongcang Gu; Pauline Barthès; Maria Kokkinaki; Serge Nef; Andreas Gnirke; Martin Dym; Bernard de Massy; Tarjei S. Mikkelsen; Henrik Kaessmann
Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.
PLOS Biology | 2012
Philippe Julien; David Brawand; Magali Soumillon; Anamaria Necsulea; Angélica Liechti; Frédéric Schütz; Tasman Daish; Frank Grützner; Henrik Kaessmann
A large-scale comparative gene expression study reveals the different ways in which the chromosome-wide gene dosage reductions resulting from sex chromosome differentiation events were compensated during mammalian and avian evolution.
PLOS Biology | 2008
David Brawand; Walter Wahli; Henrik Kaessmann
Embryonic development in nonmammalian vertebrates depends entirely on nutritional reserves that are predominantly derived from vitellogenin proteins and stored in egg yolk. Mammals have evolved new resources, such as lactation and placentation, to nourish their developing and early offspring. However, the evolutionary timing and molecular events associated with this major phenotypic transition are not known. By means of sensitive comparative genomics analyses and evolutionary simulations, we here show that the three ancestral vitellogenin-encoding genes were progressively lost during mammalian evolution (until around 30–70 million years ago, Mya) in all but the egg-laying monotremes, which have retained a functional vitellogenin gene. Our analyses also provide evidence that the major milk resource genes, caseins, which have similar functional properties as vitellogenins, appeared in the common mammalian ancestor ∼200–310 Mya. Together, our data are compatible with the hypothesis that the emergence of lactation in the common mammalian ancestor and the development of placentation in eutherian and marsupial mammals allowed for the gradual loss of yolk-dependent nourishment during mammalian evolution.
Cell Reports | 2015
Michael Keane; Jeremy Semeiks; Andrew E. Webb; Yang I. Li; Víctor Quesada; Thomas Craig; Lone Bruhn Madsen; Sipko van Dam; David Brawand; Patrícia I. Marques; Pawel Michalak; Lin Kang; Jong Bhak; Hyung-Soon Yim; Nick V. Grishin; Nynne Hjort Nielsen; Mads Peter Heide-Jørgensen; Elias M. Oziolor; Cole W. Matson; George M. Church; Gary W. Stuart; John C. Patton; J. Craig George; Robert S. Suydam; Knud Larsen; Carlos López-Otín; Mary J. O’Connell; John W. Bickham; Bo Thomsen; João Pedro de Magalhães
Summary The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.
Journal of Virology | 2008
Valérie Goldschmidt; Angela Ciuffi; Millán Ortiz; David Brawand; Miguel Muñoz; Henrik Kaessmann; Amalio Telenti
ABSTRACT The antiretroviral protein TRIM5α is known to have evolved different restriction capacities against various retroviruses, driven by positive Darwinian selection. However, how these different specificities have evolved in the primate lineages is not fully understood. Here we used ancestral protein resurrection to estimate the evolution of antiviral restriction specificities of TRIM5α on the primate lineage leading to humans. We used TRIM5α coding sequences from 24 primates for the reconstruction of ancestral TRIM5α sequences using maximum-likelihood and Bayesian approaches. Ancestral sequences were transduced into HeLa and CRFK cells. Stable cell lines were generated and used to test restriction of a panel of extant retroviruses (human immunodeficiency virus type 1 [HIV-1] and HIV-2, simian immunodeficiency virus [SIV] variants SIVmac and SIVagm, and murine leukemia virus [MLV] variants N-MLV and B-MLV). The resurrected TRIM5α variant from the common ancestor of Old World primates (Old World monkeys and apes, ∼25 million years before present) was effective against present day HIV-1. In contrast to the HIV-1 restriction pattern, we show that the restriction efficacy against other retroviruses, such as a murine oncoretrovirus (N-MLV), is higher for more recent resurrected hominoid variants. Ancestral TRIM5α variants have generally limited efficacy against HIV-2, SIVagm, and SIVmac. Our study sheds new light on the evolution of the intrinsic antiviral defense machinery and illustrates the utility of functional evolutionary reconstruction for characterizing recently emerged protein differences.
Journal of Virology | 2007
Valérie Goldschmidt; Angela Ciuffi; Millán Ortiz; David Brawand; Miguel Muñoz; Henrik Kaessmann; Amalio Telenti
ABSTRACT The antiretroviral protein TRIM5α is known to have evolved different restriction capacities against various retroviruses, driven by positive Darwinian selection. However, how these different specificities have evolved in the primate lineages is not fully understood. Here we used ancestral protein resurrection to estimate the evolution of antiviral restriction specificities of TRIM5α on the primate lineage leading to humans. We used TRIM5α coding sequences from 24 primates for the reconstruction of ancestral TRIM5α sequences using maximum-likelihood and Bayesian approaches. Ancestral sequences were transduced into HeLa and CRFK cells. Stable cell lines were generated and used to test restriction of a panel of extant retroviruses (human immunodeficiency virus type 1 [HIV-1] and HIV-2, simian immunodeficiency virus [SIV] variants SIVmac and SIVagm, and murine leukemia virus [MLV] variants N-MLV and B-MLV). The resurrected TRIM5α variant from the common ancestor of Old World primates (Old World monkeys and apes, ∼25 million years before present) was effective against present day HIV-1. In contrast to the HIV-1 restriction pattern, we show that the restriction efficacy against other retroviruses, such as a murine oncoretrovirus (N-MLV), is higher for more recent resurrected hominoid variants. Ancestral TRIM5α variants have generally limited efficacy against HIV-2, SIVagm, and SIVmac. Our study sheds new light on the evolution of the intrinsic antiviral defense machinery and illustrates the utility of functional evolutionary reconstruction for characterizing recently emerged protein differences.
Genome Biology | 2008
Ana C. Marques; Nicolas Vinckenbosch; David Brawand; Henrik Kaessmann