Abstracts for talks

(1) FCUP – Faculdade de Ciências, Universidade do Porto, Porto, Portugal; (2) CIBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal; (3) BIOPOLIS – Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal; (4) LARC/DGPC – Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal; (5) Uniarq, Faculdade de Letras, Universidade de Lisboa, Lisboa, Portugal; (6) Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey; (7) Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden; (8) Faculdade de Medicina Veterinária, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal

Iberian cattle represent an important pool of genetic diversity with a distinct evolutionary history. Local breeds display diverse mitochondrial and Y-chromosome lineages, besides the well-established African taurine ancestry also observed in their autosomes. They are considered to have high potential to reveal how trading and breeding practices shaped the genomes of cattle. However, complementary archaeogenomic data, which would allow a direct view into these past evolutionary events, are still lacking. In this study we describe newly obtained genome sequences of southern Portuguese cattle from the Medieval Islamic and post-Medieval Christian periods. A size increase of cattle was documented to have occurred along with this cultural transition. Our data also includes specimens from the Iron Age and the Roman period for broader comparisons. The amount of endogenous DNA we were able to retrieve ranged from 0.17 to 43.57% and samples were sequenced to an average of 0.38× depth of coverage. The biological sex was determined for all specimens. The population genetics analyses presented here provided further evidence of an early African influence, preceding the Moslem occupation of this territory. We also observed some level of genetic continuity between these past cattle and the extant Mertolenga native breed.

Presented by Cindy Sarmento  Eligible for best talk award

(1) IGC – Instituto Gulbenkian de Ciênca, Oeiras, Portugal; (2) 2 Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France

Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic pattern from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond ‘pattern’ and propose a theoretical framework that could help describing the temporal ‘processes’ that influence genetic variation in the context of HL&F. Since, most species worldwide have a geographically restricted dispersal (known as “isolation-by-distance”), the proposed theoretical framework consider both the effect of space and time in shaping population genetic variation. In particular, we modify the original theorical results on isolation-by-distance (Slatkin, 1991; Slatkin, 1993) and apply them to a toroidal stepping-stone model in the context of HL&F.

Presented by Gabriele Maria Sgarlata  Eligible for best talk award

(1) RSMAS – Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami FL, USA; (2) EBIO – Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA

Selection constantly reshapes the genetic and phenotypic composition of populations, yet often adaptive changes are not propagated due to e.g. prohibitively high drift or gene flow. Nevertheless, selection may still induce temporary phenotypic divergence at extremely small spatial and short temporal scales. These changes may ultimately be of higher ecological importance than long-term evolutionary trends. Selection on polygenic traits specifically may allow for repeated divergence every generation without significant reduction in standing genetic variation. The teleost Fundulus heteroclitus inhabits salt marsh estuaries that are characterized by high environmental heterogeneity (tidal ponds, creeks, coastal bays). Populations are large (>10K) and panmictic breeding results in negligible genetic structure. However, individuals demonstrate high site fidelity to microhabitats with distinct temperature and oxygen regimes. We tagged/recaptured 2000/200 individuals and confirmed residency in two disparate microhabitats: a cooler, oxygenated coastal basin and hotter, anoxic tidal ponds. After common-gardening basin and pond residents we measured fitness-related traits such as critical thermal maximum, resting metabolic rate, cardiac metabolic rate and aquatic surface respiration latency. We found significant phenotypic divergence of 5% (p=0.02) and 9% (p=0.004) among basin and pond residents in resting metabolic rate and cardiac metabolic rate respectively, suggestive of selection in microhabitats. We also identified >10,000 genome-wide single nucleotide polymorphisms using a genotyping-by-sequencing (GBS) approach. By sampling each microhabitat at two time points within a single generation we determined allele frequency change over time. Only few SNPs individually displayed significant allele frequency changes beyond that expected by random mortality. However, the proportion of SNPs showing i) non-zero allele frequency changes over time and ii) divergence among microhabitats, is significantly elevated over the neutral expectation. This pattern is consistent with selection on polygenic traits where minor allele frequency changes at multiple loci of small-effect can cause significant phenotypic shifts. Despite panmictic breeding and negligible demography F. heteroclitus displays surprising phenotypic divergence among microhabitats. This is unlikely due to environmentally induced plasticity but rather continuous selection on polygenic traits. Given sufficient standing genetic variation and large population sizes, polygenic selection may regenerate phenotypic divergence repeatedly every generation. While this does not lead to any long-term evolutionary change, such temporary phenotypic heterogeneity may be ecologically more relevant.

Presented by Moritz Ehrlich Eligible for best talk award

(1) CE3C – centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal; (2) ISEM – Institut des Sciences de l’Évolution, Université de Montpellier, Montpellier, France.

The virulence-transmission trade-off predicts that parasite fitness peaks at intermediate virulence. Despite the centrality of this hypothesis, whether the correlation between virulence and parasite fitness has a genetic basis or is environmentally driven remains to be addressed. Disentangling among these alternatives is key to identifying conditions under which parasite traits can evolve independently, which could be applied to strategies for the management of parasite virulence. Most studies in support of the trade-off hypothesis used parasite isolates that differ genetically, but also in their recent ecological and evolutionary history, as they have different geographic origins. This may lead to spurious correlations among traits, masking which factors affect the trade-off. Here, we tackled this issue by infecting host plants with inbred lines created from the same population of the macro-parasitic spider-mite Tetranychus urticae. When transmission was not possible during the infection period, we observed a hump-shaped relationship between virulence and parasite fitness, as predicted by theory. This relationship was due to within-host density dependence rather than to a genetic correlation between traits. However, when transmission to uninfected hosts occurred during the infection period, virulence was positively, environmentally and genetically correlated with parasite fitness. In this case, more virulent genotypes suffer less from host exploitation by escaping to new hosts. Therefore, the virulence-transmission trade-off depends on within-host dynamics and on the timing of transmission, rather than on a genetic correlation. This fundamental correlation may thus be easier to manipulate than previously thought.

Presented by Diogo Prino Godinho

(1) IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal; (2) INSA – Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; (3) INSA – Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal; (4) BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Portugal; (5) INSA – Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; (6) ToxOmics – Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, Nova Medical School|Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal; (7) INSA – National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.

To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimate the rate of mutation accumulation of SARS-CoV-2 and investigate the repeatability of its evolution when facing a new cell type but no immune or drug pressures. We perform experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains. From the mutations accumulated, and excluding the genes with signals of selection, we estimated a spontaneous mutation rate of 1.25×10^(-6) per nucleotide, per infection cycle for both lineages of SARS-CoV-2. We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at rate five-fold higher than the genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome towards adaptation to new environments.

Presented by Massimo Amicone  Eligible for best talk award

(1) IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal; (2) CE3C – centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal

Wolbachia is a bacterial endosymbiont that is maternally transmitted and widespread across insects and nematodes species. This endosymbiont affects many aspects of host biology and can also play a role in host defense. Wolbachia confers resistance against viral infection and affects abundance of piRNAs, an important mechanism of repressing transposable element (TE) mobilization in the germline of eukaryotes. To test this hypothesis that Wolbachia impacts TE mobilization in the host genome, we studied TE expression in flies from a panel of Drosophila melanogaster lines naturally infected with Wolbachia and for which we have information on TE insertions. We removed Wolbachia from 25 D. melanogaster genotypes from the Drosophila Genetic Reference Panel, to create a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines. We characterized Wolbachia loads in adult females from the Wolbachia-positive genotypes and measured the transcription of 14 TEs of different families in adult females from each of the Wolbachia-positive and Wolbachia negative genotypes. We found variation in TE expression which depended on Wolbachia status, type of TE, and host genotype. Differences in TE expression with versus without Wolbachia mostly depended on host genotype, rather than on TE identity. These data suggest that Wolbachia may impact TE mobilization and the generation of novel genetic variants in host genomes.

Presented by Ana Eugénio Eligible for best talk award

(1) Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro

Aging, one of the all-time challenges, is accompanied by several factors, including an increase in inflammation levels and alterations in the intestinal microbiota composition and evolution. Following a period of great fluctuations in the first years of life, the gut microbiota starts to stabilize around age three. This stability continues through adulthood but will inevitably be affected by aging, an important contributor to the loss of homeostasis. On the other hand, gut dysbiosis will also contribute to aging, e.g. by increasing gut permeability and giving rise to systemic inflammation. Nevertheless, how these events impact microbiota evolution and whether they could be involved in pathobiont selection is still unknown. Here we approach this question by comparing microbiota evolution in three sets of mice with different ages: young (6-9 weeks old), old (19 months old), and very old (25 months old). Specifically, previous studies have described the adaptation of a commensal strain of E. coli to the guts of young animals and have shown that it rapidly acquires metabolic-related mutations. In contrast, in the guts of old mice, E. coli adaptation shifts towards stress-related mutations, most likely due to an increase in inflammation and oxidative stress during aging, whereas the rise of metabolic adaptations becomes slower. Yet, to increase both the health and lifespan we need to understand how the (lucky) very old are different and how that impacts E. coli evolution. To tackle this question, we first compared the host environment that E. coli encounters upon colonization of the very old with the two previously studied age groups. For this, we measured the level of frailty, intestinal inflammation and characterized the microbiota composition. We found that the very old animals are the frailest, but do not show higher intestinal inflammation than the old mice. Interestingly, when compared to young and old animals, the very old show an increase in some health-associated bacteria, such as Akkermansia muciniphila, Oscillospira, and several Muribaculaceae members. Moreover, the adaptive pattern of E. coli colonizing the gut of the very old displays more metabolic than stress-related mutations, approaching the profile found in young animals. Together, these data raise the possibility that specific alterations to the microbiota and the gut environment during aging may not be exclusively dysbiotic and may even be associated with longevity. Future studies should try to understand whether only the healthier are able to reach very old age or whether this is a general possibility provided some reversion of dysbiosis occurs.

Presented by Rita Melo-Miranda  Eligible for best talk award

(1) cE3c – Centre for Ecology, Evolution and Environmental Changes, FCUL, University of Lisbon, Lisbon, Portugal; (2) DBA – Department of Animal Biology, FCUL, University of Lisbon, Lisbon, Portugal; (3) CESAM – Centre for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal; (4) Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Universitat Autònoma de Barcelona, Bellaterra, Spain.

Adaptive evolution is key in mediating responses to global warming and may sometimes be the only solution for species to survive. Such evolution will expectedly lead to changes in the populations’ thermal reaction norm and improve their ability to cope with stressful conditions. Conversely, evolutionary constraints might limit the adaptive response. Here, we test these expectations by performing a real-time evolution experiment in historically differentiated Drosophila subobscura populations. We address the phenotypic change after nine generations of evolution in a daily fluctuating environment with average constant temperature, or in a warming environment with increasing average and amplitude temperature across generations. Our results showed that (1) evolution under a global warming scenario does not lead to a noticeable change in the thermal response; (2) historical background appears to be affecting responses under the warming environment, particularly at higher temperatures; and (3) thermal reaction norms are trait dependent: although lifelong exposure to low temperature decreases fecundity and productivity but not viability, high temperature causes negative transgenerational effects on productivity and viability, even with high fecundity. These findings in such an emblematic organism for thermal adaptation studies raise concerns about the short-term efficiency of adaptive responses to the current rising temperatures.

Presented by Marta Santos

(1) – IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal; (2) – CCU – Champalimaud Centre for the Unknown, Lisboa, Portugal; (3) – ISPA- Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisboa, Portugal; (4) – PI and co-PI of the SocialFly Project, respectively.

Social and asocial learnings are required to cope with the complexity of the environment. They are behaviourally distinct. However, whether they use a single (general-purpose) or distinct (special-purpose) cognitive mechanisms remains elusive. A general-purpose mechanism comprises a single set of genes regulating the same biochemical pathways and neural circuits, while a special-purpose mechanism comprises two sets of genes, possibly affecting different biochemical pathways and/or neural circuits. To address this question, we firstly tested social and asocial learning abilities in 40 lines of the DGRP, a panel of several isogenic sequenced lines that together represent the genetic variation of a natural Drosophila population. For asocial learning, individual flies had to learn to avoid an oviposition-site where they associated an odour (conditioned stimulus, CS) with a bitter taste (unconditioned stimulus, US). For social learning, flies had to learn the oviposition-site choice of a group of conspecifics previously exposed to the CS and the US. Secondly, we performed a Genome-Wide Association Study – a statistical correlation between the genetic variants in the DGRP and each learning phenotype. We obtained two completely different sets of candidate genes for social and asocial learnings. Thirdly, to functionally validate the role of each gene on each learning phenotype, we used GAL4/RNAi-UAS lines to knockdown the genes. We found genes that affect both learnings and also cases of specialization. This is the first experimental evidence supporting the special-purpose cognitive mechanism hypothesis. Future work should focus on the extent of this specialization, concerning the biochemical pathways and the neural circuitry.

Financial support was granted by the Portuguese Foundation for Science and Technology through the Project “TheSocialFly” (PTDC/BIA-COM/31887/2017), Carla Henriques PhD scholarship (PD/BD/138178/2018) and Joana Marcos fellowship (203/BI/19). Financial support was also granted by ASAB, the Association for the Study of Animal Behaviour.

Presented by Carla Simões Henriques  Eligible for best talk award

(1) L’institut du thorax, Inserm UMR 1087, CNRS UMR 6291, University of Nantes, Nantes, France (2) TIMC-IMAG UMR 5525 CNRS, University Grenoble Alpes, Grenoble, France (3) Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden (4) INRAP / UMR 7264 CEPAM, CNRS-UNS Nice-Sophia Antipolis, Nice, France (5) INRAP, France; UMR 7268 (Adès) Anthropologie Bio-Culturelle, Droit, Ethique et Santé, Faculté de Médecine Site Nord, Marseille, France (6) Université de Nantes, UMR 6566 CReAAH, LARA, Nantes, France (7) Center for Evolutionary Hologenomics, University of Copenhagen, Denmark (8) Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark (9) Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark; Department of Zoology University of Cambridge, UK (10) Centre de Recherche Bretonne et Celtique, EA 4451, Université de Bretagne Occidentale, Brest, France (11) INRAP, France; UMR 6554 LETG – Brest Institut Universitaire Européen de la Mer, Plouzané, France (12) Bournemouth University, UK / UMR 8215 « Trajectoires », Paris, France (13) Commissariat à l’Energie Atomique, University of Paris-Saclay, Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Evry, France and Labex GenMed (14) Fondation Jean Dausset, CEPH, Paris, France and Labex GenMed (15) CNRS/ MNHN/ Université Paris Diderot, UMR 7206 Eco-anthropologie et ethnobiologie, Paris, France (16) UMR 1078 Génétique, Génomique fonctionnelle et Biotechnologies, Inserm, University of Brest, EFS, CHU Brest, Brest, France

Present-day France lies at the confluence of the three migration waves that mostly contributed to the genetic ancestry of modern Europeans. However, little is known about the interaction between such population movements at their edge and how this process gave rise to modern population structure.
To fill in this gap, we generated ~850 high-coverage whole-genomes together with genome-wide data for >3,000 present-day individuals from the northern half of France and incorporated them into a panel containing 100s of publicly available modern and ancient Europe-wide samples. We also present, for the first time, ancient DNA from six Medieval individuals (300-1100 CE) from Western France to gain insights into the genetic impact of what is commonly known as the Migration Period in Europe. We document extensive fine-scale population structure in Northwestern France and an overall increased population differentiation between the northern and southern sides of the river Loire accompanied by different proportions of steppe and Neolithic-related ancestries. Samples from Western Brittany show the largest levels of steppe ancestry and high levels of allele sharing with Bell Beakers-associated individuals, which are only comparable with those found in other populations lying on the northwestern edges of Europe. Together, our analysis implies that modern-day samples from Western Brittany retain, to a larger extent, the legacy of the important genetic changes that followed the arrival of people associated with the Bell Beaker complex from north-central Europe ~2500 BCE, which reflect in their genetic proximity and the sharing of disease-related alleles with other present-day Western Britons and Irish.

Presented by Isabel Alves

(1) IBUNAM – Instituto de Biología, Departamento de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, México; (2) CBS – College of Biological Sciences. University of Minnesota, Saint Paul, United States of America

Vision system in troglobitic organisms is an outstanding topic in evolutionary biology. The cavefish characid Astyanax mexicanus has been a model to address evolutionary questions regarding the visual function and the selective pressures that have evolved the differentiated morphology of cave forms relative to their surface congeners. The dim-light visual pigment rhodopsin, located in the rod photoreceptors, has been subject to numerous studies concerning vision in dark environments, such as caves. However, it was not until recently that the cone opsins and other pigments related with the visual function have acquired relevance in the evolutionary studies of cavefish species. In this study we reconstruct the phylogeny and analyze the influence of selective pressures on the visual and non-visual opsins in cave and surface populations of Astyanax mexicanus though the analysis of Next Generation Sequencing data. Therefore, 36 visual and non-visual opsins were obtained from whole genome sequences (WGS) of 22 cave and surface populations. We found evidence of relaxed selective constraints in cave forms in comparison with surface populations for most of the opsins. Furthermore, we also identified several putative “Lost of Function” (Lof) mutations in the protein-codifying genomic regions for some of the cave populations that are not present in the opsins of surface individuals. Our study reveals the differentiated action of selection on the visual pigments of cave and surface populations of this species.

Presented by Silvia Perea

(1) ESPM, University of Berkeley, California, USA; (2) Marisa Xavier Design, Portugal; (3) Zoology, University of Basel, Basel, Switzerland; (4) cE3c, Faculdade de Cie^ncias, Universidade de Lisboa, Portugal; (5) College of Life and Environmental Sciences, University of Exeter, UK; (6) College for Health and Cognition, Bath Spa University, Bath, UK ; (7) Crossmodal Cognition Laboratory, University of Bath, Bath, UK. ; (8) Centro Pedago´gico Do Jardim Zoolo´gico de Lisboa, Portugal; (9) Tutisfore, Lisbon, Portugal

39 million people have blindness worldwide and additional 246 million have impaired vision. Amounting to the difficulties deriving from sensory disability, people with blindness face socio-economic inequity and have limited access to education, a trend that is aggravated for scientific and natural history knowledge. The under-representation of people with visual impairment in the evolution research community is deeply connected with the vision-based communication of evolutionary biology and the accompanying lack of multisensory alternatives for learning. We developed an outreach project including, and dedicated to, people with blindness: evALLution. Based on an immersive and multisensory tree of life, we developed multiple haptic activities for the 20 taxa represented, including classical models for evolution research: bird beak morphology, butterfly camouflage, stickleback armor, cichlid adaptive radiations… Recurring mainly to touch and auditory narration, we were able to instruct and test participants from a wide range of ages on the basic evolution concepts of adaptation, natural selection, common ancestry and extinction. Our activities thus far have shown that regardless of age, education level and type of blindness, participants can successfully comprehend and predict evolutionary change. All it takes is creative investment in translating evolution knowledge into multisensory approaches. In a time when we strive for a more diverse and inclusive world and research community, it is imperative to gather our collective creativity to bring down any ableist barriers that obstruct anyone’s access to biodiversity and evolutionary biology. We will share our process and what we have learned along the way.

Presented by Telma Laurentino