XXI Seminario de Genética de Poblaciones y Evolución

Transcripción

XXI
Seminario de Genética de Poblaciones y Evolución
Sala Arcos - Hotel Calipolis
PROGRAMA Y RESÚMENES
PROGRAM AND ABSTRACTS
Sitio Web - Web page: http://xxisgpe.uab.es
Programa - Program
Lunes 3 de Octubre - Monday October 3rd 11:00-13:30 Llegada de los participantes. Recogida de la documentación
Arrival and registration of participants. Delivery of materials 11:15-13:30 Simposio jóvenes investigadores
Young Researcher Symposium 13:30-15:00 Almuerzo - Lunch 15:00-15:05 Bienvenida y presentación - Welcome and Presentation
Sesión 1. Evolución génica e innovación evolutiva
Session 1. Gene evolution and evolutionary innovation
Moderadores - Chairpersons
Julio Rozas (Universitat de Barcelona)
Isaac Salazar-Ciudad (University of Helsinky)
15:05-17:10 Ponencias - Contributed talks
15:05-15:30 Jordi Garcia-Fernàndez. Origins and regulation of an eutherian novelty: The
BGW cluster
15:30-15:55 Cristian Cañestro. Gene loss, pushing the limits of animal evolution
15:55-16:20 Cinta Pegueroles. Evolution of long non-coding RNAs: selective constraints in
both functional and annotated lincRNA
16:20-16:45 Jorge Ruiz-Orera. Nucleotide variation patterns of translated ORFs in lncRNAs
support widespread translation of non-functional proteins
16:45-17:10 Miguel Pérez-Enciso. Análisis de la domesticación porcina basado en rutas
metabólicas
☕ 17:10-17:35 Café - Coတee break
17:35-18:00 Marta Riutort. Comparative genetics of the diတerent reproductive strategies
in freshwater တatworms
18:00-18:25 Francisco J. Silva. Have mechanisms reducing the rates of nucleotide
substitution evolved in some ancient endosymbiont lineages?
18:25-18:50 Laura Baldo. Convergent evolution of the gut microbiota in the adaptive
radiations of African cichlid တshes
18:50-19:15 Macarena Toll-Riera. The genomic basis of evolutionary innovation in
Pseudomonas aeruginosa
19:15-20:05 ☆ Conferencia invitada - Invited address ☆
Andreas Wagner. Cryptic variation, noise, and innovation in the simplest molecular
systems
20:05-20:30 Copa de bienvenida - Welcome drink
20:30-22:00 Cena - Dinner
22:00-23:30 Música a cargo del grupo Boogie Fever - Music by group Boogie Fever
Bar-terraza Inတnity - Hotel Calipolis
Martes 4 de Octubre - Tuesday October 4th 8:00-9:00 Desayuno - Breakfast Sesión 2. Genética de poblaciones y cuantitativa
Session 2. Population and quantitative genetics
Josefa González (Institut Biologia Evolutiva)
Antonio Barbadilla (Universitat Autònoma de Barcelona)
Dmitri Petrov. To be announced
09:50-10:15 Antonio Barbadilla. Integrative population genomics in Drosophila
10:15-10:40 Harold P. de Vladar. Joint sweeps of တnite populations under stabilising
selection
10:40-11:05 Sebastián E. Ramos-Onsins. Statistics, computational tools and population
genomic analyses to search for the eတect of domestication
11:30-11:55 Miguel A. Toro. Parámetros genéticos ‘perdidos’ y ‘encontrados’ en estudios
de asociación
11:55-12:20 Aurora García-Dorado. Detección y estima de la purga genética utilizando
datos genealógicos
12:20-12:45 Jesús Fernández. Estimación multigeneracional del parentesco a partir de
marcadores moleculares
Adam Eyre-Walker. Factors that aတect the rate of adaptive evolution
13:35-15:00 Almuerzo - Lunch Sesión 3. Evolución ecológica y de poblaciones
Session 3. Ecological and population evolution
Marta Riutort (Universitat de Barcelona)
Marta Pascual (Universitat de Barcelona)
15:05-15:30 Doris Vela Peralta. Phylogenetic placement of Drosophila from Ecuador
15:30-15:55 Ana D. Caperta. Cytogenetic diversity and ecology in populations of the
halophyte Limonium vulgare and related taxa along the Portuguese coast
15:55-16:20 Marta Álvarez-Presas. New molecular markers to delve into phylogeography
and population genetic structure of two Brazilian land planarian species
16:20-16:45 Carlos Carreras. Population genomics of an endemic Mediterranean တsh:
from global to local diတerentiation caused by dispersal and adaptation
16:45-17:10 Luis Peñarrubia. Caracterización genética de la invasión de la almeja asiática
(Corbicula) en la Península Ibérica
17:35-18:00 Borja Milá. Genomic analyses reveal the role of selection and low dispersal in
driving intra-island diversiတcation of a Reunion Island songbird
18:00-18:25 Marta Barluenga. Sensory drive and sympatric speciation in Neotropical
crater lake cichlid တsh
18:25-18:50 Jorge F. Henriques. Are there genetic trade-oတs between behavioral and lifehistory traits in the soil top predator Lycosa fasciiventris?
18:50-19:15 Fernando González-Candelas. The origin of modern syphilis and emergence
of a contemporary pandemic cluster
Amparo Latorre. Dissecting the genome reduction process in endosymbiotic bacteria
20:30-22:00 Cena - Dinner
Miércoles 5 de Octubre - Wednesday October 5th 8:00-9:00 Desayuno - Breakfast Sesión 4. Genómica evolutiva y funcional
Session 4. Functional and evolutionary genomics
Mario Cáceres (Universitat Autònoma de Barcelona)
Alfredo Ruiz (Universitat Autònoma de Barcelona)
Henrik Kaessmann. The evolution of mammalian gene expression programs
09:50-10:15 Josefa González. The role of transposable element insertions in
environmental adaptation in Drosophila melanogaster
10:15-10:40 Maria Pilar Garcia Guerreiro. Desregulación de elementos transponibles en
híbridos interespecíတcos de Drosophila: causas y consecuencias
10:40-11:05 Alejandro Sánchez-Gracia. Understanding arthropod gene and genome
evolution through the comparative genomics and transcriptomics analyses of non-model
organisms
11:30-11:55 Paulino Martínez. Whole genome sequencing of turbot (Scophthalmus
maximus): adaptation to demersal life and signatures of selection across its distribution
range
11:55-12:20 Francisco Rodríguez-Trelles. Combining genomics and natural history to
understand the evolutionary biology of inversions in Drosophila subobscura
12:20-12:45 Margarida Matos. Can we predict Adaptive Evolution? A question with many
answers
Gustavo Kuhn. Satellite DNAs in Drosophila exposed: news and perspectives emerging
from the analysis of sequenced genomes
13:35-15:00 Almuerzo - Lunch Sesión 5. Evolución de humanos y primates
Session 5. Human and primate evolution
Elena Bosch (Institut Biologia Evolutiva)
Mauro Santos (Universitat Autònoma de Barcelona)
15:05-15:30 Sara Guirao-Rico. A genome wide IBD analysis in a worldwide sample of pigs
reveals a complex network of introgression events
15:30-15:55 Francesc Calafell. Lineages of men: Y chromosome analysis reveals recent,
independent expansions in Iberia and N. Africa
15:55-16:20 Martin Kuhlwilm. Chimpanzee genomic diversity reveals ancient admixture
with bonobos
16:20-16:45 Saioa López. Haplotype-based methods for the study of genetic diversity and
admixture events. Applications to modern and ancient human populations
16:45-17:10 Aida Andrés. Local adaptation in humans: Insights from modern and ancient
genomes
17:35-18:00 Haတd Laayouni. Detection of natural selection at population level: insights
from human and chimpanzee populations
18:00-18:25 Mario Cáceres. Evolutionary and functional impact of polymorphic inversions
in the human genome
18:25-18:50 Oscar Lao. Identiတcation of genetic barriers and genetic gradients by means
of a multiple regression on distance matrices (MRM) coupled to a genetic algorithm
18:50-19:15 Simón Perera. Reappraising the human mitochondrial DNA recombination
dogma
Eors Szathmary. Evolutionary neurodynamics
21:00-23:00 Cena de despedida - Conference Dinner Restaurante - Restaurant Vivero
23:00-23:40 ☆☆ Homenaje al Dr. Antonio Fontdevila - Homage to Dr. Antonio Fontdevila ☆☆
Restaurante - Restaurant Vivero
Simposio jóvenes investigadores
Young Researcher Symposium
Lunes 3 de Octubre - Monday October 3rd 11:00-11:15 Llegada de los participantes
Arrival and registration of participants 11:15-11:35 Bienvenida al I Simposio de Jóvenes Investigadores
Welcome to the I Young Reseacher Symposium 11:35-13:20 Ponencias - Contributed talks
11:35-11:50 Marta Puig Giribets. Evolution of the Hsp70 gene family at the
sequence level, genomic organization and gene expression in Drosophila
subobscura
11:50-12:05 Mayukh Mondal. Genomic analysis of Andamanese provides insights
into ancient human migration into Asia and adaptation
12:05-12:20 Laia Carreté. Genome variation in the emerging fungal pathogen
Candida glabrata
12:20-12:35 Isaac Noguera. Understanding the frequency distribution of human
polymorphic inversions
12:35-12:50 Ana S. Róis. Interspeciတc relationships in the halophyte Limonium
vulgare and related taxa (Plumbaginaceae) using the ITS1 marker
12:50-13:05 Miriam Merenciano. Multiple independent retrotransposon insertions
in the proximal promoter of a stress response gene in Drosophila melanogaster
13:05-13:20 Guillermo Friis. Testing the role of selection and demography in
driving the rapid postglacial radiation of Dark-eyed Juncos
13:20-13:30 Clausura - Closing
Resúmenes
Abstracts
Presentación - Talk 1
Lunes - Monday 15:05-15:30
Sesión 1. Evolución génica e innovación evolutiva - Session 1. Gene evolution and evolutionary innovation
ORIGINS AND REGULATION OF AN EUTHERIAN NOVELTY: THE BGW
CLUSTER
Enrique Navas1, Demian Burguera1, Cristina Vicente2, Fausto Ulloa3, Serena Mirra3,
Jose Luis Ferran4, Salvatore d'Aniello5, Luis Puelles4, Manuel Irimia6, Eduardo Soriano3,
Jaime Carvajal2, Jordi Garcia-Fernàndez1
1 Department of Genetics, Faculty of Biology, University of Barcelona 2 Gene regulation and
morphogenesis group, Centro Andaluz de Biología del Desarrollo (CABD), Seville 3 Department of Cell
Biology, Faculty of Biology, University of Barcelona, 4 Department of Human Anatomy, Faculty of
Medicine, University of Murcia 5 Department of Biology and Evolution of Marine Organisms, Stazione
Zoologica Anton Dohrn, Naples 6 EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation,
Barcelona
Two
related gene subfamilies known as BEX and TCEAL map to a genomic region
speciတc to Eutheria (placental mammals). These families are part of a gene cluster,
named “BGW cluster”, together with the ARMCX family and HNRNPH2. Some of the
BEX/TCEAL genes have been related to control the balance between proliferation and
diတerentiation, while others promote apoptosis in a p75-dependent manner, but most
of them remain poorly studied.
The ARMCX family and HNRNPH2 are derived from retrocopies of the ARMC10 and
HNRNPH1 genes respectively –conserved across bilateria, and located in autosomal
chromosomes–, whereas no orthologs have been found for the BEX/TCEAL family
outside of Eutheria. However, all these genes share an intriguing feature: a sequence
motif in their proximal promoter region that appears to be crucial for their expression,
the BGW motif. To further understand the evolution of this gene cluster, we
investigated the origin of the BEX/TCEAL genes and traced it to an atypical formation in
the ancestor of eutherians. Furthermore, novel features associated with BEX/TCEAL
suggest a more complete scenario for the origin of the cluster: the BGW motif was
already present at the HNRNPH2 locus in the ancestor of therian mammals, being
subsequently duplicated and coopted in the eutherian lineage by the BEX/TCEAL
ancestor and, posteriorly, by the ARMCX ancestral gene. Finally, we also studied the
expression of the BEX/TCEAL genes during mouse development using in situ
hybridization. We found that they are highly expressed in the brain and placenta,
which are structures that require a well-tuned control of cell cycle during their
development in eutherian mammals.
Here we propose a scenario for the origin of the BEX/TCEAL family and for the
formation of the BGW cluster where they belong. Their uncommon origin, their
pattern of expression, and their putative biological function during development
makes these genes an interesting subject of study to understand how lineage-speciတc
genes could contribute to mammalian evolution.
Volver al programa / Back to the Program
GENE LOSS, PUSHING THE LIMITS OF ANIMAL EVOLUTION
Josep Martí-Solans1, Alfonso Ferrández-Roldán1, Olga V. Belyaeva2, Miriam DiazGracia1, Marcos Plana-Carmona1, Alba Almazán-Almazán1, Anna Moncusí1, Nuria P.
Torres-Aguila1, Paula Bujosa1, Natalia S. Rojas-Galván1, Enya Duran-Bello1, Natalia Y.
Kedishvili2, Ricard Albalat1 and Cristian Cañestro1
(1) Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat
(IRBio), Universitat de Barcelona, Barcelona (Spain)
(2) Department of Biochemistry and Molecular Genetics, University of Alabama – Birmingham,
Birmingham (USA)
The bloom of Genomics is revealing a new perspective of gene loss as a pervasive
evolutionary source of genetic variation that can cause adaptive phenotypic diversity
and inတuence the evolution of species. Outside bacteria and yeast, however, the
understanding of the process of gene loss remains elusive, especially in the evolution
of animal species. Our group, using the dismantling of gene networks in the chordate
Oikopleura dioica as a case study, investigates whether gene losses are compensated
by mutational robustness, and whether biased patterns of gene losses occur in the
context of regressive or adaptive evolution. Our work illustrates how the identiတcation
of patterns of gene co-elimination can be a useful strategy to recognize gene network
modules associated to distinct functions, and how the identiတcation of survival genes
can help to recognize neofunctionalization events and ancestral functions.
EVOLUTION OF LONG NON-CODING RNAS: SELECTIVE CONSTRAINTS IN
BOTH FUNCTIONAL AND ANNOTATED LINCRNA
Cinta Pegueroles1,2, Toni Gabaldón1,2,3
(1) Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG). Dr. Aiguader, 88.
08003 Barcelona, Spain
(2) Universitat Pompeu Fabra (UPF). 08003 Barcelona, Spain.
(3) Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona,
Spain.
Despite
long non-coding RNAs are largely transcribed in all studied eukaryotic
genomes, their functionality is still under debate since they are usually expressed at
low levels and they are poorly conserved across species. In addition, it was previously
suggested that in those species having an small eတective population size such as
human, selection may be not strong enough to counteract the eတect of drift. We have
evaluated signatures of selection in a curated dataset of experimentally characterized
human lncRNAs, as a reference for truly functional lncRNAs, and a large set of
annotated intergenic lncRNA (lincRNA). We focused in three main types of analysis:
conservation across species, patterns of polymorphism within a species, and
relationships between sequence constraints and secondary structure. We found
evidence of purifying selection acting on lncRNAs. In addition, RNA secondary
structure seems to constrain sequence variation in lncRNAs. Importantly, this relation
is independent of the GC content and the presence of splice-related motifs. Our
results reinforce the idea that numerous predicted lncRNAs are indeed functional.
NUCLEOTIDE VARIATION PATTERNS OF TRANSLATED ORFS IN LNCRNAS
SUPPORT WIDESPREAD TRANSLATION OF NON-FUNCTIONAL PROTEINS
Jorge
Ruiz-Orera1
Messeguer2,
M.Mar
Pol
Verdaguer-Grau2,
José
Luis
Villanueva-Cañas1,
Xavier
Albà1,3
(1) Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar
Research Institute, Universitat Pompeu Fabra, Barcelona, Spain.
(2) Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain.
(3) Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
Any cell expresses thousands of transcripts that contain short, non-conserved, open
reading frames and which are assumed to be non-coding. The functions of the vast
majority of these long non-coding RNAs (lncRNAs) remain unknown. Intriguingly,
ribosome proတling experiments have provided evidence that a large fraction of
lncRNAs is translated (e.g. Ruiz-Orera et al., 2014). Many lncRNAs are evolutionary
young and they could play an important role in the evolution of new coding and noncoding functions (Ruiz-Orera et al., 2015).
Here we have employed ribosome proတling sequencing data from eight mouse tissues
or cell types to investigate what drives the translation of lncRNAs and which are the
functional consequences of this activity. Using the three-nucleotide read periodicity
that characterizes actively translated regions in transcripts we have detected
translation of about 1,500 lncRNAs, about one third of the initial lncRNA dataset. We
have employed ~330,000 synonymous and non-synonymous mouse single nucleotide
variants to infer the strength of purifying selection acting on the translated proteins.
We have identiတed hundreds of mouse lncRNAs that are not conserved in human and
which translate non-functional proteins. We have found that the nucleotide hexamer
composition of the ORFs has a signiတcant inတuence on the translatibility of these
lncRNAs. The translation of lncRNAs တlls a gap in our understanding of de novo protein
coding gene emergence.
Ruiz-Orera et al. (2014). Long non-coding RNAs a source of new peptides. Elife 3,
e03523.
Ruiz-Orera et al. (2015). Origins of de novo genes in human and chimpanzee. Plos
Genetics 11, e1005721.
ANÁLISIS DE LA DOMESTICACIÓN PORCINA BASADO EN RUTAS
METABÓLICAS
Jorge Leno-Colorado1, Antonio Reverter2, Miguel Pérez-Enciso1,3
(1) Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB),
Universitat Autònoma de Barcelona, Bellaterra 08193. España.
(2) CSIRO Agriculture, Queensland Bioscience Precinct, St. Lucia 4067, QLD, Australia
(3) ICREA, Carrer de Lluís Companys 23, Barcelona 08010, España.
El
objetivo de nuestro trabajo es el análisis de posibles huellas genómicas de la
domesticación en cerdos, utilizando la vía metabólica como unidad del análisis.Hemos
analizado un total de 163 genomas porcinos (Sus scrofa) de todo el mundo que
provienen de bases de datos públicas y obtenidas en nuestro laboratorio. Los
genomas fueron clasiတcados en 4 grandes grupos: jabalíes asiáticos (ASWB, n = 20),
que contiene jabalíes de China, Corea del Sur y Rusia; cerdos domésticos asiáticos
(ASDM, n = 60), incluyendo 10 razas chinas como Meishan o Wuzhishan; jabalíes
europeos (EUWB, n = 20) de diferentes regiones de Europa como España, Italia, Grecia
y Holanda; y cerdos domésticos europeos (EUDM, n = 63). Se han obtenido todas las
vías metabólicas y sus genes a partir de la base de datos NCBI Biosystems (Geer et al.
2010). Como medida de diferenciación, usamos el Fst. Realizamos dos análisis:
comparando ASDM con ASWB, EUDM con EUWB. La obtención de un estadístico para
cada vía, se hizo en dos etapas. En la primera obtuvimos un valor de probabilidad (Pvalue) empírico combinando mediante el estadístico de Fisher los Fsts de cada uno de
los SNPs de cada gen (eliminando los que están en muy alto desequilibrio). En una
segunda etapa se repitió el proceso para todos los genes de cada ruta, y el P-value
တnal se calculó mediante permutación. En nuestros resultados encontramos varias
vías metabólicas importantes que parecen ser distintas entre cerdos salvajes y
domésticos, algunas de ellas están relacionadas con el metabolismo de ácidos grasos,
azúcares y proteínas o con señales hormonales que están involucradas en el
comportamiento del animal, como puede ser la dopamina. En conclusión, el análisis
de vías es un enfoque prometedor para detectar señales de selección y
domesticación.
COMPARATIVE GENETICS OF THE DIFFERENT REPRODUCTIVE
STRATEGIES IN FRESHWATER FLATWORMS
Marta Riutort1, Laia Leria1, Eduard Solà1, Miquel Vila-Farré2,
(1) Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat
(IRBio), Universitat de Barcelona, Barcelona, Catalonia (Spain)
(2) Max Planck Institute of Molecular Cell Biology and Genetics, Dresden (Germany).
The way how an organism reproduces plays a crucial role upon its genetic evolution.
Sexual reproduction increases the genetic variability of the populations due to
recombination and outcrossing. On the other hand, in asexual reproduction oတspring
is genetically identical to the parents, and the accumulation of deleterious mutations
can lead asexual populations to extinction. Freshwater တatworms of the genus Dugesia
show a wide variety of reproductive strategies even in the same species: they can
reproduce laying cocoons (either sexually or by parthenogenesis) and also asexually
by တssion (thanks to their great regeneration capabilities).
The main objective of this work is to investigate how genetic variability is generated by
the diတerent reproductive strategies using D. subtentaculata as a model species.
We have sequenced three molecular markers bearing diတerent types of information
(nuclear exons and introns and a mitochondrial gene) of individuals belonging to eight
natural populations with diတerent types of reproduction. We have analysed the
genetic variability for the three markers at diတerent levels (intra-individual, population,
by type of reproduction,…) by estimating population genetic parameters.
The preliminary results show an extremely high haplotype mosaicism within
individuals no matter their type of reproduction. However, the nucleotide diversity is
signiတcantly higher in individuals of mixed and တssiparous populations. Moreover, all
the haplotypes of the exclusively sexual populations are private, while the rest of
individuals share haplotypes between distantly distributed populations.
These data provide new insights into the evolution of the diတerent types of
reproduction helping us to understand how asexually reproducing organisms
overcome the problems associated to the absence of sex.
HAVE MECHANISMS REDUCING THE RATES OF NUCLEOTIDE
SUBSTITUTION EVOLVED IN SOME ANCIENT ENDOSYMBIONT
LINEAGES?
Francisco J. Silva1, Diego Santos-Garcia2
(1) Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain.
(2) Department of Entomology, Hebrew University of Jerusalem, Rehovot, Israel.
The availability of complete genome sequences of bacterial endosymbionts with strict
vertical transmission to the host progeny opens the possibility to estimate molecular
evolutionary rates in diတerent lineages and understand the main biological
mechanisms inတuencing these rates. The sequencing of the genomes of four strains of
the primary endosymbiont of whiteတies (Portiera aleyrodidarum) showed that the
rates of nucleotide substitution were unexpectedly very low in three of the lineages, in
spite of the fact that their gene repertories were strongly reduced with almost no DNA
repair systems. A positive correlation was also observed between the rates of
synonymous and nonsynonymous substitutions. We have extended and compared the
rates of evolution for nonsynonymous and synonymous substitutions in nine bacterial
endosymbiont lineages, belonging to four clades (Baumannia, Blochmannia, Portiera
and Sulcia) primary endosymbionts of several insect species. The main results are the
observation of a positive correlation between both rates with diတerences among
lineages of up to three orders of magnitude and that the substitution rates decrease
over long endosymbioses. To explain these results we propose three mechanisms. The
တrst, variations in the e†ciencies of DNA replication and DNA repair systems, is unable
to explain most of the observed diတerences. The second, variations in the generation
time among bacterial lineages, would be based on the accumulation of fewer DNA
replication errors per unit time in organisms with longer generation times. The third, a
potential control of the endosymbiont DNA replication and repair systems through the
transfer of nuclear-encoded proteins, could explain the lower rates in long-term
obligate endosymbionts. Because the preservation of the genomic integrity of the
harbored obligate endosymbiont would be advantageous for the insect host, biological
mechanisms producing a general reduction in the rates of nucleotide substitution per
unit of time would be a target for natural selection.
CONVERGENT EVOLUTION OF THE GUT MICROBIOTA IN THE ADAPTIVE
RADIATIONS OF AFRICAN CICHLID FISHES
Laura Baldo1, Joan L. Pretus1, Juan L. Riera1, Zuzana Musilova2, Walter Salzburger2
(1) Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona
(2) Zoology Institute, University of Basel, Switzerland
African
cichlids, with their spectacular radiations driven by adaptation to diတerent
trophic niches, provide a powerful comparative system for understanding the
evolutionary dynamics of the host-gut microbiota association following host speciation
and ecological divergence. Presence of natural replicates in host ecomorphs following
diet convergence makes the system particularly useful to explore the role of the gut
microbiota as a trophic trait, while accounting for other two confounding factors in
shaping these microbial communities, host geography and phylogeny. If the gut
microbiota plays a key role in the host adaptation to a trophic niche by optimizing
nutrients extraction and absorption, then this trait should mirror the adaptation of the
other eco-morphological traits of cichlids, such as gut and jaw morphologies, rather
than phylogeny. Therefore, we expect compositional and functional microbial
divergence and convergence across species in function of the diet, and repeatability of
such processes across radiations.
To test these predictions here we characterized the intra- and interspeciတc variation of
the gut microbiota of 29 wild cichlid species from two african lakes: Tanganyika
(Zambia) and Barombi Mbo (Camerroon). We found a strong taxonomic and functional
microbial divergence of herbivores from carnivores and a remarkable convergence in
the gut microbiota of herbivores across distantly related species at each lake,
supporting a primary role of the gut in the cichlid trophic adaptation.
THE GENOMIC BASIS OF EVOLUTIONARY INNOVATION IN
PSEUDOMONAS AERUGINOSA
Toll-Riera M1,2,3, San Millan A1, Wagner A2,3,4, MacLean RC1.
(1) Department of Zoology, University of Oxford, Oxford, United Kingdom.
(2) Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
(3) The Swiss Institute of Bioinformatics, Lausanne, Switzerland.
(4) The Santa Fe Institute, Santa Fe, New Mexico, United States of America.
Novel traits play a key role in evolution, but their origins remain poorly understood.
Here we address this problem by using experimental evolution to study bacterial
innovation in real time. We allowed 380 populations of Pseudomonas aeruginosa to
adapt to 95 diတerent carbon sources that challenged bacteria with either evolving
novel metabolic traits or optimizing existing traits. Whole genome sequencing of more
than 80 clones revealed profound diတerences in the genetic basis of innovation and
optimization. Innovation was associated with the rapid acquisition of mutations in
genes involved in transcription and metabolism. Mutations in pre-existing duplicate
genes in the P. aeruginosa genome were common during innovation, but not
optimization. These duplicate genes may have been acquired by P. aeruginosa due to
either spontaneous gene ampliတcation or horizontal gene transfer. High throughput
phenotype assays revealed that novelty was associated with increased pleiotropic
costs that are likely to constrain innovation. However, mutations in duplicate genes
with close homologs in the P. aeruginosa genome were associated with low pleiotropic
costs compared to mutations in duplicate genes with distant homologs in the P.
aeruginosa genome, suggesting that functional redundancy between duplicates
facilitates innovation by buတering pleiotropic costs.
This paper was recently published in Plos Genetics
Toll-Riera M.*, San Millan A.*, Wagner A., MacLean RC. (2016). The genomic basis of
metabolic evolutionary innovation in Pseudomonas aeruginosa. PLoS Genet.
12(5):e1006005. DOI: 10.1371/journal.pgen.1006005
CRYPTIC VARIATION, NOISE, AND INNOVATION IN THE SIMPLEST
MOLECULAR SYSTEMS
Andreas Wagner
Dept. of Evolutionary Biology and Environmental
Winterthurerstrasse 190 CH-8057 Zurich Switzerland
Studies,
Phenomena
Y27-J-54.
University
of
Zurich,
such as cryptic variation have တrst been discovered in complex
multicellular organisms and their complex morphological traits. To study them in such
systems is made di†cult by the fact that complex traits are aတected by many genes
whose interactions are poorly understood. I will discuss laboratory evolution
experiments that highlight the advantages of much simpler systems, such as evolving
RNA and protein molecules in studying these phenomena. These systems can help
understand the signiတcance of cryptic variation, robustness, and noise for evolutionary
adaptations and innovations on all scales of biological organization.
Martes - Tuesday 09:00-09:50
Sesión 2. Genética de poblaciones y cuantitativa - Session 2. Population and quantitative genetics
TO BE ANNOUNCED
Dmitri A. Petrov
Department of Biology, Stanford University, USA
--Volver al programa / Back to the Program
INTEGRATIVE POPULATION GENOMICS IN DROSOPHILA
Antonio Barbadilla1, Sònia Casillas1, Raquel Egea1, Marta Coronado1, Sergi Hervàs1,
David Castellano1, Isaac Noguera1, Roger Mulet1, Esteve Sanz1, Isaac Salazar-Ciudad2,
Irepan Salvador2, Alfredo Ruiz1
(1) Institut de Biotecnologia i de Biomedicina & Departament de Genètica i Microbiologia, Universitat
Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
(2) University of Helsinki, Helsinki (Finland)
La genómica de poblaciones ha abierto nuevas líneas de indagación tanto en el nivel
de la variación genómica como en el del nivel multiómico. Nuestra participación en un
análisis de genómica de poblaciones pionero en la especie Drosophila melanogaster
nos ha permitido proponer nuevas metodologías para medir el potencial adaptativo
de un genoma o cartograတar la selección en una unidad anatómica o morfológica. Se
ha cuantiတcado por primera vez el coste de ligamiento de un genoma (la interferencia
Hill-Robertson, iHR) y descrito la selección en el espacio y en el tiempo del ciclo vital de
D. melanogaster. Mediante una aproximación interdisciplinar, integrando métodos y
conocimientos de genómica, genética de poblaciones, biología del desarrollo, y
bioinformática, se han abordado los siguientes objetivos: (a) la descripción de los
patrones de variación y iHR a lo largo de los genomas de D. melanogaster y Drosophila
simulans analizado centenares de genomas completos secuenciados en varias
poblaciones del espectro geográတco de distribución actual de estas especies; (b) la
elaboración de un mapa de la adaptación y el constreñimiento selectivo en el embrión
y la larva de D. melanogaster. La era actual de la genómica de poblaciones promete
revelarnos တnalmente cuál es la verdadera naturaleza de la variación genética.
PALABRAS CLAVE: genómica de poblaciones, interferencia Hill-Robertson, evo-devo
molecular, Drosophila
JOINT SWEEPS OF FINITE POPULATIONS UNDER STABILISING SELECTION
Harold P. de Vladar
Parmenides Foundation, Pullach (Germany)
Most quantitative traits are thought to be under stabilising selection. However, how
this mode of selection aတects the alleles that compose the trait is not entirely clear,
particularly for unequal eတects on the trait. Moreover, understanding how selection
combines with mutation and drift is even more puzzling. In a recent analyses it was
shown that in inတnite populations (i.e. without genetic drift), the alleles of a
quantitative character fall into two classes. It the eတects are above a threshold, 4 mu/S,
where mu is the allelic mutation rate and S the intensity of stabilising selection, then
the alleles remain near တxation. Alleles of eတect lower than the threshold remain at
intermediate frequencies of ~1/2. Also, there are several stable combinations that
allow the trait to nearly match the optimum value. In this talk I present results of a
similar system under genetic drift in stationary state. The picture is diတerent than in
inတnite populations because eventually all alleles will be တxed. However, the alleles of
small eတect are less constrained by selection and can freely wander the space of
genetic combinations, but they still contribute less to the trait and negligibly to the
genetic variance. Peak shifts of alleles of large eတect can occur. However, it is shown
that most of these shift are unlikely to occur at single loci at a time, and, instead,
several alleles at diတerent loci stochastically sweep at the same time. In this way, the
trait remains close to the optimum while alleles of large eတect switch states without
going through a တtness valley.
STATISTICS, COMPUTATIONAL TOOLS AND POPULATION GENOMIC
ANALYSES TO SEARCH FOR THE EFFECT OF DOMESTICATION
Sebastián E. Ramos-Onsins1, Luca Ferretti2, Sara Guirao1, Porတdio Hernández-Budé3,
Joan Jené1, Carlos Montemuiño3, Javi Navarro3, Alejandro Sánchez-Gracia4,5, Gonzalo
Vera1, Mireia Vidal-Villarejo1
(1) Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB. Ediတci CRAG, Campus UAB.
08193 Bellaterra, Spain. (2) The Pirbright Institute, Woking, United Kingdom.
(3) Departament d'Arquitectura de Computadors i Sistemes Operatius (DACSO). Arquitectura i
Tecnología de Computadors. Escola d'Enginyeria ·Carrer de les Sitges. Campus de la UAB. 08193
Bellaterra, Spain.
(4) Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028,
Barcelona, Spain.
(5) Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona,
Spain.
We aim to understand the eတects of selection due to domestication by scanning the
levels and patterns of genomic variation in commercial interesting organisms such as
Sus scrofa (pig), Cucumis genus (melon, cucumber) or Prunus genus (peach, almond).
To achieve this, we work on three diတerent lines: (i) we search for statistics and
methods to measure the genome variability and to disentangle selective patterns from
demography in collaboration with theoreticians; (ii) we develop software for the
analysis of high throughput data, mainly in collaboration with computer engineers; (iii)
we make genome-wide comparative analysis of nucleotide variability in domestic
species (and also versus wild populations, if extant) to describe the patterns and levels
of variation and also perform computational simulations of evolutionary models in
order to analyze and to interpret the available data. We developed a new algorithm (PFcaller) designed to extract the variability
information from genome sequencing data, specially for low read depth data and for
polyploidy and pooled sequence datasets. We also developed a computational
solution (ngaSP) for the analysis of genome variability using NGS data, which
integrates our own-in-house but also external applications. This solution is an open
source code designed to include new calculations provided by the scientiတc
community. Volver al programa / Back to the Program
PARÁMETROS GENÉTICOS ‘PERDIDOS’ Y ‘ENCONTRADOS’ EN ESTUDIOS
DE ASOCIACIÓN
Miguel A. Toro
Deprtamento de Producción Agraria, ETSIA, UPM, 28040 Madrid
Recientemente,
en estudios de asociación, el tema de la ‘missing heritability’ ha
recibido mucha atención, aunque no tanto el comportamiento de otros parámetros
genéticos. En primer lugar hemos analizado la relación entre la varianza genética
(aditiva y dominante) de un QTL y la varianza genética (aditiva y dominante) ‘aparente’
explicada por un marcador poniendo de maniတesto que solo coinciden si el ligamiento
es perfecto (el QTL y el marcador están completamente ligados y tienen las mismas
frecuencias). Este ligamiento perfecto no es posible si el QTL es trialélico. En segundo
lugar utilizando un modelo de un QTL y dos loci marcadores se muestra que es
posible que aparezcan varianzas epistáticas ‘aparentes' incluso si el QTL es aditivo. Por
último en un contexto aditivo y utilizando un modelo de dos QTLs y dos marcadores
se muestra que la correlación genómica entre dos caracteres puede ser mayor, igual o
menor que la correlación genética e incluso de signo distinto.
DETECCIÓN Y ESTIMA DE LA PURGA GENÉTICA UTILIZANDO DATOS
GENEALÓGICOS
Aurora García-Dorado1, Jinliang Wang2, Eugenio López-Cortegano*1
(1) Departamento de Genética, Facultad de Biología, Universidad Complutense. 28040, Madrid
(2) Institute of Zoology, Regent's Park, London NW1 4RY, UK
La depresión consanguínea se debe sustancialmente a que el componente recesivo
de los efectos deletéreos (d, denominado aquí coeတciente de purga) se expresa en los
homocigotos generados por consanguinidad. Ello desencadena a su vez la purga
genética, consistente en la selección en contra de d.
Se ha acumulado evidencia de que, en poblaciones naturales, el lastre de
consanguinidad B es mucho mayor que el estimado en diseños de laboratorio, pero es
de esperar que la purga sea también más intensa. Por tanto, resulta necesario estimar
la depresión consanguínea y la purga con datos obtenidos en la naturaleza donde,
gracias a los esfuerzos en conservación, se dispone a menudo de registros
genealógicos que pueden completarse utilizando información molecular.
Después de haber desarrollado un modelo para predecir las consecuencias conjuntas
de la consanguinidad y la purga, presentamos aquí su ampliación al tratamiento de
datos de eတcacia en individuos con genealogías conocidas.
En primer lugar, la ecuación exponencial que predice la eတcacia media se reformula
para la eတcacia individual Wi, y se demuestra que la pendiente esperada del logaritmo
de Wi sobre la consanguinidad es [ln(1-2d)/2d]B, pudiendo ser por tanto,
sustancialmente mayor que B en valor absoluto.
En segundo lugar, se derivan ecuaciones genealógicas para los coeတcientes de
consanguinidad y parentesco purgados, es decir, corregidos por la reducción en
frecuencia de los deletéreos atribuible a la purga.
Finalmente, presentamos un software (PURGd) que calcula dichos coeတcientes y
estima d y la tasa de depresión consanguínea. Si no hay eတcacias nulas, PURGd puede
analizar la regresión lineal para el logaritmo de la eတcacia, aunque, como se ha dicho,
se obtendrá una estima sesgada de B. Alternativamente, PURGd puede estimar d y B
ajustando directamente la ecuación exponencial por métodos numéricos.
Una exploración preliminar de datos simulados muestra que este método,
implementado en PURGd, discrimina si ha ocurrido purga y proporciona estimas del
lastre de consanguinidad y el coeတciente de purga que tienen buen valor predictivo. El
método propuesto puede ser pues de gran ayuda para el análisis y valoración del
papel de la purga genética en la determinación de las consecuencias de la
consanguinidad sobre la eတcacia, proporcionando información útil desde el punto de
vista evolutivo y conservacionista.
ESTIMACIÓN MULTIGENERACIONAL DEL PARENTESCO A PARTIR DE
MARCADORES MOLECULARES
Jesús Fernández1, Miguel Ángel Toro2
(1) INIA, Ctra. Coruña Km. 7,5, 28040 Madrid
(2) Departamento de Producción Agraria, ETSIA, UPM, 28040 Madrid
Además
de los problemas derivados de su dependencia del conocimiento de las
frecuencias alélicas ancestrales, muchos de los estimadores de parentesco a partir de
información molecular no son capaces de diferenciar más que un rango limitado de
tipos de relación. Por ejemplo, solo pueden diferenciar entre hermanos o individuos
no emparentados. Es más, sólo son eတcaces para relaciones muy cercanas (hermanos,
medios hermanos, padre-hijo). Uno de estos métodos, incluido en el grupo de
estimadores de reconstrucción genealógica, se basa en maximizar la correlación entre
la matriz de parentesco molecular y la matriz calculada a partir de genealogías usando
ancestros virtuales. De esa manera puede estimar relaciones más complejas que otros
estimadores mediante la creación de genealogías más “profundas”. Sin embargo, una
limitación que presenta es que los individuos estudiados (genotipados) deben
pertenecer a la misma generación (es decir, no pueden ser ancestros unos de los
otros). Hemos extendido el método anterior para que sea capaz de trabajar con
individuos no contemporáneos que pertenezcan a diferentes generaciones.
Simulaciones por ordenador han demostrado que este método es capaz de
reconstruir genealogías de tamaño moderado que comprenden unas pocas
generaciones usando un número factible de marcadores. La precisión mejora cuando
se dispone de alguna información demográတca (por ejemplo, el conocimiento de la
fecha de nacimiento de los candidatos permite descartar algunos individuos como
ancestros y/o descendientes). El método es también capaz de incorporar la
información sobre los parentescos reales que ya se conozcan. Este estimador podría
ser muy útil para determinar la estructura de poblaciones, especialmente cuando ésta
no es regular como ocurre en poblaciones salvajes o no sujetas a manejo especíတco.
Un caso especial es el de determinar los parentescos entre los individuos fundadores
de un núcleo en cautividad a partir de un población natural reducida. Se está
elaborando un software de uso libre que se distribuirá una vez တnalizado.
FACTORS THAT AFFECT THE RATE OF ADAPTIVE EVOLUTION
Adam Eyre-Walker
School of Life Sciences, University of Sussex (UK)
In
many species a substantial proportion of amino acid substitutions have been
inferred to be due to adaptive evolution. However, the rate of adaptive evolution is
unlikely to be the same for all genes in the genome. In my talk I will explore three
factors that can potentially aတect the rate of adaptive evolution: the rate of
recombination, the rate of mutation and the age of the gene. I will show that low rates
of recombination depress the rate of adaptive evolution and that ~30% of all
potentially adaptive mutations are lost by Hill-Robertson interference due to a lack of
su†cient recombination. I will also present evidence that genes with lower rates of
mutation have depressed rates of adaptation and that younger genes have
substantially higher rates of adaptive evolution than older gene
Sesión 3. Evolución ecológica y de poblaciones - Session 3. Ecological and population evolution
PHYLOGENETIC PLACEMENT OF DROSOPHILA FROM ECUADOR
Doris Vela Peralta1, Miguel Pinto2
(1) Laboratorio de Genética Evolutiva, Escuela de Ciencias Biológicas, Pontiတcia Universidad Católica del
Ecuador, Quito-Ecuador
(2) Instituto de Ciencias Biológicas, Escuela Politécnica Nacional, Quito-Ecuador
In Ecuador, more than 100 species of the genus Drosophila have been described in
the past 20 years, and this pattern continues with several new species being
discovered each year. This high diversity of Drosophila could be related with the
geographical location of Ecuador and with the high variety of natural ecosystems in
the Andean mountains.
Taxonomic classiတcation of Drosophila species is based in characteristics of the
genitalia and general morphological traits The category “species group” is a level not
recognized by The Taxonomic Code, however has been used frequently by Drosophila
taxonomist for clustering species with similar phenotypic and ecological
characteristics. The species group classiတcation should be reviewed, and phylogenetic
relationships should be conတrmed, but molecular data are lacking for Neotropical
species. On the other hand, abundant information of Drosophila species from other
geographic regions is available in databases like GenBank.
Our objective was to generate DNA barcodes (a region of the COI gene) to place the
Ecuadorian Drosophila species in the Drosophilidae phylogeny to understand better
the radiation of fruit တies in the Neotropical region. The phylogenetic relationships
were established using maximum likelihood and Bayesian analyses.
Additionally to mitochondrial markers, new nuclear markers should be generated to
improve the phylogenetic classiတcation of neotropical species, this will allow us to
conတrm the classiတcation proposed in base to morphological traits or to reorganize the
previous established relationships. The high biodiversity of Ecuador requires of new
approaches to identify and classify the species. These approaches should be based in
molecular markers in addition to morphological traits (integrative taxonomy). Very
little is known about the Drosophila species from Ecuador yet, despite years of work;
however integrative taxonomy looks promising to speed up Drosophila discoveries in
the region.
CYTOGENETIC DIVERSITY AND ECOLOGY IN POPULATIONS OF THE
HALOPHYTE LIMONIUM VULGARE AND RELATED TAXA ALONG THE
PORTUGUESE COAST
Sílvia Castro1, João Loureiro1, Joana Costa1, Pedro Arsénio2, Dalila Espírito Santo2, Ana
D. Caperta2
(1) Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Calçada
Martim de Freitas 3000-456 Coimbra, Portugal
(2) Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de
Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal
Limonium spp. (Plumbaginaceae), typically found in coastal areas and saline steppes
(Erben, 1993; Kubitzki, 1993), harbour signiတcant diversity. The polyploid (2n = 4x = 36
chromosomes) Limonium vulgare shares morphological a†nities with the closely
related L. maritimum (Cortinhas et al., 2015), but there is no information on the ploidy
level of the later species. In this study, we addressed the (1) geographical patterns, (2)
cytotype distribution and diversity within and among populations, and (3) compared
the habitat of these species along the Portuguese coast. Individuals from natural
populations were sampled and DNA ploidy levels were estimated using တow
cytometry. Chromosome counts were also made to conတrm ploidy level estimations.
Furthermore, occurrence data points were characterized regarding climatic factors
and surface lithology. Our results showed that L. vulgare was scattered in saltmarshes
all over the coast and have a broader distribution than L. maritimum, which tend to be
distributed in rocky formations in northern Portugal. In both species, most
populations showed constancy in ploidy levels, while mixed-ploidy populations and
aneuploid individuals were also detected in L. vulgare. Although there are
morphological and cytogenetic a†nities between species, our results provide evidence
of ecological diတerentiation between L. vulgare and L. maritimum.
NEW MOLECULAR MARKERS TO DELVE INTO PHYLOGEOGRAPHY AND
POPULATION GENETIC STRUCTURE OF TWO BRAZILIAN LAND
PLANARIAN SPECIES
Marta Álvarez-Presas1, Fernando Carbayo2, Alejandro Sánchez-Gracia1, Eduard OcañaPallarés3, Julio Rozas1, Marta Riutort1
(1) Dept. de Genètica, Microbiologia i Estadística i Institut de Recerca de la Biodiversitat, Universitat de
Barcelona, 08028 Barcelona, Spain
(2) Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades, Universidade de São
Paulo, 03828-000 São Paulo (Brazil)
(3) Multicellgenome Lab, Institut de Biologia Evolutiva (UPF-CSIC), 08003 Barcelona, Spain
A well-resolved phylogeny and population genetic analyses are pivotal for any study
aiming to characterize the distribution of biodiversity and the processes that originate
and maintain it. Terrestrial planarians (Tricladida, Platyhelminthes), having low
mobility, are ideal for this type of studies. Although being non-model organisms we
have begun to beneတt from the possibility of using next-generation sequencing, which
allows rapid and economical production of large amounts of raw data without prior
knowledge of the genome. In recent publications we have analysed the genetic
diversity distribution of Cephaloတexa bergi to test the state of conservation of the
remaining fragments of Brazilian Atlantic Forest (AF). The results showed high levels of
nucleotide diversity indicating a pre-Pleistocenic origin for populations’ diversity.
Hence, it was proposed the existence of refugia during the Pleistocene in unpredicted
regions, plus complex secondary contacts among populations. However the markers
used (Cox1 and ITS-1) lacked power to give support to any of the alternative
hypotheses posed. Now, in order to better analyse the factors that have shaped the
current distribution pattern of genetic diversity, we will focus on a smaller region, the
conserved areas of the state of São Paulo, covering diတerent parameters (altitude,
coastal vs interior mountains, etc.) and using new markers. The presence of São Paulo
city and all the infrastructures around it will moreover allow us to assess the impact of
human activity on the conservation of AF. We have conducted Illumina HiSeq
sequencing for two species (C. bergi and Imbira marcusi) in four diတerent localities in
order to တnd new mitochondrial and nuclear markers that provide information on
genetic divergence within and between populations. We are at present testing the new
markers with a တnal goal of doing a small-scale study of the genetic diversity
distribution for the two species and infer the events and parameters that had shaped
it.
POPULATION GENOMICS OF AN ENDEMIC MEDITERRANEAN FISH: FROM
GLOBAL TO LOCAL DIFFERENTIATION CAUSED BY DISPERSAL AND
ADAPTATION
Carlos Carreras1, Víctor Ordóñez1, Enrique Macpherson2, Marta Pascual1
(1) Department de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, Av.Diagonal
643, 08028 Barcelona, Spain.
(2) Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, 17300 Blanes Girona,
Spain.
High-throughput sequencing technologies allow genotyping thousands of markers on
a genome-wide approach. This is a crucial advantage when studying species with large
eတective population sizes, as low numbers of markers may compromise the detection
of population structuring. Furthermore, when designing networks of protected areas,
it is essential to work from global to a local spatial scale as well as with non-model
organisms, as they comprise most of the biodiversity. To assess the potential of these
new sequencing technologies applied to non-model species, we used Genotyping-bySequencing (GBS) to analyse 412 individuals of a common littoral တsh (Symphodus
tinca) from 16 locations collected in three diတerent areas of its distribution: Western
Mediterranean, Adriatic/Ionian region and Black Sea. We obtained a total of 4,553
polymorphic SNPs. All the individuals clustered in three diတerentiated groups,
matching the three regional sampling areas, but the overall structure masked the local
တne-scale structuring and thus a hierarchical approach was needed. In this study, we
analysed the Adriatic/Ionian region in order to clarify the relationships among
populations within this region. We identiတed 83 outlier SNPs to be potentially under
directional selection and 3,932 neutral SNPs, both showing signiတcant structuring
within the basin (FST = 0.1350 and FST = 0.0046, respectively). Some of the adaptive
SNPs could be related to environmental factors as revealed with a BlastN search
against the closest-related တsh genome available, the Nile Tilapia (Oreochromis
niloticus). Two strong barriers to gene တow were observed indicating a larger genetic
diတerentiation than previously detected, the main one diတerentiating Tremiti Islands,
in the northwest, from all the other samples (Fst range 0.013-0.021, P< 0.001) and the
second one separating east and south-west localities (Fst range 0.004-0.006, P< 0.001).
Population genomics and adaptation studies in ecologically non-model relevant
species are တnally at hand. These new genomic approaches reveal a genetic
structuring that shows the role of selection in biodiversity assessments and could
change our vision when designing networks of protected areas.
CARACTERIZACIÓN GENÉTICA DE LA INVASIÓN DE LA ALMEJA ASIÁTICA
(CORBICULA) EN LA PENÍNSULA IBÉRICA
Luis Peñarrubia1, Rosa Maria Araguas1, Oriol Vidal1, Carles Pla1, Jordi Viñas1, Nuria
Sanz1
(1) Laboratori d’Ictiologia Genètica, Departament de Biologia, Universitat de Girona. Campus Montilivi, E17003, Girona, Spain.
La almeja asiática (Corbicula sp.) es una especie invasora de bivalvos de aguas dulces
originaria de Asia, el Medio Este, África y Australia. Sin embargo, su actual rango de
distribución incluye masas de agua a lo largo de todo el mundo. Esta especie produce
grandes impactos tanto a nivel ecológico como económico en los ecosistemas donde
se establece. Se han descrito tres grandes linajes que predominan en el rango de
invasión dentro de esta especie, que juntos forman un complejo de especies capaz de
hibridar individuos de los diferentes linajes. Todos ellos presentan un sistema de
reproducción asexual, donde un único individuo adulto hermafrodita puede generar
una descendecia compuesta por individuos clones del mismo progenitor gracias a la
androgénesis; y donde existen procesos de captura mitocondrial entre individuos del
mismo o de diferente linaje, generando transferencia de información entre ellos.
En este estudio, recolectamos 175 individuos adultos de almeja asiática procedentes
de diferentes localizaciones de la Península Ibérica junto a diferentes localizaciones de
Europa y USA. Nuestro objetivo consistia en caracterizar genéticamente la estructura
genética a lo largo dediferentes poblaciones de la Península Ibérica y evaluar la
distribución de los diferentes linajes dentro de ellas. Utilizamos una combinación de
dos marcadores genéticos, el gen nuclear 28S y el gen COI mitocondrial, que nos
permitió caracterizar tanto la herencia paterna como materna.
Nuestros resultados mostraron 7 haplotipos diferentes en el gen COI mitocondrial,
junto a 10 haplotipos en el gen 28S nuclear a lo largo de los 175 individuos. El análisis
တlogenético de estos haplotipos agrupó todos los individuos dentro de los clusters
correspondientes a los tres linajes invasores de almeja asiática. La distribución
geográတca de los haplotipos de ambos marcadores detectó una elevada divergencia
genética entre los indiviuos del Delta del río Ebro y el resto de las localizaciones
Ibéricas, indicando que ocurrieron al menos dos episodios de invasión diferentes.
Además, esta distribución sugiere que ha habido posteriores contactos secundarios
entre las localizaciones ibéricas y otras localizaciones de Europa. Por último, nuestros
resultados revelaron que la hibridación nuclear entre linajes derivada de la
androgénesis, con más frecuencia de lo que se había detallado en previos estudios,
contribuye a mantener los niveles de diversidad génica durante el proceso de invasión
de la almeja asiática
GENOMIC ANALYSES REVEAL THE ROLE OF SELECTION AND LOW
DISPERSAL IN DRIVING INTRA-ISLAND DIVERSIFICATION OF A REUNION
ISLAND SONGBIRD
Borja Milá1, Yann Bourgeois2, Boris Delahaie2, Josselin Cornuault2, Joris Bertrand2,
Christophe Thébaud2
(1) Museo Nacional de Ciencias Naturales, CSIC, Madrid 28006, Spain.
(2) Laboratoire Ecologie et Diversité Biologique, Université Paul Sabatier, Toulouse, France.
Oceanic islands provide unique scenarios in which to identify the factors involved in
population divergence and speciation. The Mascarene gray white-eye (Zosterops
borbonicus) shows several geographically-structured plumage color forms on the
small yet ecologically complex island of Reunion (2,500 km2). We use mtDNA,
microsatellites, genome-wide SNPs and pehenotypic data to investigate the
evolutionary history of this unique intra-island radiation. A preliminary tree based on
20,000 SNPs obtained by RADseq, reveals that Z. borbonicus is divided into two main
clades corresponding to ecologically diတerent highland and lowland areas, separated
by a steep genetic and phenotypic cline. In turn, the three color forms in the lowlands
form reciprocally monophyletic clades, with most high-Fst variants found to be located
on the Z sex chromosome. Phylogenetic and pedigree analyses revealed that the
sympatric gray and brown individuals in the highlands represent a true genetic
polymorphism, driven by a single genomic region on chromosome 1, a locus not
previously known to host genes related to melanic pigmentation. Our genomic and
morphometric results show the early role of ecology in dividing populations into
highland and lowland forms, and the existence of independent lineages in the
lowlands suggests the existence of premating isolating barriers to reproduction, likely
due to sexual selection on plumage traits. Despite being good တyers, our results
indicate that dispersal in the gray white-eye is extremely limited and suggest the role
of selection in restricting gene တow between incipient evolutionary lineages.
SENSORY DRIVE AND SYMPATRIC SPECIATION IN NEOTROPICAL CRATER
LAKE CICHLID FISH
Barluenga, M.
Museo Nacional de Ciencias Naturales, CSIC, 28006 madrid
Environmental
heterogeneity provides diverse visual environments to which
organisms adapt in order to detect food, avoid predators or တnd mates. We study the
adaptation of visual systems in Neotropcial cichlid တsh to the local conditions of
several crater lakes, but also to microhabitats within lakes. We hypothesize that the
diversity of light environments tunes the တsh’s visual system, which could aတect mating
and either cause speciation, or reinforce diတerences among diverging species.
Speciation through sensory drive is a mechanism that might explain rapid
diversiတcation in sympatry, and be a key to explaining the extreme cichlid diversity.
ARE THERE GENETIC TRADE-OFFS BETWEEN BEHAVIORAL AND LIFEHISTORY TRAITS IN THE SOIL TOP PREDATOR LYCOSA FASCIIVENTRIS?
Jorge F. Henriques1, Mariángeles Lacava2, Celeste Guzman3,Eva De Mas3, Sara
Magalhães1, Jordi Moya-Laraño3
(1) cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências,
Universidade de Lisboa, Lisboa, Portugal
(2)Laboratorio de Ecología del Comportamiento, Instituto de Investigaciones Biológicas Clemente
Estable, Avenida Italia 3318, Montevideo, Uruguay
(3)Functional and Evolutionary Ecology, Estacio´n Experimental de Zonas A ´ ridas, CSIC, Carretera de
Sacramento s/n, 04120-La Can˜ada De San Urbano, Almeria, Spain
With
the increasing number of studies concerning animal personality, or the
recognition of intra-individual consistency in behaviour leading to inter-individual
diတerences in behavior as raw material for evolution, the တeld of behavioral ecology
has found a cornerstone. Despite several studies concerning animal personality traits
such as boldness or aggressiveness, the factors aတecting consistency in interindividual diတerences in behavior is poorly understood. In particular the heritability of
such personalities and potential genetic trade-oတs or correlations with life-history
traits, remain to be identiတed.
In this study, we evaluate the additive genetic variation and the heritability of selected
behavioral and life-history traits. To this aim, we conducted a half-sib split-brood
design to evaluate additive genetic eတects, heritability and genetic correlations in a
series of behavioral and life-history traits of the predator Lycosa fasciiventris, a
common wolf spider in the Iberian Peninsula. Spiderlings of 50 sire and 100 dam
families were raised under two feeding treatments, in which 3 spiderlings within each
brood were fed three times more food than the remaining 9 spiderlings. Behavioral
traits (boldness and/or aggressiveness) were assessed recurring to analysis of video
recordings.
Our preliminary results show negligible heritability for body size at birth and
assimilation e†ciency, but moderately high heritability for body condition at birth.
Together, this set of data may provide accurate quantitative genetic estimates in
functional traits for a soil top predator, which may allow to predict the outcome of ecoevolutionary feedback loops within soil food webs.
THE ORIGIN OF MODERN SYPHILIS AND EMERGENCE OF A
CONTEMPORARY PANDEMIC CLUSTER
Natasha Arora1,2, Verena Schuenemann3, Leonor Sánchez-Busó4, Denise Kühnert5,
Lorenzo Giacani6, Arturo Centurión-Lara6, Steven J. Norris7, David Smajs8, Philipp P.
Bosshard9, Kay Nieselt10, Johannes Krause11, Homayoun C. Bagheri1, Fernando
González-Candelas4 and their group members
(1) Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
(2) Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
(3) Institute for Archaeological Sciences, University of Tübingen, Germany
(4) Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia. CIBER in Epidemiology and
Public Health, Spain.
(5) Department of Biosystems Science and Engineering, Computational Evolution, ETH Zurich,
Switzerland
(6) University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, and
Department of Global Health, Seattle, WA USA
(7) Department of Pathology and Laboratory Medicine, UTHealth McGovern Medical School, Houston, TX
USA
(8) Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
(9) Department of Dermatology, University Hospital of Zurich, Switzerland
(10) Center for Bioinformatics, University of Tübingen, Germany
(11) Institute for Archaeological Sciences, University of Tübingen, Germany
Syphilis
swept across the world in the 16th century as one of most prominent
documented pandemics and is re-emerging worldwide despite the availability of
eတective antibiotics. Little is known about the genetic patterns in current infections or
the evolutionary origins of the disease due to the non-cultivable and clonal nature of
the causative bacterium Treponema pallidum subsp. pallidum. In this study, we have
used DNA capture and next generation sequencing to obtain whole genome data from
syphilis patient specimens and from treponemes propagated in the lab. A total of 39
genomes were included in the analyses, encompassing 31 T. pallidum subsp. pallidum
(TPA), 7 T. pallidum subsp. pertenue (TPE) and one T. pallidum subsp. endemicum
(TPN) Phylogenetic analyses indicate that the syphilis strains examined share a
common ancestor posterior to the 15th century. Moreover, most contemporary
strains are azithromycin resistant, and form part of a global dominant cluster that
began diversifying from a common ancestor only in the mid-20th century. This cluster
has the population genetic and epidemiological features indicative of the emergence
of a pandemic lineage.
DISSECTING THE GENOME REDUCTION PROCESS IN ENDOSYMBIOTIC
BACTERIA
Amparo Latorre
(1) Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Genética Evolutiva. Universitat de València,
Valencia 22085, Spain.
(2) Fundación para el Fomento de la Investigación Sanitaria de la Comunitat Valenciana (FISABIO),
Genómica y Salud, Valencia, 46020, Spain.
Endosymbiosis
between bacteria and insects is a common phenomenon, usually
related to the diet upgrade of the hosts due to the metabolic complementation with
their symbionts. During the transition from free-living to intracellular life styles the
bacteria undergo many structural and metabolic changes, being genome reduction a
general characteristic in all studied systems. A model case is Buchnera aphidicola, the
obligate endosymbiont of most aphids, whose role is to supply nutrients that are
lacking in the aphid’s phloem diet, mainly essential amino acids and some vitamins.
Apart from Buchnera, many aphids harbor secondary endosymbionts. Among these,
Serratia symbiotica is a very interesting case for the study of genome erosion. In
members of the Aphidinae subfamily S. symbiotica is of facultative nature and harbor
large genomes (from 3.6Mb to 2.6Mb), whereas in the Lachninae subfamily it has
established co-obligate associations with Buchnera. However, the three co-obligate S.
symbiotica genomes analyzed in our laboratory are indeed very diတerent. They show
strikingly diတerences in genome sizes (2.5Mb, 1.7Mb and 0.7Mb), number of CDS
(1,600, 677 and 495), localizations (extracellular/intracellular), presence/absence of IS
(insertion sequences) and the amount of non-coding DNA. Comparative genomics of
all these cases, together with the available genomes of closely related free-living
Serratia, gives us a very unique opportunity to study in detail the genome reduction
process (from free-living to reduced obligate endosymbiont) within a single taxon
evolving in a similar biological niche (aphid-Buchnera).
Miércoles - Wednesday 09:00-09:50
Sesión 4. Genómica evolutiva y funcional - Session 4. Functional and evolutionary genomics
THE EVOLUTION OF MAMMALIAN GENE EXPRESSION PROGRAMS
Henrik Kaessmann
Group leader in the DKFZ-ZMBH Alliance ZMBH - Center for Molecular Biology Heidelberg University Im
Neuenheimer Feld 282 69120 Heidelberg Germany
Shared mammalian traits include lactation, hair and relatively large brains with unique
structures. Individual lineages have, in turn, evolved distinct anatomical, physiological
and behavioral characteristics relating to diတerences in reproduction, life span,
cognitive abilities and disease susceptibility. Regulatory mutations aတecting gene
expression (rather then mutations altering the sequence of the gene product)
probably explain many or even most phenotypic diတerences among species. The
advent of high-throughput RNA sequencing (RNA-seq) approaches now allows for
accurate and sensitive assessments of transcript sequences and expression levels at a
genome-wide scale. We have been generating comprehensive sets of RNA-seq data for
a large collection of germline and somatic tissues from representatives of all major
mammalian lineages (placental mammals, marsupials, and the egg–laying
monotremes) and evolutionary outgroups (e.g., birds). In conjunction with various
high-throughput genomic/epigenomic data, we are using these transcriptome datasets
to study the functional (expression) evolution of mammalian genomes across gene
types, species/lineages, tissues, developmental stages, cell types, chromosomes and
sexes. I will present recent selected highlights of this endeavor.
THE ROLE OF TRANSPOSABLE ELEMENT INSERTIONS IN
ENVIRONMENTAL ADAPTATION IN DROSOPHILA MELANOGASTER
Lain Guio1, Miriam Merenciano1, Anna Ullastres1, Maite G. Barrón1, Vivien Horváth1,
José Luis Villanueva-Cañas1, Josefa González1
(1) Institute of Evolutionary Biology (CSIC-UPF), Barcelona. Spain.
Transposable elements are likely to play a role in adaptive evolution because they are
powerful mutagens that create a great variety of mutations. However, the role of
transposable elements in adaptation has been understudied due to methodological
limitations. The availability of next-generation sequencing techniques allows us to
study transposable element-induced adaptations to an unprecedented scale. We have
performed a genome-wide screening looking for transposable element-induced
adaptations in Drosophila melanogaster. While previous studies included only a
subset of the transposable element insertions present in the reference genome, we
have now analyzed the majority of the euchromatic insertions. We have used a
computational pipeline, T-lex2, to estimate the frequencies of these 1,621 insertions in
61 natural populations including one African population from the ancestral range of
the species. We have identiတed 203 insertions with signiတcantly diတerent frequencies
within and outside of Africa. So far, we have been able to map four candidate
transposable element insertions to their ecologically relevant phenotypic eတect and to
pinpoint the molecular mechanism underlying them. Currently, we are investigating
the role of transposable element-induced mutations in immune response.
DESREGULACIÓN DE ELEMENTOS TRANSPONIBLES EN HÍBRIDOS
INTERESPECÍFICOS DE DROSOPHILA: CAUSAS Y CONSECUENCIAS
Valèria Romero-Soriano1, Laurent Modolo2, Hélène Lopez-Maestre2, Bruno Mugat3,
Eugénie Pessia2, Séverine Chambeyron3, Cristina Vieira2, Maria Pilar Garcia Guerreiro1
(1) Departament de Genètica i Microbiologia. Universitat Autònoma de Barcelona, 08193 Bellaterra
(Barcelona), Spain.
(2) Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Villeurbanne, France.
(3) Institut de Génétique Humaine, CNRS, UPR1142, 34396 Montpellier Cedex 5, France
El
estrés genómico causado por la hibridación interespecíတca puede ocasionar la
activación de elementos transponibles (ETs), tanto en animales como en plantas.
Estudios previos realizados en nuestro grupo mostraron que hasta 28 familias de
elementos podrían ser movilizadas en híbridos entre las especies D. buzzatii y D.
koepferae, así como alteraciones de los patrones de expresión de los elementos
Osvaldo y Helena. Hasta la fecha se desconocen los mecanismos responsables de esta
activación así como sus causas. En este trabajo evaluamos el impacto de la hibridación
en el tamaño del genoma de los híbridos de estas dos especies a través de cuatro
generaciones. Los resultados muestran la existencia de una expansión genómica, que
afecta a las hembras del primer retrocruce; lo que constituye la primera evidencia en
animales de que el aumento del tamaño del genoma en híbridos interespecíတcos
puede estar asociado a la movilización de ETs.
En la segunda parte del trabajo se intentan explicar las posibles causas de la
desregulación de los ETs. Con este propósito se realizó un estudio global en gónadas
del transcriptoma de los ETs, así como de los RNAs pequeños que los regulan
(piRNAs), tanto en las especies parentales como en híbridos mediante la técnica de
RNaseq. Los resultados muestran que alrededor del 15% de los ETs están
desregulados en ovarios de la F1. Estos resultados no pueden ser completamente
explicados por diferencias en las cantidades de piRNAs entre las especies parentales.
Adicionalmente observamos que los genes que codiတcan para las proteínas implicadas
en la síntesis de estos piRNAs, presentan patrones de expresión diferencial entre las
dos especies parentales. Por lo tanto, la divergencia funcional de la via piRNA entre D.
buzzatii y D. koepferae podría ser otro de los factores implicados en las
incompatibilidades observadas en híbridos así como en la desregulación de los ETs.
No obstante, algunos ETs no tienen piRNAs asociados. Esto nos lleva a pensar en la
existencia de rutas de regulación alternativas y de modiတcación de las marcas de las
histonas, asociadas a ETs, que merecen ser exploradas en el futuro.
UNDERSTANDING ARTHROPOD GENE AND GENOME EVOLUTION
THROUGH THE COMPARATIVE GENOMICS AND TRANSCRIPTOMICS
ANALYSES OF NON-MODEL ORGANISMS
Alejandro Sánchez-Gracia1, Cristina Frías-López1, José F. Sánchez-Herrero1, Joel
Vizueta1, Paula Escuer-Pifarré1, Albert Ferrer-Mata1, Nuria E. Macías-Hernández2,
Miquel A. Arnedo2 & Julio Rozas1
(1) Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat
(IRBio), Universitat de Barcelona
(2) Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals and Institut de Recerca de la
Biodiversitat (IRBio), Universitat de Barcelona
Oceanic island biotas have been long recognized as simpliတed natural experiments of
evolution, providing tractable case studies for assessing the genomic basis of
adaptation and the mechanisms that generate biodiversity. Using the terrestrial
radiation of the spider Dysdera (Dysderidae: Araneae) in the Canary Islands as a model
system, we are investigating the global genomic determinants of species
diversiတcation, with a special focus on the genetic changes associated with dietary
specialization in this genus. We are using comparative genomics and transcriptomics
approaches to identify the speciတc nucleotide changes, both in coding and non-coding
regulatory sequences, the diတerences in gene copy number and the diတerential
expression patterns associated with phenotypic divergence in this genus. We have
compared the transcriptomes of two pairs of generalist and specialist Dysdera species
(regarding to the type of diet), using the transcriptome of a generalist outgroup
species as a reference, and we are sequencing and assembling the complete genome
of a pair of these species and of this reference.
On the other hand, we are also interested in the contribution of rapidly evolving gene
families in genome organization and evolution. Currently, we are extending our
previous comparative genomics study on arthropod chemosensory gene families to
various chelicerate genomes (with public available genome sequence) and also to the
tardigrade and onychophoran model species, Hypsibius dujardini and Euperipatoides
rowelli, respectively. At the same time, and to gain insights into the speciတc members
of these gene families involved in smell and taste of some of these lineages, we have
obtained and analyzing the transcriptomes of candidate chemosensory structures in
our spider model (D. silvatica), one myriapod (Strigamia maritima) and the
onychophoran E. rowelli. We are integrating our results with available genomic and
trasncriptomic information in other representative species with the တnal goal of
understanding the origin and evolution of the molecular components of the
chemosensory system in arthropods and their contribution to genome architecture in
these ancient lineages.
WHOLE GENOME SEQUENCING OF TURBOT (SCOPHTHALMUS
MAXIMUS): ADAPTATION TO DEMERSAL LIFE AND SIGNATURES OF
SELECTION ACROSS ITS DISTRIBUTION RANGE
Martínez P, Bouza C, Rubiolo JA, Prado FD, Vera M, Robledo D, Hermida M, Taboada X,
Vilas R, Fernández C, Pardo BG, Viñas A, The Aquatrace consortium, The Turbot
Genome consortium
Departamento de Xenética, Universidade de Santiago de Compostela, Spain
Turbot is a very appreciated marine species showing the highest world aquaculture
production among တatတsh and important တsheries in Atlantic Europe. As a တatတsh
(Pleuronectiformes), a group with a controversial phylogeny and evolutionary origin,
the turbot is adapted to demersal life. Also, because of its wide distribution range, this
species lives in a variety of temperature and salinity regimes. Here, we report the
turbot genome assembly integrated with all previous transcriptomic and mapping
data and apply this valuable resource to identify genomic signatures related to
adaptation to its particular lifestyle and to the environment diversity across its
distribution range. Genome assembly resulted in 544 Mb (contig-N50: 31.2kb; scaတoldN50:4.2Mb). A total of 22,751 protein-coding genes were identiတed, more than 85%
being functionally annotated. The genome (>90%) was anchored to the turbot genetic
map (~600 markers) enabling to investigate teleost chromosome evolution by
comparative mapping. Orthology and paralogy relationships were analyzed regarding
other vertebrates to characterize syntenic relationships and duplication events in
teleost evolution, and to investigate speciတc duplications of the တatတsh lineage related
to adaptations to demersal life. Our data suggest a reတned vision of turbot to adapt to
benthic life supported by the presence of duplicated green-sensitive opsin genes along
with other duplicated genes related to vision. This observation contrasts with the
decayed visual system reported in other တatတsh like tongue sole (Cynoglossus
semilaevis). Another diတerence between both species is related to the metabolic
machinery involved in preventing oxidation of membrane polyunsaturated fatty acids
(PUFA), which appears to be related to their diတerent thermal preferences. Conversely,
the expansion of the olfactory system is shared by turbot and tongue sole, suggesting
a common origin. Recent studies have suggested the presence of adaptive divergence
of turbot populations, especially related to salinity and temperature in the Atlantic
area. We used a panel of 755 SNPs in 22 sampling sites across the European
distribution range to identify selection signals under diတerent temperature and salinity
regimes. A total of 23 outliers suggesting divergent selection were identiတed, being 17
related to the Atlantic area, four to the Baltic Sea and two exclusive when comparing
Baltic and Black Sea. Most outliers were located in the turbot map and some of them
associated with previously reported QTL. These results provide useful information for
conservation of တsheries and boosting aquaculture breeding programs of this species.
COMBINING GENOMICS AND NATURAL HISTORY TO UNDERSTAND THE
EVOLUTIONARY BIOLOGY OF INVERSIONS IN DROSOPHILA
SUBOBSCURA
Rosa Tarrío1, Francisco Rodríguez-Trelles1
(1) Departament de Genetica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva
(GGBE), Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
Chromosomal inversions are ubiquitous features of genomes with an impact on the
evolution of recombination. Inversions are di†cult to investigate by population
genomics means, because they typically create a pattern of cryptic, chromosomespeciတc population substructure that is not accounted for by most current costeတective next-generation sequencing designs. Drosophila furnishes a way out to this
drawback, because of the availability of giant polytene chromosomes and balanced
lethal stocks for the identiတcation and isolation of gametes, yet at considerable
experimental cost. To be worth the eတort, this approach should be targeted to an
appropriate model system, ideally one whose descriptive phase is accomplished and
exhibits exploitable patterns. The endemic Palearctic species D. subobscura exhibits
one of the known richest inversion polymorphisms that aတects all its တve acrocentric
chromosomes, thereby it should qualify as ideal for research on the population
genomics of inversions. But according to the prevailing view, the inversion
polymorphisms of D. subobscura are “semi-rigid” because they vary only latitudinally,
which limits the interest of this species for its use in experimental designs at more
manageable spatiotemporal scales. A critical look to the information supporting this
view, however, reveals inappropriate designs and downplay of contrary evidence,
which suggests that the system’s description stage might have been closed
prematurely. We decided to reopen the issue using a longitudinal cross-sectional
monitoring approach at increasingly တne-grained scales of space, including geography,
altitude and mountain slope aspect, and time, from interdecadal to intraseasonal.
Against the dominant view, our results show that the chromosomal inversion
polymorphisms of D. subobscura vary neatly and consistently across all assayed
spatiotemporal scales, and do so as if the inversions diတered in their eတects on the
thermal adaptation of their carriers. We plan to use the newly identiတed dimensions of
variation to conduct a cross-sliding-window analysis of chromosome-wide nucleotide
diversity patterns for alternative inversions. This approach should help us to identify
the molecular targets of natural selection and test alternative models of the role of
inversions in local adaptation.
CAN WE PREDICT ADAPTIVE EVOLUTION? A QUESTION WITH MANY
ANSWERS
Margarida Matos1**, Inês Fragata1,2**, Marta A.Santos1,3, Gonçalo S. Faria1,4, Mauro
Santos5, Soတa G. Seabra1** & Pedro Simões1**
(1) cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências,
Universidade de Lisboa, Lisboa, Portugal.
(2) Instituto Gulbenkian de Ciência, Oeiras, Portugal
(3) CEDOC – Centro de Estudos de Doenças Crónicas, Lisboa, Portugal
(4) School of Biology, University of St Andrews, St Andrews, UK
(5) Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, España
**These authors contributed equally
How capable are populations to adapt to environmental changes? Will populations of
contrasting histories converge, both at the phenotypic and genomic level, when
adapting to a common environment? In spite of the importance of this issue, few
studies have addressed it. Taking advantage of Drosophila subobscura natural
diတerentiation, we founded in a common lab environment populations derived from
contrasting European latitudes. We then followed their real-time evolutionary
dynamics, both in phenotypic traits and chromosomal inversion frequencies. Initially,
the populations were highly diတerentiated for all traits. While phenotypic convergence
occurred in few generations in the laboratory, after 40 generations populations
remained diတerentiated at the karyotypic level. Thus, despite the role of selection,
history played an important role in the evolutionary dynamics of the frequencies of
chromosomal inversions. We are further characterizing by pool-seq the genomic
temporal changes of the populations derived from the latitudinal extremes (Portugal
and Netherlands). Allele frequency variation in SNPs with signal of selection revealed
that initially diတerentiated populations followed diတerent genetic routes during
adaptation, with no genetic convergence detected between them. We are now
investigating the dynamics of selected variants to explore if there are common genes
involved in the evolutionary changes of these populations. Our overall data indicate
hitherto that similar phenotypic optima were reached through diတerent genetic paths,
suggesting that history plays an important role but does not constrain adaptive
evolution. The signature of history and its impact on the evolutionary dynamics may
thus have diတerent outcomes depending on the level that is being assessed. Ongoing
directions include the analysis of the evolution of the genetic content of speciတc
inversions and to test how much the (un)predictability of evolutionary patterns is
contingent on the biological levels under study.
SATELLITE DNAS IN DROSOPHILA EXPOSED: NEWS AND PERSPECTIVES
EMERGING FROM THE ANALYSIS OF SEQUENCED GENOMES
Gustavo Kuhn
Universidade Federal de Minas Gerais, Belo Horizonte (Minas Gerais, Brasil)
Satellite DNAs consist of tandemly repeated DNA sequences with repetition grades
usually within the range of 103 to 107. Long and homogeneous arrays made of
satDNA repeats are located in the heterochromatin, but recent studies also revealed
the presence of short arrays dispersed along the euchromatin. The collection of
satDNAs makes large portions (usually more than 30%) of animal and plant genomes.
Although satDNAs do not code for proteins, they may play important cellular roles,
including participation in chromatin packaging, centromere formation/maintenance
and gene regulation. Despite their abundance, diversity and sometimes widespread
genomic distribution, our knowledge about several features of satDNAs is still limited.
In the past decades, satDNAs have been mostly studied from a small sample of cloned
repeats obtained by biased experimental approaches (usually by restriction digestion
and/or PCR), isolated from one or few species. Experimental strategies for the
identiတcation of satDNAs were expensive, time-consuming and insu†cient for the
identiတcation of the whole collection of satDNAs from any chosen genome. Nextgeneration sequencing technologies have recently provided a revolution in the
number of species with sequenced genomes, while new and e†cient bioinformatic
tools have been speciတcally developed towards genome-wide identiတcation of
repetitive DNAs. We are taking advantage of the large reservoir of genomic sequences
from several Drosophila species to conduct an in-depth investigation on satDNAs
through a combination of bioinformatic, cytogenomic and phylogenetic approaches.
During my talk, I will show examples coming from diတerent Drosophila species that
help to illustrate how the results are improving our understanding about the origin,
genomic distribution, mobility and evolution of satDNAs and increasingly highlighting
their importance in shaping eukaryotic genomes.
Sesión 5. Evolución de humanos y primates - Session 5. Human and primate evolution
A GENOME WIDE IBD ANALYSIS IN A WORLDWIDE SAMPLE OF PIGS
REVEALS A COMPLEX NETWORK OF INTROGRESSION EVENTS
Sara Guirao-Rico1, Jordi Leno-Colorado1, Miguel Pérez-Enciso1,2
(1) Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Bellaterra, Barcelona,
Spain.
(2) ICREA, Pg Lluis Companys 23, 08010 Barcelona, Spain.
The species Sus scrofa was independently domesticated in Asia and in Europe from
the local wild boars in each continent, about 9,000 year ago, while both clades had
diverged ca. 1 MYA. It is known that international pig breeds are the result of
introgressing Asian pigs into local European pigs during the 17th century onwards, and
hence these European breeds are actually genetic mosaics of highly divergent
haplotypes. The percentage of Chinese germplasm has been estimated to be 20 - 30%,
depending on breeds and methods employed. Some European breeds, like Iberian
and Mangalitza, are thought not to be introgressed with Asian pigs. Although the
impact of the introgression has been recently studied by Bosse et al. (2014), important
aspects remain to be elucidated; among them, what has been the real impact of this
event in porcine variability, whether it was a single or multiple introgression event, its
geographical origin and the impact of introgression on genetic architecture of complex
traits.
To investigate these issues, here we present the most comprehensive analysis to date
of the haplotype structure and relationships across pig breeds. We used an enlarged
sample (compared to Bosse et al. 2015) comprising 228 complete wild boar and pig
genomes from diတerent populations worldwide that contained a total of 21 M SNPs.
This allowed us to identify introgressed genomic regions, the geographical origin of
Asian germplasm and the distribution pattern of these fragments in each European
pig genome. The analysis indicate a an intricate network of genetic relationships
among domesticated populations Our results show that the Asian to Europe တow was
not a homogeneous, single pulse event, but rather revealed numerous admixture
events with multiple origin sources. We observe that the contribution of the Northern
Chinese haplotypes is higher than the Southern Chinese ones, similar to what has
been observed for a low-recombining region of the X-chromosome (Ai et al. 2014,
Groenen 2016). Moreover, the extent of introgression and its origin diတered between
European breeds. International pig breeds were the more introgressed and the Iberian
and Mangalitza breeds, the less ones. Interestingly, the British local rare breeds exhibit
an intermediate level of introgression.
LINEAGES OF MEN: Y CHROMOSOME ANALYSIS REVEALS RECENT,
INDEPENDENT EXPANSIONS IN IBERIA AND N. AFRICA
Neus Solé-Morata1, Patricia Villaescusa2, Vadim Urasim3, Jaume Bertranpetit1, Marian
Martínez de Pancorbo2, David Comas1, Francesc Calafell1
(1) Institut de Biologia Evolutiva (CSIC-UPF), Barcelona
(2) BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU,
Vitoria-Gasteiz
(3) Yfull, Moscow
The analysis of the complete sequences of the Y chromosomes in the 1000 Genomes
project has revealed that a number of haplogroups increased rapidly in frequency
bursts of extreme expansion in diတerent populations at historical times linked to
migrations and technological innovations.
Here we present the analysis of two such haplogroups that expanded independently
on either side of the Gibraltar Straits: R1b-DF27 in Iberia and E-M81 in N. Africa. R1bDF27 was recently discovered as a sister group to R1b-U152 and R1b-L21; all three are
subclades of R1b-P312, a common haplogroup in W Europe, with frequencies ranging
from 50% to >90% in the Basque Country and Ireland. We have genotyped DF27 and a
number of its derived SNPs in populations from Spain, Portugal and France. Its
frequencies are ~40% in most of Spain and Portugal, but reach 74% in native Basques;
on the contrary, they drop to 5-10% in France, even in populations close to the
Pyrenees. We also genotyped 16 Y-STRs, which allowed us to estimate the age of DF27
at 3,400 years ago. Both the variance of the Y-STR repeat sizes and the age estimates
were similar across N Iberia, which makes it di†cult to pinpoint an exact place of
origin for DF27. We are currently trying to တt a demographic model to explain the
burst of DF27 in the last 110 generations.
E-M81 is found at high frequencies (up to 75%) in NW Africa, but is also present in NE
Africa, the Middle East, and at low frequencies (<10%) in Iberia and Sicily. For the တrst
time, we analyze whole Y chromosome sequences from 32 males selected for
belonging to the E-M81 haplogroup. The analysis of whole Y chromosome sequences
has enabled the discovery of new variants deတning new subclades within the E-M81
branch. Those variants, as well as 16 Y-STRs, have been genotyped in more than 200
North African samples. We have found that E-M81 subclades show no discernible
geographical structure, which is probably due to the recent age (we estimated ~2,000
years ago) and rapid expansion of this haplogroup.
CHIMPANZEE GENOMIC DIVERSITY REVEALS ANCIENT ADMIXTURE WITH
BONOBOS
Martin Kuhlwilm1, Marc de Manuel1, Peter Frandsen2,3, Vitor Sousa4, Jessica
Hernandez-Rodriguez1, Lukas F.K. Kuderna1, The Chimpanzee Diversity Consortium,
Aida M. Andrés5, Aylwyn Scally6, Laurent Exco†er4, Chris Tyler-Smith7, Sergi
Castellano5, Yali Xue7, Christina Hvilsom3, Tomas Marques-Bonet1,8,9
(1) Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona,
Catalonia 08003, Spain.
(2) Department of Biology, Bioinformatics, University of Copenhagen, 2200 Copenhagen, Denmark.
(3) Research and Conservation, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
(4) Swiss Institute of Bioinformatics, 105 Lausanne, Switzerland.
(5) Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher
Platz 6, Leipzig, 04103, Germany.
(6) Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
(7) Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
(8) CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology
(BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
(9) Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.
Due
to an almost complete absence of fossils, the evolutionary history of
chimpanzees can best be explored using genetic data from present-day populations.
Here, we analyzed the complete genomes of 75 wild-born chimpanzees and bonobos
from ten diတerent countries in Africa to decipher the complex demographic history of
our closest living relatives. We တnd that the central chimpanzees carry the largest
amount of ancestral variation and that population structure at regional scale makes
genetic diversity a good predictor of the geographic origin, making it possible to reassign chimpanzees of unknown provenance. Multiple lines of evidence from allele
sharing, properties and ages of haplotypes, as well as demographic models based on
the allele frequency spectrum suggest ancient gene တow from bonobos into the
ancestors of central and eastern chimpanzees more than 200 thousand and less than
500 thousand years ago, probably with subsequent spread to Nigeria-Cameroon
chimpanzees. Additionally, more recent gene တow from bonobos into central
chimpanzees implies at least two phases of secondary contact, contributing at least
~1% to the central chimpanzee genome. Admixture thus appears to have been
widespread during hominid evolution.
HAPLOTYPE-BASED METHODS FOR THE STUDY OF GENETIC DIVERSITY
AND ADMIXTURE EVENTS. APPLICATIONS TO MODERN AND ANCIENT
HUMAN POPULATIONS
Saioa López1, Ayele Tarekegn2, Neil Bradman2, Mark G Thomas1, Garrett Hellenthal1
(1) Department of Genetics, Evolution and Environment, University College London, London, UK
(2) The Henry Stewart Group, London, UK
Unravelling the ancestral history of populations is becoming more approachable in
the era of genome-wide data analyses. We use a "chromosome painting" approach
that exploits linkage among neighbouring SNPs, and has been shown to be more
powerful than commonly-used algorithms (like PCA, STRUCTURE or ADMIXTURE) to
identify population structure and infer and date admixture events among populations.
Furthermore, we describe a novel Bayesian mixture model that represents both
modern and ancient individuals as mixtures of other sampled individuals based on
shared haplotype patterns.
We apply these approaches to world-wide human samples, including new genomewide data from 1,157 Ethiopian individuals (belonging to 77 diတerent
ethnic/occupational groups) and 355 individuals from Sudan (belonging to 37 ethnic
groups). These regions are where the တrst remains of anatomically modern humans
were found and exhibit some of the highest levels of genetic diversity in the world.
Thus they are ideal places to study the processes that have driven recent human
evolution over several diတerent time scales. For example, we identify which modern
groups are most related genetically to a previously described 4500-year-old Ethiopian
genome, and precisely how those modern groups' genomes have changed due to drift,
admixture and selection eတects. We provide a comprehensive picture of the genetic
diversity across these regions, and use this information to investigate the
topographical and sociological features that promote interactions leading to genetic
exchange or imposing barriers to genetic intermixing.
LOCAL ADAPTATION IN HUMANS: INSIGHTS FROM MODERN AND
ANCIENT GENOMES
Felix M Key1, Joshua Schmidt1, Muslihudeen A. Abdul-Aziz1, Qiaomei Fu2, Frédéric
Romagné1, Benjamin Peter3, Mauro d’Amato4, Megan Dennis5, Michael Lachmann6,
Aida M Andrés1 (1) Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
(2) Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Beijing,
China
(3) Department of Human Genetics, University of Chicago, Chicago, IL, USA
(4) BioDonostia Health Research Institute, Donostia, Spain
(5) UCDavis Genome Center, Davis, CA, USA
(6) Santa Fe Institute, Santa Fe, NM, USA
Humans inhabit today a wide variety of environments, but the colonization of many of
them started only a few thousands of years ago, as modern humans migrated out of
Africa. This raises the question of whether (and if so, how) human populations have
biologically adapted to their diverse local environments. For years, modern genome
data suggested a limited role of positive selection and local adaptation on human
population diတerentiation. Combining ancient and modern human genomes I will
show that local adaptation has indeed contributed to the (modest) genetic
diတerentiation that exists among human groups. In Europe, more locally adaptive
alleles are of hunter-gatherer than farmer origin, as expected from early huntergatherers inhabiting Europe long before the arrival of southern farmers. The nature of
these adaptive alleles is diverse and includes newly adaptive mutations, segregating
variants that were previously mildly advantageous or under balancing selection, and
introgressed alleles from other human groups. The eတects of these alleles are also
diverse, as they aတect numerous phenotypes. I will discuss in detail the evidence for
strong, local positive selection having raised the frequency of cold-adaptive alleles in
human populations living in high latitudes.
DETECTION OF NATURAL SELECTION AT POPULATION LEVEL: INSIGHTS
FROM HUMAN AND CHIMPANZEE POPULATIONS
Haတd Laayouni, Begoña Dobon, Sandra Walsh, Jessica Nye, Mayukh Mondal, Ludovica
Montanucci, Jaume Bertranpetit.
Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
Evolutionary
analysis at the molecular level provides new tools to biology by
considering the action of natural selection in genes and groups of genes on their
functional setting of molecular pathways of their gene products. By comparing
genomic data of diတerent populations within a single species, we can distinguish
between selection at large or short scales, allowing detection (and sometimes
measurement) of natural selection in the form of positive selection and purifying
selection.
Whole genome sequences from African populations from Ethiopia, as well as whole
genome sequences from diတerent Chimpanzee populations are analyzed. Results are
discussed in the light of new opportunities and limitations of detecting positive
selection analyzing whole genome sequences.
EVOLUTIONARY AND FUNCTIONAL IMPACT OF POLYMORPHIC
INVERSIONS IN THE HUMAN GENOME
Carla Giner-Delgado1,2, † , Sergi Villatoro1, † , Magdalena Gayà-Vidal1, † , Jon Lerga-Jaso1,
Meritxell Oliva1, David Castellano1, David Izquierdo1, Isaac Noguera1, Lorena
Pantano1, Marta Puig1, Mario Cáceres1,3
(1) Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra
(Barcelona), Spain.
(2) Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra
(Barcelona), Spain.
(3) ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain
† These authors contributed equally to this work.
For
a long time Drosophila inversion polymorphism has been a big paradigm in
evolutionary biology. However, due to the di†culty of their study, little is known about
the role of inversions in other organisms. Here we present the တnal results of INVFEST,
an ambitious project towards the complete characterization of polymorphic inversions
in the human genome. First, we have determined the distribution of 45 inversions in
550 individuals from seven populations of the 1000 Genomes Project, which
represents the largest population genetics study of human inversions so far. Inversion
frequency spectrum showed considerable variation (MAF = 0.5-49.7%), with a bias
towards intermediate frequencies and signiတcant diတerences among populations (Fst =
0.01-0.49) in several cases. In particular, by using diတerent tests we have found that
distribution patterns of some inversions are not consistent with a neutral scenario and
suggest events of positive or balancing selection. Second, the analysis of the
nucleotide variation within the inverted region revealed that inversions mediated by
inverted repeats (N = 26) show an unexpectedly high degree of recurrence, with most
of them occurring on diတerent haplotypes in humans and showing also diတerent
orientations in chimpanzees and gorillas. This contrasts with inversions with simple
breakpoints (N = 19), which are unique and can be tagged by SNPs. Finally, we have
identiတed diတerent functional eတects of the inversions, ranging from gene breakage,
inversion of alternatively spliced exons, and generation of new fusion transcripts. Our
integrative analysis therefore illustrates the dynamic nature of the genome and
represents a key step in deတning the evolutionary impact of this type of structural
variants at diတerent levels.
IDENTIFICATION OF GENETIC BARRIERS AND GENETIC GRADIENTS BY
MEANS OF A MULTIPLE REGRESSION ON DISTANCE MATRICES (MRM)
COUPLED TO A GENETIC ALGORITHM
Iago Maceda1,2, Oscar Lao1,2
(1) CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology
(BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
(2) Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
Despite the broad genetic homogeneity existing in the human genome, a small and
signiတcant proportion of human genetic variation is not randomly distributed among
individuals. It has been shown that most of human population substructure is
explained by geography so the genetic diတerentiation between any two individuals
tends to correlate with the geographic distance of their sampling locations. Whether
this geographic diတerentiation is smooth (clinal) or sharp (barrier) is still a contentious
topic in the scientiတc community. Previous population based algorithms for identifying
genetic barriers focus on identifying sharp genetic discontinuities between spatial
neighbours (i.e. Monmonier algorithm) or spatially classifying populations into
genetically homogeneous groups (i.e. SAMOVA). Nevertheless, none of them consider
the fact that within a given geographic region deတned by a genetic barrier, populations
will tend to show genetic gradients due to isolation by distance.
In the present study we combined a meta-heuristic approach called genetic algorithm
with well-established geostatistical techniques to develop a new algorithm for
identifying clusters of spatially related populations showing similar genetic gradients.
We တrst show the performance of the proposed algorithm on simulated datasets
under diတerent demographic and spatial scenarios. Next, we applied it to publicly
available human databases.
REAPPRAISING THE HUMAN MITOCHONDRIAL DNA RECOMBINATION
DOGMA
Simón Perera1, Amanda Ramos1,2, Luis Alvarez3, Maria Guardiola1, Manuela Lima2,
Maria Pilar Aluja1 and Cristina Santos1
(1) Unitat Antropologia Biològica, Department Biologia Animal, Biologia Vegetal i Ecologia, Universitat
Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain.
(2) Departamento de Biologia, Universidade dos Açores, Ponta Delgada, Portugal; Instituto de
Investigação e Inovação em Saúde, Universidade do Porto, Portugal; and Instituto de Biologia Molecular
e Celular (IBMC), Universidade do Porto, Porto, Portugal.
(3) i3S-Instituto de Investigação e Inovação em Saúde/IPATIMUP-Institute of Molecular Pathology and
Immunology of the University of Porto, Porto, Portugal.
Correspondence to: [email protected]
The
value of mitochondrial DNA (mtDNA) as a major tool for human evolutionary
studies relies on the assumption that it does not recombine. Evidences accumulating
during the last ten years have, however, questioned this “dogma”. Direct evidence of
recombination has been limited to studies with diseased individuals. On what
concerns indirect tests of recombination, ambiguous results have been obtained,
partly because such studies have been applied to small datasets and were mainly
conceived to analyse nuclear DNA. The main goal of this work was to test for
recombination in human mtDNA using both direct and indirect approaches. We
applied the single molecule PCR (smPCR) procedure to directly test for recombination
in two multiheteroplasmic individuals without any overt pathology. Moreover, we
tested for recombination in the whole mitochondrial genomes of more than 16 000
individuals. We analysed the existence of recombination in the global dataset, as well
as in macrohaplogroup- and haplogroup-deတned sequence subsets, with the
neighbour-similarity score (NSS) test, which was shown to be the best adapted for
analysing recombination in mtDNA. Direct and indirect evidence of recombination
were found. Indirect evidences of past recombination events were found for a
signiတcant number of the deတned haplogroup- and macrohaplogroup- subsets, as well
as for a signiတcant number of theof the partitions in the global dataset. Overall, we
present robust evidence for human mtDNA recombination. This တnding poses new
research questions, which compel to revise the current dogma of absence of
recombination in human mtDNA, as well as the current evolutionary knowledge
derived from the study of this molecule in humans.
EVOLUTIONARY NEURODYNAMICS
Eörs Szathmáry1,2
(1) Institute for Advanced Studies Koszeg, Hungary
(2) Parmenides Center for the Conceptual Foundations of Science, Pullach-Munich, Germany
We
present a proof-of-principle model for Darwinian evolutionary search for
candidate solutions in the brain. While previous selectionist approaches resting on the
elimination of surplus neurons and connections are empirically well supported, our
question here is whether the brain could also implement a truly evolutionary system
constituted by units that multiply with hereditary variation on which selection in
repeated rounds can act. We argue that the brain can potentially host this
evolutionary implementation, because all its components are present, and would
certainly be extremely useful for generating new variation in cognitive tasks. These
components are: recurrent attractor networks for memory, the cortex/basal ganglia/
thalamus/cortex loop for evaluation, and implicit or unconscious working memory to
store interim candidate solutions. We employ attractor networks with palimpsest
memory that operate under a Hebbian-like modiတed covariance rule, allowing them to
store correlated information without catastrophic forgetting in regular attractor
basins. The same architecture can be used for fast search among stored solutions (by
selection) and for evolutionary search when novel candidate solutions are generated
in successive iterations. Novelty is generated in three ways: (i) noisy recall of patterns
from the attractor networks, (ii) noise during transmission of candidate solutions as
messages between networks, and, (iii) spontaneously generated, untrained patterns in
spurious attractors. We discuss the implications of our ideas for high-level cognitive
processes, such as stochastic search in the language of thought.
Simposio jovenes investigadores - Young Researchers Symposium
EVOLUTION OF THE HSP70 GENE FAMILY AT THE SEQUENCE LEVEL,
GENOMIC ORGANIZATION AND GENE EXPRESSION IN DROSOPHILA
SUBOBSCURA
Marta P. Giribets, Mª Pilar García Guerreiro, Francisco Rodríguez-Trelles, Rosa Tarrío.
(1) Grup de Recerca de Genòmica, Bioinformàtica i Evolució, Dept. de Genètica i Microbiologia,
Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
The
species D. subobscura is native to the temperate Palearctic region, having
recently colonized South and North America. The species displays a rich inversion
polymorphism in all its တve acrocentric chromosomes, whose spatiotemporal
distribution patterns clearly attest that they are adaptive. Particularly interesting are
two O chromosome gene arrangements with north-south clinal geographic
distributions, namely the warm-climate associated O3+4 and the cool-climate
associated OST. An early heat shock experiment from our laboratory identiတed the
thermal-stress-inducible Hsp70 locus, which in D. subobscura is known to be located
within the O3+4 arrangement, as a candidate gene responsible for alleged diတerences
in thermal adaptation between the two arrangements. It was found that, တies
homokaryotypic for O3+4 exhibited increased basal levels of Hsp70 that remained
stably high after exposure to heat-shock, in contrast with OST and O3+4+8, which
exhibited the typical inducible behavior. Although constantly high levels of HSP70 in
O3+4 might be detrimental for the cell, they might be advantageous in moderately
warm environments. We decided to explore this issue in depth, using a two-tiered
approach consisting in တrst characterizing the nucleotide sequence and genomic
organization of the Hsp70 family, and second assessing its gene expression levels
considering both mRNA and protein. We used isochromosomal isogenic strains, and
included the four most common arrangements of interest, namely OST, O3+4, O3+4+8
and O3+4+16. Our preliminar results show that the Hsp70 gene family of D. subobscura
consists of two closely spaced, highly similar copies placed in divergent orientation,
and that this organization is conserved across all the four assayed gene arrangements.
A comparative sequence analysis across lines indicates that the coding regions are
under strong purifying selection. Diတerences in basal HSP70 levels between
arrangements, as quantiတed by ELISA, are nonsigniတcant statistically, and are
uncorrelated with the observed cis-regulatory variation. We plan to continue our study
with the corresponding mRNA expression analyses.
Resúmenes jóvenes investigadores
Abstracts Young Researcher
Presentación jóvenes investigadores - Talk Young Researcher 1
GENOMIC ANALYSIS OF ANDAMANESE PROVIDES INSIGHTS INTO
ANCIENT HUMAN MIGRATION INTO ASIA AND ADAPTATION
3
Mayukh Mondal1, Ferran Casals2, Tina Xu , Giovanni M. Dall’Olio4, Marc Pybus1, Mihai
3
G. Netea5, David Comas1, Haတd Laayouni1,6, Qibin Li , Partha P. Majumder7, Jaume
Bertranpetit1,8
(1) Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
(2) Servei de Genòmica, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
(3) BGI Shenzhen, Yantian District, Shenzhen, 518083, China
(4) Computational Biology, Target Sciences, GSK R&D, GlaxoSmithKline , Stevenage, Hertfordshire ,
United Kingdom
(5) Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
(6) Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra,
Catalonia, Spain
(7) National Institute of BioMedical Genomics, Kalyani, West Bengal 741251, India
(8) Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology,
University of Cambridge, Cambridge, United Kingdom.
To
shed light on the peopling of South Asia and the origins of the morphological
adaptations found there, we analyzed whole-genome sequences from ten
Andamanese individuals and compared them with 60 individuals from mainland
Indian populations with diတerent ethnic histories, and with publicly-available data from
other populations. We show that all Asian and Paciတc populations share a single origin
and expansion out of Africa, contradicting an earlier proposal of two independent
waves. We also show that populations from South and Southeast Asia harbor a small
proportion of ancestry from an unknown extinct hominin, which is absent from
Europeans and East Asians. The footprints of adaptive selection in the genomes of the
Andamanese show that their characteristic distinctive phenotypes (including very
short stature) do not reတect an ancient African origin, but instead result from strong
natural selection on genes related to human body size.
GENOME VARIATION IN THE EMERGING FUNGAL PATHOGEN CANDIDA
GLABRATA
Laia Carreté1,2, Cécile Fairhead3, Toni Gabaldón1,2,4
(1) Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG), the Barcelona
Institute of Science and Technology (BIST). Dr. Aiguader, 88. 08003 Barcelona, Spain
(2) Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF).
(3) Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des
Sciences, Orsay Cedex, F 91405, France.
(4) Institució Catalana d’Estudis Avançats (ICREA)
Infections
caused by pathogenic yeasts are becoming of increasing medical
importance. Candida glabrata is one of the most common pathogenic fungi in
humans, ranking as the second causative agent of candidiasis worldwide. Despite its
genus name C. glabrata is only distantly related to the model pathogen Candida
albicans and belongs to the Nakaseomyces, a clade more closely related to
Saccharomyces cerevisiae (Gabaldón et al., 2013). This indicates that virulence to
humans has independently and recently emerged within this clade. Considering that
virulence properties can vary signiတcantly among strains of the same species, it is
important to study the detailed genetic background of pathogenic and commensal
isolates.
Here, we use a genome re-sequencing approach to analyse the variability among 32
diတerent genomes from clinical and commensal C. glabrata samples from diတerent
countries. We surveyed single-nucleotide polymorphism, ploidy, copy number
variation and genomic re-arrangements. Our results show that the sequenced strains
are structured in six genetically diတerentiated clusters, which do not cluster by
geographical origin or site of infection. Despite an overall high similarity at the
sequence level, most diတerences between strains consist of gene losses and gains,
often involving cell-wall proteins. We တnd evidence for active recombination between
distinct subpopulations, which is remarkable for species considered as asexual. In
accordance we တnd genomic evidence for active mating type switching, although we
report a high incidence of failed switching events leading to aberrant mating type
conတgurations.
Gabaldón et al.: Comparative genomics of emerging pathogens in the Candida
glabrata clade (2013). BMC Genomics 14:623.
UNDERSTANDING THE FREQUENCY DISTRIBUTION OF HUMAN
POLYMORPHIC INVERSIONS
Isaac Noguera1, David Castellano1, Sergi Villatoro1, Mario Cáceres1,2
(1) Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra
(Barcelona), Spain.
(2) Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
Chromosomal inversion polymorphism has been a paradigm in evolutionary biology.
Since early on it was shown that inversions have adaptive eတects in diတerent
organisms, but very little is known about the action of selection on inversions,
especially in humans. A key evolutionary eတect of inversions is that they suppress
recombination as heterozygotes due to the generation of lethal unbalanced gametes.
It is also known that there are two main generation mechanisms of inversions in
humans (associated maybe to diတerent mutation rates): mediated and non-mediated
by inverted repeats (IRs). Thus, it is essential to assess the role of mutation, drift and
selection in the population behavior of these two types of inversions. In this work, we
took advantage of a large-scale genotyping eတort of 44 inversions in 550 individuals
from seven populations to carry out a global analysis of inversion frequency in
humans. First, we built generalized linear mixed models to predict how the frequency
varies according to the presence and size of IRs at their breakpoints, inversion
positional eတects, such as distance to closest gene, number of captured genes, gene
location, and features associated with the eတect of inversions in recombination, such
as inversion length and local recombination rate. Next, we compared the observed
frequency against that predicted by our models in order to identify outliers and
therefore inversion candidates to be under selection. Our models တt better the data
when we distinguish inversions according to the presence (~30% of the variation
explained) or absence (~50% of the variation explained) of IRs in their breakpoints,
with inversion genetic length and inversion positional eတects, respectively, as main
and secondary factors aတecting the variation in inversion frequencies. Inversion
physical length is negatively correlated with both local recombination rate and
inversion frequency (while controlling for each other and gene content). Moreover,
inversions aတecting coding regions are at signiတcantly lower frequency than intergenic
or intronic inversions. These results suggest that human polymorphic inversions are
under strong purifying selection due to its role in promoting the generation of
unbalanced gametes. Finally, we report two inversions that show clear signs of positive
selection that deserve further molecular and phenotypic characterization.
INTERSPECIFIC RELATIONSHIPS IN THE HALOPHYTE LIMONIUM
VULGARE AND RELATED TAXA (PLUMBAGINACEAE) USING THE ITS1
MARKER
Ana S. Róis1,2, Flávio Sádio1, Miguel Fernandes2, Miguel Guara Requena3, Dalila
Espírito Santo1, Ana D. Caperta1
(1) Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de
Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal
(2) Escola de Psicologia e Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias
(ULHT), Campo Grande, 376, 1749-024 Lisboa, Portugal
(3) Departamento de Botánica, Facultad de Ciencias Biológicas, Universidad de Valencia, Spain
The
closely related halophytes Limonium vulgare Mill., Limonium narbonense and
Limonium maritimum (Plumbaginaceae) form a remarkably biodiverse taxonomic
complex group distributed throughout European Atlantic and Mediterranean coastal
regions. However, species boundaries of these species are morphologically
ambiguous. In this study we investigated the interspeciတc relationships of individuals
representative of these species using the Internal Transcribed Sequence 1 (ITS1) of the
nuclear rDNA as a marker. Genetic analyses revealed that populations of these species
are poorly diတerentiated, appearing to be very homogeneous. Network analysis
showed haplotype sharing within and among species’ populations of diတerent ploidy
levels. Phylogenetic analysis indicates that L. vulgare and L. maritimum Portuguese
populations are genetically more related with Spanish L. vulgare populations than with
L. narbonense. Our results show that morphological diတerentiation among these
species is correlated with few genetic diတerentiation across its huge range. We discuss
these data in light of these species reproductive strategies.
MULTIPLE INDEPENDENT RETROTRANSPOSON INSERTIONS IN THE
PROXIMAL PROMOTER OF A STRESS RESPONSE GENE IN DROSOPHILA
MELANOGASTER
Miriam Merenciano1, Anna Ullastres1, M.A.R. de Cara2, Maite G. Barrón1, Josefa
González1
(1) Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
(2) Laboratoire d'Ecoanthropologie et Ethnobiologie, UMR 7206, CNRS/MNHN/Universite Paris 7,
Museum National d'Histoire Naturelle, F-75116 Paris, France.
Promoters
are structurally and functionally diverse gene regulatory regions. The
presence or absence of sequence motifs and the spacing between the motifs deတnes
the properties of promoters. Recent alternative promoter usage analyses in
Drosophila melanogaster revealed that transposable elements signiတcantly contribute
to promoter diversity. In this work, we analyzed in detail one of the transposable
element insertions, named FBti0019985, that has been co-opted to drive expression of
CG18446, a candidate stress response gene. We analyzed strains from diတerent
natural populations and we found that besides FBti0019985, there are another eight
independent transposable elements inserted in the proximal promoter region of
CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed
the sequence of the nine roo insertions and we investigated whether the diတerent
insertions were functionally equivalent by performing 5'-RACE, gene expression, and
cold-stress survival experiments. We found that diတerent insertions have diတerent
molecular and functional consequences. The exact position where the transposable
elements are inserted matters, as they all showed highly conserved sequences but
only two of the analyzed insertions provided alternative transcription start sites, and
only the FBti0019985 insertion consistently aတects CG18446 expression. The
phenotypic consequences of the diတerent insertions also vary: only FBti0019985 was
associated with cold-stress tolerance. Interestingly, the only previous report of
transposable elements inserting repeatedly and independently in a promoter region in
D. melanogaster, were also located upstream of a stress response gene. Our results
suggest that functional validation of individual structural variants is needed to resolve
the complexity of insertion clusters.
TESTING THE ROLE OF SELECTION AND DEMOGRAPHY IN DRIVING THE
RAPID POSTGLACIAL RADIATION OF DARK-EYED JUNCOS
Guillermo Friis1, Angeles de Cara2, Borja Milá1
(1) National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid,
Spain
(2) Museum national d’Histoire naturelle, Paris, France
Rapid
evolutionary radiations likely result from the combined eတects of selective
pressures and demographic processes. The Dark-eyed Junco of North America
includes several phenotypically divergent forms which have arisen within the last
15,000 years. Phylogeographic analyses have revealed low diတerentiation among these
forms in mtDNA, along with haplotype frequencies congruent with a demographic
expansion from Central America to Canada, suggesting a diversiတcation process during
a northward recolonization following the last glacial maximum (LGM). Here we
combine whole-genome and genotyping-by-sequencing (GBS) data to (i) reconstruct
the phylogenetic relationships among Dark-eyed Junco forms; (ii) test the recentdivergence and population-expansion hypotheses using MSMC (multiple sequentially
Markovian coalescent) and G-Phocs (generalized phylogenetic coalescent sampler);
and (iii) infer the number of loci under selection involved in lineage diတerentiation
using Bayescan. Genome-wide SNPs obtained from GBS data resolved Dark-eyed
Junco forms into reciprocally monophyletic lineages, congruently with geographic and
phenotypic patterns. Furthermore, a rooted maximum likelihood phylogeny revealed a
striking pattern of diversiတcation consistent with a northward sequence of
cladogenetic events. Both MSMC and G-Phocs revealed recent demographic
expansions for all of forms, reinforcing the hypothesis of multiple lineage
diတerentiation driven by a postglacial northward expansion. Bayescan genomic
surveys revealed no speciတc regions of high diတerentiation but rather a large number
of highly divergent variants scattered across the genome, suggesting the role of
selection acting on numerous independent loci from the early stages of the
diversiတcation. Our analyses show that juncos represent one of the fastest radiations
documented in birds, driven by demographic and selective factors.
Lista de participantes
List of attendants
Nombre / Name
Centro / Center
Aguadé, Montserrat
Universitat de Barcelona (Spain)
Alba, Mar
Parc de Recerca Biomèdica de Barcelona (Spain)
Alonso, Santos
Universidad del País Vasco, EHU (Spain)
Álvarez, Marta
Andres, Aida
Max Planck
(Germany)
Angeles, De Cara
CNRS / Museum National d'Histoire Naturelle, Paris (France)
Baldo, Laura
Barbadilla, Antonio
Universitat Autònoma de Barcelona (Spain)
Barluenga, Marta
Museo Nacional de Ciencias Naturales, Madrid (Spain)
Barrón Aduriz, Maite
Institut Biologia Evolutiva (CSIC-UPF), Barcelona (Spain)
Bertranpetit, Jaume
Blevins, William
Universitat Pompeu Fabra (Spain)
Bosch Fuste, Elena
Cáceres, Mario
Calafell Majo, Francesc
Calvo Martín, Juan Manuel
Cañestro, Cristian
Caperta, Ana D
Instituto Superior de Agronomia (ISA), Lisboa (Portugal)
Carreras Huergo, Carlos
Carreté Muñoz, Laia
Fundació Centre de Regulació Genòmica, Barcelona (Spain)
Casillas, Sònia
Comas, David
Coronado, Marta
De Vladar, Harold
Parmenides Foundation, Pullach (Germany)
Delprat, Alejandra
Dobon Berenguer, Begoña
Dolgova, Olga
Institute
for
Evolutionary
Anthropology
Escuer, Paula
Eyre-Walker, Adam
University of Sussex (UK)
Fernández Martín, Jesús
Instituto Nacional de Investigacion y Tecnologia Agraria y
Alimentaria, Madrid (Spain)
Fontdevila, Antonio
Frías López, Cristina
Friis, Guillermo
Museo Nacional de Ciencias Naturales, Madrid (Spain)
García Guerreiro, Mª Pilar
García-Dorado, Aurora
Universidad Complutense de Madrid (Spain)
Garcia-Fernandez, Jordi
Giner Delgado, Carla
González Pérez, Josefa
Gonzalez-Candelas, Fernando
Universidad de Valencia (Spain)
Guirao Rico, Sara
Centre de Recerca en AgriGenòmica (CRAG), Barcelona
(Spain)
Henriques, Jorge
Centre for Ecology, Evolution and Environmental Changes,
FCUL, Lisboa (Portugal)
Hervás, Sergi
Horvath, Vivien
Kaessmann, Henrik
Heidelberg University (Germany)
Kuhlwilm, Martin
Universitat Pompeu Fabra (Spain)
Kuhn, Gustavo
Universidade Federal de Minas Gerais Belo Horizonte (Brasil)
Laayouni, Haတd
Lao, Oscar
Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Barcelona
(Spain)
Latorre, Amparo
López Cortegano, Eugenio
Universidad Complutense de Madrid (Spain)
López, Saioa
University College London (UK)
Marquès Bonet, Tomàs
Martínez Portela, Paulino
Universidad de Santiago de Compostela (Spain)
Matos, Margarida
Centre for Ecology, Evolution and Environmental Changes,
FCUL, Lisboa (Portugal)
Merenciano, Miriam
Milá, Borja
Museo Nacional de Ciencias Naturales (CSIC), Madrid (Spain)
Mixao, Veronica
Fundació Centre de Regulació Genòmica, Barcelona (Spain)
Mondal, Mayukh
Moreno Merchan, Antoni
Moya, Andrés
Negre, Bàrbara
Noguera, Isaac
Orengo, Dorcas J
Pascual Berniola, Marta
Pegueroles, Cinta
Fundació Centre de Regulació Genòmica (CRG), Barcelona
(Spain)
Peñarrubia, Luis
Universitat de Girona (Spain)
Perera Del Rosario, Simón
Pérez, Nuria
Pérez-Enciso, Miguel
(Spain)
Petrov, Dmitri Stanford University (USA)
Pla, Carles
Puerma Rodríguez, Eva M
Puig, Marta
Ramos Onsins, Sebastián E
(Spain)
Rech, Gabriel
Riutort León, Marta
Rodríguez-Trelles, Francisco
Róis, Ana Soတa
Instituto Superior de Agronomia, University of Lisbon; and
Lusofona University of Humanities and Technologies
(Portugal)
Rozas, Julio
Ruiz Orera, Jorge
Fundació Institut Mar d'Investigacions Mèdiques, Barcelona
(Spain)
Ruiz, Alfredo
Salazar-Ciudad, Isaac
University of Helsinki, Helsinki (Finland)
Sánchez, Alejandro
Sanchez-Herrero, José Francisco Universitat de Barcelona (Spain)
Santos, Cristina
Santos, Mauro
Segarra, Carmen
Silva Moreno, Francisco J
Universitat de València (Spain)
Subirana, Juan A
Fundació Institut Mar d'Investigacions Mèdiques, Barcelona
(Spain)
Szathmáry, Eörs
Eötvös University, Budapest (Hungary)
Tarrío, Rosa
Toll Riera, Macarena
University of Zurich (Switzerland)
Toll Riera, Macarena
Toro, Miguel Angel
Universidad Politécnica Madrid (Spain)
Ullastres Coll, Anna
Vela, Doris
Pontiတcia Universidad Católica del Ecuador (PUCE)
Villanueva Cañas, Jose Luis
Vizueta, Joel
Wagner, Andreas
Walsh Capdevila, Sandra
99 participantes / attendants
Patrocinadores
Sponsors

XXI Seminario de Genética de Poblaciones y Evolución

Transcripción

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