Abstracts for Posters

(1) CIBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (2) Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; (3) 3BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; (4) ISEM – Institut des Sciences de l’Évolution Montpellier, Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier, France

Hybridization leading to genetic exchanges between species is a ubiquitous evolutionary process that impacts the evolutionary trajectories of species since the split from a common ancestor. Characterizing patterns of genomic divergence and introgression between species, and the selective and demographic processes underlying the genetic exchanges, provide important insights on fundamental evolutionary mechanisms. It allows, for example, understanding how the genomes of the diverging entities become isolated (speciation), or the adaptive impact of interspecific genetic exchanges. Here, we will address these relevant evolutionary questions studying the process of divergence between two hare species from Europe: the broom hare (Lepus castroviejoi), distributed in the Cantabrian Mountains in Northern Spain, and the Italian hare (L. corsicanus), present in Central and Southern Italy, Sicily and introduced in Corsica. These species are the result of a recent split from a common ancestor and occupy geographic areas with environmental similarities in the Iberian and Italian Peninsulas. Both show evidence of ancient introgression from an arctic/boreal hare, the mountain hare (L. timidus) currently distributed in northern Eurasia and the Alps. Moreover, the broom hare possibly also hybridized with its current neighbouring species in the Iberian Peninsula. We will use this system and whole genome sequencing data to characterize and model the process of divergence between the sister broom and Italian hares, and infer the dynamics of ancient and possibly current hybridization affecting the species. These hybridization events resulted from complex dynamics of transient and novel contacts among south European hare species during the post-glacial environmental changes, which we will reconstruct. This work will allow understanding the relative importance of demographic and selective events shaping the divergence and genetic exchanges among species.

Presented by João Souto  Eligible for best poster award

(1)CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal; (2) 2Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; (3) BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; (4)National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK; (5)National Veterinary Institute (SVA), SE75189 Uppsala, Sweden

Anthropogenic changes in climate and habitats pose important challenges to biodiversity, forcing species to move or risk extinction unless they are able to adapt to the new environments. Among the most striking impacts of climate change are the important shifts of the distribution of species, such as retractions or fragmentations of vulnerable species or expansions of favoured ones. This is particularly relevant when species are invading the range of retracting close relatives and they hybridize. Introgressive hybridization may endanger the survival of species, introducing maladaptive variation, but may also create opportunities for adaptation, if the introgressed variation increase their adaptive potential in the new environmental settings. Quantifying the impact of introgressive hybridization in the interspecific dynamics of species facing climate change is therefore of utmost importance. Here, we investigate the genetic interaction between Lepus timidus (mountain hare), a retracting artic/boreal species well adapted to cold environments, and Lepus europaeus (brown hare), an invading temperate species, in two contact areas, in Sweden and Scotland, where an invasion-retraction dynamics between the species is known. By using genome-wide single nucleotide polymorphism data from both species, we will characterize the patterns of genetic structure and genetic diversity on the two focal areas, inspect historical and contemporaneous patterns of hybridization during the range replacement, and model the demographic dynamics of the interacting species.

Presented by Juliana Sofia Alves Eligible for best poster award

(1) MPI Evol Bio – Max Planck Institute for evolutionary biology, Plön, Germany

Repetitive sequences are frequent in vertebrate genomes. Both transposable elements and structural variation can leave a footprint of high repetitiveness in the genome. Their complement, high-complexity and transposon-free regions have long been associated with developmental genes, like the Hox cluster.

High-complexity regions can be identified by their dissimilarity to other genomic regions. We calculate the genome complexity of the human genome using the published program macle, and identify all unique regions, showing that these regions are strongly enriched for genes involved in neuron differentiation and morphogenesis processes. We further estimate that duplications older than 120 Million years have diverged to the point of being considered unique.

We expand this dissimilarity search to compare pairs of genomes and look for functionally significant lineage-specific regions (LSR) between the human and chimpanzee genomes.

Presented by Beatriz Vieira Mourato Eligible for best poster award

(1) CE3C – centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal; (2) Department of Environment and Natural Resources, Bermuda; (3) ISPA – Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal

Pterodroma cahow, also known as Bermuda petrel, is an endangered seabird species, endemic to the Bermuda Islands. The settling of colonizers in the islands in the 17th century caused a drastic decline on this species to the point that was though as extinct. Surprisingly, in 1951, a few pairs were found breeding in a few remote islets, which brought up an ambitious conservation programme, that has led to an incredible recovery until the present day. The approach embraced in cahow’s recovery in the last years enabled the gathering of such ecology data considered very rare among wild populations and more commonly on captive ones. This project aims to bring a deeper knowledge on the Bermuda petrel through a genetic approach, comprising a high throughput sequencing technique (ddRAD-seq) and further bioinformatic tools. The main goals are to estimate cahow’s genomic diversity and compare it to other sister taxa; estimate levels of inbreeding and relatedness and test its putative impact on the hatching success of the last few years; find genomic signatures of its demographic history, which is presumed to rely on a period of high diversity and abundance of individuals until an intense genetic bottleneck followed by an ongoing expansion. Also, this project intends to learn about the dynamic between drift and selection through sequencing and analysis of two immune system genes (TLRs), described as being under selection in many avian species.

Presented by Rita Afonso Eligible for best poster award

(1) INIAV – National Institute for Agrarian and Veterinarian Research, Oeiras, Portugal; (2) cE3c – Centre for Ecology, Evolution and Environmental Changes, FCUL University of Lisbon, Lisbon, Portugal

Antibiotics have become a serious threat to human, animal, and ecosystem health. Their overuse has had a serious impact on bacteria and has led to an alarming increase in antibiotic resistance which is particularly worrying in the case of pathogenic bacteria. The exposure to antibiotics is a driver of bacterial genome evolution, and as such, the genomic location of the resistome and the virulome may have a critical role on this dynamic. Recent works have demonstrated that there is a positive correlation between antibiotic resistance and virulence in microbial communities’ metagenomes. In this work we aimed at evaluating the co-occurrence of antibiotic resistance, and virulence factor genes in the same genomic location in a dataset composed of 16632 bacterial complete reference genomes (from RefSeq). For that we have searched for all the gene orthologues to the Resfinder and MUSTARD antibiotic resistance (ARs), and the VFDB virulence factor (VFs) databases, and assigned them a genomic location: either on plasmids or on chromosomes. We concluded that an additional category of genomic element should be considered for those antibiotic resistance and virulence factor encoding genes that are present in both plasmids and chromosomes of the same bacterial genome, which may correspond to mobile genomic elements, such as Integrative and Conjugative Elements (ICE). Our results show that ICEs are enriched with ARs while VFs are preferentially located in chromosomes. We also show the distribution of the different categories of each ARs and VFs, and co-occurrences per genomic element.

Presented by Helena Darmancier Silveira Eligible for best poster award

(1) IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal

Iron is critical in host-microbe interactions, and its availability is under tight regulation in the mammalian gut. Antibiotics and inflammation are known to perturb iron availability in the gut, which could subsequently alter host-microbe interactions. Here, we show that an adaptive allele of iscR, encoding a major regulator of iron homeostasis of Escherichia coli, is under fluctuating selection in the mouse gut. In vivo competitions in immune-competent, immune-compromised, and germ-free mice reveal that the selective pressure on an iscR mutant E. coli is modulated by the presence of antibiotics, other members of the microbiota, and the immune system. Ex vivo assays show that iron availability is an important mediator of the iscR allele fitness benefits or costs. We identify Lipocalin-2, a host’s innate immune system protein that prevents bacterial iron acquisition, as a major host mechanism underlying fluctuating selection of the iscR allele. Our results provide a remarkable example of strong fluctuating selection acting on bacterial iron regulation in the mammalian gut.

Presented by Hugo Barreto Eligible for best poster award

(1) Departamento de Didáctica de las Ciencias, Universidad de Jaén, Jaén, Spain; (2) Departamento de Didáctica de las Ciencias Experimentales, Universidad de Granada, Granada, Spain.

Evolutionary Biology is a fundamental discipline that explains the evolution of all organisms in the planet. Despite this essential assignment, teaching Biological Evolution is not free of obstacles and several pedagogical difficulties of diverse origin has been reported in the literature regarding this discipline. In that respect, we have interviewed six pre-service and three in-service teachers of secondary education from Granada (Spain) to look into their perceptions about teaching difficulties when dealing with Evolutionary Biology. Interestingly, we found that pre-service teachers observe a higher number of difficulties than in-service teachers related to teaching-learning processes associated with Evolutionary Biology. However, both groups of teachers agree on the kind of difficulties detected: the teleological thinking, substitution of species, the concept of population, an anthropocentric view of Biological Evolution and the nature of science. These obstacles for the understanding of Evolutionary Biology were detected when teachers referred to the students more than to themselves. With this in mind, we designed a sequence of activities for the 4th year of the secondary education in order to address misconceptions about Biological Evolution. These activities start from a reflective discussion around memes as a playful thread and continue with cross-curricular activities to consider the integrative nature of Evolutionary Biology as a way to reinforce a meaningful knowledge of the discipline.

Presented by María Martín-Peciña  Eligible for best poster award

(1) University of Vigo, CINBIO, Vigo, Spain; (2) Chirurgische Klinik, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; (3) Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, and German Cancer Consortium (DKTK); Partner Site Berlin, German Cancer Research Center (DKFZ), Berlin, Germany.

Despite significant improvements in metastatic colorectal cancer (mCRC) survival, tumor recurrence remains a critical clinical concern, as most patients will relapse within a short time period, primarily in the liver. While the high genetic heterogeneity, often observed in mCRC tumors, is expected to contribute to the observed variation in therapeutic response and patient survival, our current understanding of the mechanisms that metastatic cells use to resist treatment is so far limited. Importantly, unlike conventional sequencing strategies of bulk tumor samples – which collectively average the genomic information stemming from highly heterogeneous clonal populations -, single-cell DNA sequencing technologies currently enable the identification of specific malignant cell lineages that would be impossible to distinguish otherwise. As such, here we use heterochronous single-cell DNA sequencing data to identify specific malignant cell lineage/s responsible for the relapse in a mCRC patient with recurrent hepatic metastasis. By leveraging a robust Bayesian phylogenetic approach with sophisticated molecular profiling methods we explored () the evolutionary history of metastatic spread, () the timing and clonality of cancer progression and () somatic variants and molecular patterns potentially contributing to the acquisition of therapeutic resistance.

Presented by João Alves

(1) Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Germany (2) Matthias Fischer, Max Planck Institute for Medical Research, Heidelberg, Germany

Species interactions shape population dynamics and community diversity. Such interactions are not fixed, but lay along a parasitic-mutualistic continuum where cost and benefits change by the interplay of ecological and evolutionary processes. In addition, species interactions might be disrupted by chemical exposures derived from anthropic activities, which in microbial communities can result in rapid evolutionary changes relevant at ecological time scales. Here, we use a marine heterotrophic flagellate to test host, virus and virophage trait changes under antiviral exposures (oseltamivir of 0.1 mg/L of oseltamivir what is with Predicted No Effect Concentrations (PNEC)). Communities were established in chemostats for 50 days (~100 host generations) under three antiviral treatments: control, no exposure; pulse, one pulse of 0.1 mg/L; and, disturbed, one pulse of 0.1 mg/L every day. Host, virus and virophage population dynamics and species ratio changed depending on antiviral exposure. Host population traits diversified from ancestor populations, It suggests they evolved during the experiment. Specifically, host survived virus infections, interestingly, especially host clones coming from the disturbed treatments where virus pressure was expected to be lower due to antiviral exposure. Virus and virophage trait changes are still under study. To conclude, we show host diversification from ancestral populations influenced by antiviral pressures.

Presented by Ana del Arco

Poster P11 Session 1, Room 3

(1) Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal; (2) Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium; (3) Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium; (4) Data Science Institute, I-Biostat, Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium; (5) Unité Bioinformatique Evolutive, Département de Biologie Computationelle, Institut Pasteur, Université de Paris, Paris, France; (6) Hub Bioinformatique et Biostatistique, Département de Biologie Computationelle, Institut Pasteur, Université de Paris, Paris, France; (7) Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; (8) Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia; (9) National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil; (10) Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium; (11) Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil; (12) Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 – Muséum National d’Histoire Naturelle, CNRS, EPHE, SU, UA, Paris, France; (13) Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium

Zika virus (ZIKV), a mosquito-borne virus of the Flaviviridae family that induces microcephaly in newborns, caused a public health emergency of international concern in 2016 due to its rapid spread in the Americas. Although the overall number of ZIKV-related cases has declined sharply after 2016, the virus might still be circulating unnoticed. The virus was first isolated in 1947 in non-human primates in Africa and the first suggestion of inter-human transmission came from its detection in the antropophilic mosquito, Aedes aegypti, in 1966, in South-East Asia. The first reported outbreaks occurred in the Pacific islands of Micronesia in 2007. In 2013, in French Polynesia, an outbreak was associated with increased congenital and neurological syndromes, from where it radiated to the Americas. Following the American outbreaks, intensified surveillance efforts provided an opportunity to understand the patterns of genetic diversity, evolution and spread of ZIKV. We analyzed a curated dataset of 505 publicly available full-length coding region sequences with associated metadata that included geographical origin and collection date. Maximum likelihood tree reconstruction showed two main genetic clusters that separated the African from non-African sequences. We further examined the non-African (previously denominated “Asian”) cluster with a Bayesian model-based hierarchical clustering approach and identified substructures within it. We reported a genetic distance between Pre-American and American lineages of 5 %, while the distance between American subgroups was limited to ~0.5 %. This reduced genetic distance is expected from a very recent diversification. Ancestral character reconstruction indicated a spread from South-East Asia to Polynesia and from there reaching South America, particularly Brazil. Subsequently, multiple diversification events occurred in other South-Central American and Caribbean countries, giving rise to the North American cluster. The large number of low-frequency mutations that were detected in sequences originating from epidemic regions and that are distributed homogeneously across the genome, agrees with a demographic expansion scenario. We detected nine sites with evidence of positive selection that also harbored increased frequencies of alternative amino acids in particular clades, for example, the non-African clade, the Central American clade and the Caribbean/North American clade. When restricting the detection of selection to the period of the earlier expansion of ZIKV in the Americas, we were able to identify another two sites with evidence of selection. We were unable to find evidence of recombination within ZIKV. The genetic subgroups that we identified in this study are the basis for a proposal of a new nomenclature that will constitute a helpful framework for future studies on ZIKV genomic variation.

Presented by Sofia Seabra

(1) NHM – Natural History Museum, London, UK; UCL – University College London, UK

A latitudinal diversity gradient in species richness is one of the most consistently recognised patterns across a wide variety of terrestrial and aquatic habitats, but diversity patterns in the deep ocean (>200m) have rarely been investigated. Here, we have compiled and analysed a dataset of more than 250,000 coordinate records spanning the entirety of the world’s oceans and covering the full taxonomic diversity of the Asteroidea, an entire class of charismatic marine invertebrates. We find evidence for a latitudinal gradient in diversity in shallow (0-200m) waters of both the Northern and Southern hemispheres, but diverging patterns of latitudinal species richness between the hemispheres with depth. The abyssal fauna (2000-6000m) is dominated by largely cosmopolitan species, with peaks in northern temperate and Antarctic/sub-Antarctic waters. We have used measurements of sea-floor environmental variables to investigate potential contributory factors shaping these observed patterns. We have also compiled a secondary database, containing geographic and bathymetric range and substrate preference for ~99% of currently described taxa and used this in combination with our coordinate dataset to analyse for the first time the interrelationships between global regional assemblages in this group. We identify the Philippines and the Caribbean as hotspots of global diversity, with high regional diversity around the Antarctic Peninsula and along the chain of the Aleutians. Finally, we produce the first global bathymetric overview of the Asteroidea and show that most families are shallow tropical specialists with deep sea diversity dominated by a highly restricted set of specialised families.

Presented by Hugh Carter Eligible for best poster award

(1) CESAM – Center for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal; (2) Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA; (3) Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.

Body temperature is a crucial variable in animals that affects nearly every aspect of their lives. Here we analyze for the first time largescale patterns in the evolution of body temperatures across terrestrial vertebrates (tetrapods: including amphibians, mammals, birds and other reptiles). Despite the traditional view that endotherms (birds and mammals) have higher body temperatures than ectotherms, we find they are not significantly different. However, rates of body-temperature evolution are significantly different, with lower rates in endotherms than ectotherms, and the highest rates in amphibians. We find that body temperatures show strong phylogenetic signal and conservatism over 350 million years of evolutionary history in tetrapods, and some lineages appear to have retained similar body temperatures over time for hundreds of millions of years. Although body temperatures are often unrelated to climate in tetrapods, we find that body temperatures are significantly related to day-night activity patterns. Specifically, body temperatures are generally higher in diurnal species than nocturnal species, both across ectotherms and, surprisingly, across endotherms also. Overall, our results suggest that body temperatures are significantly linked to phylogeny and diel-activity patterns within and among tetrapod groups, rather than just climate and the endotherm-ectotherm divide.

Presented by Matthew Moreira Eligible for best poster award

(1) NHMUK – Department of Life Sciences, Natural History Museum, London, UK; (2) UOB – School of Biological Sciences, University of Bristol, Bristol, UK; (3) NMNH – Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., US; (4) CU – Department of Earth Sciences, University of Cambridge, Cambridge, UK

Members of the gastropod superfamily Stromboidea are characterised by their elaborate shell morphologies and diverse eye structures. Estimates of visual acuity from histological data suggest surprisingly fine resolution vision in the large eyes of families Rostellariidae, Seraphsidae and Strombidae. In contrast, the small eyes of Aporrhaidae, Struthiolariidae and Xenophoridae provide much coarser resolution. Due to this variation in eye types and visual capabilities, the superfamily therefore provides an excellent opportunity for eye evolution studies. To this end, we use Sanger sequencing data for three mitochondrial genes (COI, 12S and 16S) and one nuclear gene (28S) to build a robust phylogenetic framework of the superfamily. Morphological traits (including eye size, aperture size, and lens diameter) are mapped onto the phylogeny to identify key transition points in the evolution of large, camera-type eyes and further explore how visual structures vary across the group. The stromboid fossil record is excellent, which allows for the use of fossil calibrations in phylogenetic analyses, to determine when these complex eyes originated.

Presented by Alison Irwin Eligible for best poster award

(1) CE3C – centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal

Genomic scans of differentiation are widely used to detect outliers potentially under divergent selection. However, the effect of removing deleterious mutations can confound these analyses. In addition, work done on migration and its effects on deleterious mutations are scarce while works measuring the effects of deleterious mutations on the genome focus on diploid autosomes, excluding for example haplodiploid populations. To quantify this effect, we model migration and deleterious mutations, using stochastic simulations of 100Kb chromosomes with SLiM. We compare genetic differentiation patterns in sex-limited hemizygous chromosomes (e.g. X/Z sex-chromosomes or haplodiploid autosomes) with diploid autosomes. Our results predict that background selection (BGS) increases differentiation, but this effect vanishes with increasing migration rates. For recessive and slightly deleterious mutations, we predict diploid chromosomes to be affected by associative overdominance (AOD) at low recombining regions, creating valleys of differentiation while maintaining diversity. Interestingly, such results were also found in hemizygous chromosomes but at a much narrower range of the parameter space. In addition, we report on the transition zone between AOD and BGS, which depends on the dominance of deleterious mutations and is influenced by the hemizygosity of the genome, with haplodiploids presenting the transition much sooner than diploids.

Our results indicate that AOD can exist in haplodiploids, contrary to our initial thoughts, and that migration has an impact on the differentiation between populations, eroding the peaks produced by BGS while also lowering the effects of AOD albeit at a much slower rate.

Presented by Gonçalo Caneira Eligible for best poster award

(1) NHM – Department of Life Sciences, The Natural History Museum, London, UK; (2) UoB – School of Earth Sciences, University of Bristol, Bristol, UK

Post-processing of trees often focuses on (multi)sets of phylogenetic trees on the same leaf set, which can be summarised or investigated using a variety of consensus and clustering methods. One post-processing method identifies islands of trees, the disconnected components of a graph where vertices are trees and edges connect sufficiently similar trees. This approach cannot be easily extended to (multi)sets of trees with partially overlapping leaf sets, such as those generated for phylogenomic studies, due to the confounding effects introduced by small trees (with small distances to potentially disparate larger trees) and by pairs of trees with insufficiently overlapping leaf sets. In an attempt to identify informative clusters of trees with partially overlapping leaf sets, we define a new subsetting approach that successively extracts subsets we term “clumps” from a set of trees. Clumping overcomes the problem of undefined distances between insufficiently overlapping input trees, by instead measuring the distances of the trees to a supertree computed for the as yet unclumped input trees. Clumps are those trees that are sufficiently similar to the supertree, with the supertree recalculated for the remaining trees after each round of clumping. Weighting is used to obviate problems otherwise caused by small input trees. While clumps were developed with the goal of minimising the negative effects introduced by small trees and avoiding comparisons of trees with non-overlapping leaf sets, they can be applied to (multi)sets of trees with identical taxonomic sampling. Time permitting we will introduce the concept of clumps, an analytical pipeline and an empirical example of clumping.

Presented by Ana Serra Silva Eligible for best poster award

(1) CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; (2) Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; (3) BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; (4) CNRS/MNHN/Université de Paris – UMR 7206 Ecoanthropology, Paris, France.

Recently admixed populations provide unique opportunities to understand how complex admixture processes influence genetic diversity. Since the 15th century, admixture triggered by European colonization and the Atlantic Slave Trade (AST) has been marked by sex-specific demographic processes leaving a peculiar signature along the genome. According to historical sources, much more males than females were forcibly displaced from Africa during the AST. However, population genetics studies revealed a strong sex-bias towards unions between African females and European males. In the patriarchal colonial context, enslaved and non-enslaved people formed two almost isolated communities, but unions between enslaved females and non-enslaved males were more likely tolerated. For this reason, the specific history of socio-cultural constraints on mating at play during admixture has strongly influenced genetic diversity of Afro-descendant populations.

We aim at reconstructing complex sex-specific admixture histories on the archipelagos of Cabo Verde and Sa~o Tome´ e Principe, two of the earliest European peopling colonies in Sub-Saharan Africa and commercial platforms crucial to the history of AST. Both the archipelagos were not inhabited when the Portuguese first settled the islands in the 15th century. Portuguese settlers then intensified the peopling with enslaved Africans and tolerated the formation of a biologically and culturally admixed society. Although similar, the colonisation history of both archipelagos markedly differed, influencing processes of genetic admixture and the formation of creole cultures. We genotyped more than 2.5 million Single Nucleotide Polymorphisms (SNP) on autosomes, X-chromosome, NRY-chromosome and mitochondrial DNA from 350 individuals sampled on the main inhabited islands of both archipelagos.

We propose a novel method and accompanying computational and bioinformatics tools to infer, from autosomal and sex-specific genetic data, the complex sex-specific admixture history of admixed populations using Approximate Bayesian Computation (ABC). The recently developed software package MetHis, together with existing Machine Learning algorithms, allows for ABC inference of complex admixture histories based on explicit simulation of diploid (autosomal) genetic data under random mating. The aim of our project is to implement a sex-specific version of the MetHis software allowing for the joint simulation of diploid, haplo-diploid (X-chromosome), and haploid (NRY-chromosome, mtDNA) data under explicitly parameterized non-random mating. After in silico benchmarking of our method, will be able to disentangle female and male demographic processes during admixture in Cabo Verde and São Tomé e Príncipe to formally test which sex-specific admixture history best explains the observed genetic diversity in either archipelagos.

Presented by Marta Ciccarella  Eligible for best poster award

(1) IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal; (2) IMT – Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, Toulouse, France; (3) INSA – Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France; (4) ENAC – Ecole Nationale de l’Aviation Civile, Université de Toulouse, Toulouse, France; (5) GenPhySE-, Génétique Physiologie et Systèmes d’Elevage, Université de Toulouse, Castanet Tolosan, France; (6) EDB – Laboratoire Évolution & Diversité Biologique, Université de Toulouse, Midi-Pyrénées, Toulouse, France.

Reconstructing the demographic history of species has an enormous importance for evolutionary and conservation biologists. The pairwise sequentially Markovian coalescent (PSMC) of Li and Durbin [1] uses the distribution of heterozygous sites along the genome of a single diploid individual to reconstruct the population demographic history. However, it also requires the use of a reference genome, which is mostly unavailable for non-model species. This causes people to use reference genomes from other species, which can introduce a bias when calling SNPs and lead to spurious results [2]. In this study, we assess the impact of the reference divergence by using high-quality reference genomes from increasingly divergent species. We first infer a human PSMC, using reference genomes from human, chimpanzee, a Western lowland gorilla, a Sumatran orangutan, a Northern white-cheeked gibbon, and a rhesus macaque. To further investigate the impact of the reference divergence, we compared the PSMCs inferred for each of these primates using as reference both its conspecific and the other primates’ references assemblies. Results suggest that the divergence of the reference generate biases on the demographic inference. While we were able to recover a similar shape using the closer species as reference, the PSMC curves tended to be shifted towards the recent past and lower effective sizes, with increasingly divergent references showing a bigger shift or a drastic change of the curve shape. We also wanted to investigate whether using a de novo assembly from the target non-model species as reference would be a better approach compared to the use of a high-quality reference from a closely related species. To assess the impact of the quality of the reference on the PSMC, we generated de novo assemblies for the Chimpanzee and the Gray mouse lemur, we then compared the PSMC inferred using these as references versus using the high-quality reference genome for the same species. Results indicate that using a short read de novo assembly as reference, produces a very close demographic inference as the one obtained using a high-quality reference genome. Results also suggest that a de novo assembly might lead to a more accurate inference than the one obtained using a high-quality reference genome from a close species. This approach can be a valuable tool to infer the PSMC for species for which there are no high-quality reference genomes available.

Ref:

1. Li, H., Durbin, R., 2011. Nature 475 (7357), 493–496.

2. Günther, T., Nettelblad, C., 2019. PLoS Genet 15(7): e1008302. https:// doi.org/10.1371/journal.pgen.1008302

Presented by Margarida Henrique

(1) ISEB – Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland

Plants in the genus Erysimum (Brassicaceae) have gained the ability to produce cardenolides in addition to the conserved glucosinolate defences of all Brassicaceae. Cardenolides are a class of potent toxins that are functionally and biosynthetically unrelated to glucosinolates. Consistent with a co-evolutionary escape by the plant, several glucosinolate-adapted herbivore species no longer accept Erysimum as host plant. While some herbivores still feed on Erysimum, there appears to have been no evolution of specific resistance to cardenolides in any Erysimum herbivore. To study the consequences of phytochemical novelty and diversification for herbivore resistance, we expose a lepidopteran insect (Plutella xylostella) – with partial susceptibility to cardenolides – to strong selective pressures, and aim to observe the evolution of cardenolide resistance in action. Genomic responses to selection will be assessed using whole genome sequencing of pooled individuals. Candidate loci contributing to cardenolide resistance will be validated using CRISPR/Cas9 genome-edited Plutella xylostella reference lines on artificial ‘cardenolide’ diets.

Presented by Erik van Bergen

(1) cE3c – Centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal

From Fisher’s characterization of adaptation in 1930, until now with the genomics era, understanding adaptation has been a topic under active research. In many taxa, there is evidence of local adaptation to different environments across the species range. Yet, little is known about how populations can adapt to new environments leading to local adaptation, especially when there is potential for gene flow. Theoretical studies predict that advantageous alleles in a given local environment can be lost due to gene flow, preventing adaptation. At the same time, other studies have shown that gene flow can bring new alleles that speed up local adaptation. To fulfil this knowledge gap, one can use experimental evolution, since it provides the possibility to control different selective pressures exerted in all replicated populations which in turn helps disentangle the impact of drift, migration and selection. More recently it was possible to combine Experimental Evolution with next-generation sequencing (NGS) and sequencing whole genomes of pools of individuals (PoolSeq), allowing to obtain estimates of allele frequencies at multiple SNPs for several replicated populations at different time points (Evolve and reseq). Therefore, I aim to tackle how populations can adapt to new environments by studying phenotypic and genomic changes through time in experimental evolution populations of Tetranychus urticae adapting to cadmium with and without gene flow. Namely, I aim to: (1) assess if populations can adapt to cadmium by analyzing changes in life-history traits through time; (2) identify genomic regions involved in adaptation to cadmium in the absence of gene flow; (3) compare genomic patterns of diversity and differentiation in regimes with and without migration; and (4) verify if the observed genomic patterns fit theoretical predictions, by simulating populations evolving according to the conditions used in experimental evolution. Here, we will present the plan for my Master thesis, describing the data and comparisons that we will do to achieve these goals.

Presented by Marta Ferreira  Eligible for best poster award

(1) cE3c – Centre for ecology, evolution and environmental changes, FCUL, Lisbon, Portugal; (2) DBA – Departamento de Biologia Animal, FCUL, Lisbon, Portugal; (3) ISEM – Institut des Sciences de l’Evolution, University of Montpellier, France

Costly reproductive interactions between species, termed reproductive interference, have recently regained attention as being a major driver of species exclusion. Thus, it is expected that, following secondary contact, sympatric populations engaging in these interactions will evolve strategies to mitigate or avoid reproductive interference in order to persist. Here, we tested this expectation using a system comprised of two closely related spider mites, Tetranychus urticae and T. cinnabarinus, which have been shown to engage in interspecific crosses that produce mostly sterile hybrids. We allowed these species to evolve in either allopatry or sympatry for 30 generations before testing the strength of reproductive interference in the system. By comparing offspring production by each species when alone versus in the presence of heterospecifics, we confirmed that both suffer from reproductive interference. However, the response of each species to reproductive interference did not change after evolution in sympatry, indicating that spider mites were unable to avoid costly interactions. This finding has important implications for spider mite population dynamics and distribution in nature, and raises the question of whether other strategies, such as niche partitioning, can serve as alternate means of avoiding reproductive interference.

Presented by Miguel A. Cruz  Eligible for best poster award

(1) CIDTFF.UA, Centro de Investigação em Didática e Tecnologia na Formação de Formadores, Universidade de Aveiro, Aveiro, Portugal; (2) Alpoente, Agrupamento de escolas de Albufeira Poente, Albufeira, Portugal; (3) inED, Centro de investigação e Inovação em Educação, Politécnico do Porto, Porto, Portugal; (4) IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; (5) Universidade do Minho, Centro de Investigação em Educação, Braga, Portugal; (6) CeiED – Centro de Estudos Interdisciplinares em Educação e Desenvolvimento da Universidade Lusófona, Portugal

A recent analysis of Portuguese basic education biology curricula shows that some of the fundamental key ideas of evolution are not explicitly mentioned in the mandatory essential learnings to be achieved by the students. Although not specifically mentioned, these learning goals can still be taught in these grades by the teachers. To understand how evolution is explored in these educational levels, the textbooks from “Study of the environment” (from the 1st to the 4th grade) and “Natural Sciences” (from the 5th to the 9th grade) that are most used in Portugal were analysed. This educational resource was chosen for analysis because several studies show that textbooks are one of the resources that teachers use most in their classes. Using the Framework to Assess the Coverage of biological Evolution (FACE) we analysed the text, exercises, laboratorial activities and images appearing in these books. Each book was independently analysed by two researchers that identified and coded each unit of analysis that contained a FACE evolution key idea. When distinct results were obtained for a unit of analysis, they were discussed by the researchers until consensus was reached or otherwise removed from the analysis. According to our results, the FACE categories most often found in Portuguese basic education textbooks are “Evidence for evolution”, “History of life” and “Scientific Practices”. The categories “Evolutionary processes”, “Nature of Science” and “Studying evolution” are less frequent in these textbooks. Approximately 25% of the subcategories are not addressed in any of the textbooks, showing that several key evolution ideas are still missing in these basic educational resources. Our results suggest that, although textbooks explore more evolution key ideas than those explicitly mentioned in the oficial curricula for basic education in Portugal, several evolution key ideas are still missing or are scarcely mentioned, highlighting the importance of being explicitly addressed in the official curricula.

Presented by Xana Sá Pinto

Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal

The Azores offers a unique stage for studying the impact of human-mediated processes on the genetic composition of honey bee populations. Through beekeeping activities, humans can shape gene pools directly, by selective breeding or by mediating gene flow between geographically isolated lineages, and indirectly, by introducing novel parasites and pathogens. These processes can change dramatically and rapidly in insular populations, due to their geographical isolation and their typically small effective population sizes. Recently, we performed a genetic survey of the Azorean honey bee populations (N=474) using a combination of mtDNA and SNP markers. This survey revealed a very heterogeneous composition across the archipelago, which has been shaped by historical and contemporary human-mediated processes. The most ubiquitous haplotypes (62%) were of African ancestry (sub-lineage AIII), supporting an introduction of the Iberian honey bee Apis mellifera iberiensis from the north of mainland Portugal during historical times. However, a tentative breeding program in the 1980s, involving the importation of honey bee queens from a highly divergent eastern European lineage (aka lineage C), associated with the accidental arrival of the dangerous ectoparasitic mite Varroa destructor in 2000, led to a dramatic change in the composition of populations from Pico, Faial and Graciosa and, to a lesser extent, from Terceira, São Miguel, Flores, and especially Santa Maria. The SNP and mitochondrial data were not concordant (r2=0.082). In São Miguel, most of the individuals did not show any signal of C-lineage introgression in the nuclear genome although 27% of the colonies harbored a C-lineage mitotype. Contrarily, in Terceira and São Jorge, C-lineage mitotypes were undetected, yet many individuals (84%) showed some level of nuclear introgression (0.050=Q-values=0.181). Graciosa, Pico, and Faial harbour the most introgressed population, as revealed by both markers, and the latter two islands are also colonized by V. destructor. Santa Maria harbours the best preserved population, with virtually no C-lineage introgression at both nuclear and mitochondrial compartments, and it is free of V. destructor. This is the first genetic study performed in the Azores, offering unique baseline data that can be used for better managing and preserving Azorean populations.

Presented by Dora Henriques

(1) Departamento de Genética, Universidad de Granada, Granada, Granada, Spain; (2) Departamento de Didáctica de las Ciencias, Universidad de Jaén, Jaén, Spain; (3) Department of Organismal Biology – Systematic Biology, Uppsala University, Uppsala, Sweden; (4) School of Biological Sciences, University of East Anglia, Norwich, UK.

B chromosomes are supernumerary and dispensable elements that are found in the genome of many eukaryotes in addition to the standard set of chromosomes, also known as A chromosomes. They often behave like genomic parasites for the host genome, but the true nature of this intragenomic conflict is still poorly understood. Here, we address this issue by means of a comprehensive RNA-seq experiment, comparing transcriptomes of B-carrying and B-lacking male and female embryos and adults, including legs and gonads, of the grasshopper Eyprepocnemis plorans. The results showed that B chromosome presence is associated with gene expression changes for a high number of A chromosome genes, in addition to those inherent to the protein-coding genes located in the B chromosome. The highest number of differentially expressed genes (DEGs) due to B presence was found in gonads (ovary= 643 DEGs, testis= 306 DEGs), followed by embryos (female= 95 DEGs, male= 130 DEGs) and finally in hind legs (female= 81 DEGs, male= 36 DEGs). Furthermore, while B-carrying embryos showed a pronounced up-regulation of transposable elements (~38% of all DEGs), gene expression changes in B-carrying adults mainly involved protein-coding genes (~50%, considering both up- and down-regulations). In particular, these changes were more apparent in the ovary with ~36% of protein-coding DEGs showing down-regulation, a figure being only ~15% in testis. Moreover, we found a slight increase of DEGs in embryos that received a maternal B in respect to embryos which inherited a paternal B chromosome. These findings outline a scene in which the B chromosome in testis, where they are eliminated postmeiotically from spermatids, triggers fewer changes in gene expression than in ovaries. Finally, the meaning of the higher transcriptional effects of B chromosome presence on the ovary could entail a response to manage the B-drive that takes place in this organ for E. plorans, as these chromosomes show a transmission advantage during female meiotic drive during oogensis.

Presented by María Martín-Peciña

(1) CESAM – Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal; (2) GEAL – Grupo de Etnologia e Arqueologia a Lourinhã, Museu da Lourinhã, Lourinhã, Portugal

The vertebral column consists of repetitive skeletal elements, organized in homologous series, the vertebrae, and is of paramount importance for evolutionary analyses. Its standardization is regulated by an extremely conserved group of Hox genes that regulate embryonic development. From over 30,000 amniote species there are almost 10,000 reptiles that present a large variation of pre-sacral vertebral count. Mammals (Synapsida) and reptiles (Sauropsida) show great divergences in the plasticity of their axial development since the beginning of tetrapod evolution. Curiously, there is still no consensus on how to define cervical vertebrae. The more common definition is topological: all vertebrae anterior to the first vertebra connected to the sternum by a complete rib. Synapsids are an extremely typical example of conservation, with 7 cervical vertebrae. Exceptions include the genera Bradypus, Choloepus, and Trichechus. In the case of sauropsids, they have greater plasticity, reaching up to 72 cervical vertebrae in Elasmosaurus platyurus. However, they also demonstrate segmental conservation in the Crocodylia and Testudinata clades, with 9 and 8 cervical vertebrae, respectively. On the other hand, in birds they range from 10 in Nymphicus hollandicus to 25 cervical vertebrae in Cygnus. There are multiple studies centered on the variation of the vertebral count as a whole or on the conserved cervical regionalization of mammals. To clarify how cervical regionalization evolved over millions of years, we conducted a comprehensive survey of pre-sacral vertebral counts focusing on intraspecific and interspecific variations in more than 400 tetrapod taxa (extinct and extant). We mapped vertebral counts into amniotic phylogeny as well as into more detailed trees within the group. This allowed to test several hypotheses regarding the relationship between the number of presacral vertebrae vs: total size, total weight, and length of the neck. We also calculated intraspecific variation in order to find patterns of variation. Finally, we used embryos from 3 model species Gallus gallus, Anas platyrhincus, and Coturnix coturnix to analyze the frequency with which these meristic changes occurred. Our study demonstrates a substantial variation in the number of cervical vertebrae in some species of the most diverse groups of tetrapods, suggesting the absence of strong selection against intraspecific and interspecific changes in the number of cervical vertebrae. Contrary to the initial hypothesis, the inverse relationship between intraspecific variation and increase in cervical vertebrae numbers may be explained by developmental constrains that limit the intraspecific variation in long neck species.

Presented by Rita Martins  Eligible for best poster award

CE3C – centre for ecology, evolution and environmental changes, FCUL University of Lisbon, Lisbon, Portugal

Due to climate change, organisms are being increasingly exposed to longer and more intense periods of heat stress, which critically affect their life-history traits. Reproduction is generally more sensitive to high temperatures than survival, although most studies focus on the latter trait. This suggests that populations will be affected by climate change earlier than predicted by current knowledge. To test the influence of temperature on reproduction, we addressed how sub-lethal high temperatures affect this trait in Tetranychus urticae, a haplodiploid agricultural pest of great economic importance. Although several studies have tackled the effect of temperature on this species, as well as their reproductive behaviour, few have addressed the interaction temperature – reproductive behaviour. First, we measured fertility and survival of both sexes at high temperatures, to identify the temperature that critically impairs fertility but not survival. This is seen in females by decreased fecundity and in males by reduced ratio of female offspring. Results showed that 36 ºC best fits this condition, with males being more sensitive than females. Then, we measured how this temperature affected offspring paternity share, as the pattern of first male sperm precedence seen in this species may change when the first male is sterile due to temperature. Results suggest that this is the case. Moreover, females mated with sterilized males had higher remating eagerness, which led to restored offspring sex-ratio levels after they remated with fertile males. We also tested if, and how fast, sterilized males regain fertility once placed at an optimal temperature. Results indicate that there is no recovery at least after two days at an optimal temperature. This project thus provides new insights regarding the effects of climate change on reproductive traits in an important crop pest, paving the way to future studies in both sexual selection and adaptation to abiotic stresses.

Presented by Sofia Costa Eligible for best poster award

(1) EAWAG – Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland; (2) University of Jyväskylä, Finland

Human activity is a major driver of environmental change and can act as a significant evolutionary force. Although responses of organisms to anthropogenic changes are extensively studied, most work to date does not integrate responses of host-associated microbiomes, even though they can be a key determinant of host fitness. Chemical pollutants – often introduced to streams via wastewater treatment plant effluents – are pervasive anthropogenic stressors that can affect the fate of individuals, populations, and ecosystems. We use Asellus aquaticus, a freshwater isopod with high environmental tolerance, to study the impact of pollution on organismal fitness and to explore the hypothesis that gut-microbiome may mediate adaptation to environmental stress. We specifically aim to understand how wastewater contaminants, including chemical compounds and microbes, affect A. aquaticus’ performance and microbiome. Laboratory and semi-natural flume experiments revealed that chemical pollution can lead to mortality of the host at high concentrations, while more realistic concentrations affect growth and feeding rates (i.e. host performance). 16S amplicon sequencing of digestive tissues further revealed that exposure to wastewater can also alter composition of the gut microbiota. Our results provide insight into host-microbiome responses to anthropogenic change.

Presented by Elvira Lafuente

1 – Instituto Gulbenkian de Ciência, Oeiras, Portugal; 2 – ISPA-Istituto Universitário; 3 – Champalimaud Centre for the Unknown, Lisboa, Portugal; *PI and co-PI of the SocialFly Project, respectively

Dopamine is a neuromodulator that controls the formation of appetitive and aversive memories during the associative learning process. Mate-choice copying (MCC) is a type of associative learning during which females observe the mating interactions of other females and copy their choices. MCC is known to be regulated by dopamine but is unclear whether it depends on appetitive or aversive memories, as females can learn to copy preferences (appetitive memory) or rejections (aversive memory). As motivation is necessary for reproduction and appetitive learning increases motivation, MCC probably involves the formation of appetitive memories. To find out, we studied the role of appetitive (PAM) and aversive (PPL1) dopaminergic neurons in modulating MCC, in Drosophila melanogaster. We used transgenic lines to silence dopaminergic signalling in the PAM and PPL1 clusters. We compared the behaviour of transgenic with control flies. We found that PAM flies were incapable of MCC, unlike control flies. PPL1 flies also failed to learn but learned better than PAMs (although the sample size is small). This confirms that the formation of appetitive memories during MCC is certainly an adaptive mechanism. For this reason, there may be a smaller contribution from aversive memories, however, our study leaves this hypothesis still open.

Presented by Joana Marcos

(1) IGC – Instituto Gulbenkian de Ciência, Oeiras, Portugal

Background and objectives: Social networks can influence the ecology of gut bacteria shaping the species composition of the gut microbiome in humans and other animals. Gut commensals can also evolve and adapt at a reasonable pace when colonizing healthy hosts. Here, we aimed at assessing the impact of the host’s social regime on bacterial molecular evolution in the mammalian gut. Methodology: Using an in vivo experimental evolution approach, we investigated how the pattern of molecular adaptation of Escherichia coli colonizing the mouse gut is influenced by the host’s social environment. Results: We found high transmission rates of newly colonizing E. coli strains in mice inhabiting the same environment, with horizontal gene transfer (HGT) events between phylogenetic distinct E. coli strains being pervasive under these conditions. A simple population genetics model of mutation-selection-migration predicts that, after hundreds to thousands of generations of gut adaptation, the level of parallelism of evolutionary events is greatly enhanced in co-housed mice when compared to animals living asocially. Moreover, under a social regime, evolutionary events reach global higher frequencies and can lead to swamping of locally selected evolutionary events. Conclusions and implications: The observed pattern of mutation and HGT sharing under sociality is consistent with a massive role of migration shaping the adaptive evolution of new strains that invade the gut microbiomes of healthy hosts. Strong directional selection is observed, where fixation of alleles and swamping of locally selected evolutionary events are to be expected, which may have important implications for the spread of antibiotic resistant strains across mammalian microbiomes.

Presented by Nelson Frazão