Pigmentation patterns in Rajidae (class Chondrichthyes): the genetic basis of spots revealed by transcriptome analysis

Ferrari, A.1, 2, Leslie, R.3, Scarcella, G.4, Cariani, A.1, Tinti, F.1 and Salzburger, W.2

1 Dept. BiGeA, University of Bologna, Italy
2 Zoological Institute, University of Basel, Switzerland
3 Dept. of Environmental Affairs&Agriculture, Forestry and Fisherie of Cape Town, Rep. of South Africa
4 CNR-ISMAR, Ancona, Italy

Animal patterning has always been investigated as one of the possible drivers involved in the enigmatic mechanism of speciation. However, the molecular basis of skin pigmentation and its adaptive meaning are still poorly investigated. Therefore, this topic is one of the most intriguing among Evolutionary biologists. Skates are bottom dwelling cartilaginous fishes inhabiting worldwide oceans and whose phylogeographic structures were widely influenced by hydro-geographical isolation resulting from paleo-climatological events. Some recently diverged species show a strikingly stable external morphology and particular dorsal patterning which could have been implicated with cryptic speciation events. In order to investigate the genetic basis of eyespots in skates, we performed transcriptomic profiling of different skin tissues from five nominal species. More specifically, we first conducted Illumina based RNA-sequencing of different skin pattern motifs of (i) recently diverged species in comparison to their sibling species (Raja clavata, R. straeleni and R. asterias respectively) and (ii) species showing a convergent pigmentation and strong monophyly (the Mediterranean R. miraletus and the South African R. ocellifera). We then assembled a reference transcriptome of R. miraletus based on Ion Torrent NGS. This enabled us to quantify differential gene expression between species and eyespot patterns. Our results provide the basis for examining the connection between pigmentation patterns in skates and their diversification.

Hurdles out of Africa: how climate shaped the history of human migrations

Eriksson A.

Department of Zoology, University of Cambridge, UK, Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal (KAUST), Saudi Arabia

Geographic and environmental factors shape migrations, population bottlenecks and local movements of individuals, and thereby the patterns of genetic variation within a species. For humans, large ethnically and geographically diverse genetic datasets have recently become available, including a rapidly increasing number of ancient samples. However, the richness of data presents challenges to methods aimed at analysing differences between small numbers of populations. I will discuss how spatially explicit models and Bayesian methods of inference can be used to address some of these difficulties, using the influence of climate and geography on the spread of anatomically modern humans out of Africa into Eurasia and the Americas as a case study, as well as the current limitations of this approach and how they might be addressed. Finally, as humans expanded out of Africa they encountered environments that differed dramatically from those where our species originated. This would have presented both challenges and opportunities, and set the stage for adaptation. However, the effects of specific adaptations on genetic variation can be confounded by the general demographic response to the new environments, such as local population bottlenecks. I will discuss how climate-informed spatial models can help to disentangle these factors by providing clear signatures of different forms of selection in specific geographic contexts.

Lifestyle and DNA base composition in polychaetes

Tarallo A. 1, Gambi M.C. 1, D'Onofrio G. 1

1 Stazione Zoologica A. Dohrn, Napoli

A comparative analysis of polychaete species, classified as motile and low-motile forms, highlighted that the former were characterized not only by a higher metabolic rate (MR), but also by a higher genomic GC content. The fluctuation of both variables was not affected by the phylogenetic relationship of the species. Thus, present results further support that a very active lifestyle affects at the same time MR and GC, showing an unexpected similarity between invertebrates and vertebrates. In teleost, indeed, a similar pattern has been also observed comparing migratory and non-migratory species. Till now a cause–effect link between MR and GC has not been proved yet, but the fact that the two variables are significantly linked in all the organisms so far analyzed is, most probably, of relevant biological and evolutionary meaning. Present results fit very well within the frame of the metabolic rate hypothesis proposed to explain the DNA base composition variability among organisms. On the contrary, the thermostability hypothesis was not supported. At present, no data about the recombination rate in polychaetes were available to test the biased gene conversion (BGC) hypothesis.

Rapid adaptive phenotypic change following colonization of a newly restored habitat

Lo Cascio Sætre C., Coleiro C., Austad M., Gauci M., Sætre G.P., Voje K.L. and Eroukhmanoff F.

Real-time observation of adaptive evolution in the wild is rare and limited to cases of dramatic, often anthropogenic, environmental change. Here, we present the case of a small population of reed warblers (Acrocephalus scirpaceus) over a period of 19 years (1996 – 2014) after colonizing a restored wetland habitat in Malta. Our data show that body mass has decreased in the population, following a trajectory consistent with a population ascending an adaptive peak, a so-called Ornstein-Uhlenbeck process. We corroborate these findings with genetic and ecological data, revealing that individual survival is correlated with body mass, and more than half of the variation in mean-population fitness is explained by variation in body mass. Despite a small effective population size, an adaptive response has taken place within a decade. A founder event from a large, genetically variable source population to the southern range margin of the reed warbler distribution likely facilitated this process.

Episodic Positive Selection drove the evolution of Old World Arenaviruses

Forni D.1, Pontremoli C. 1, Mozzi A. 1, Cagliani R. 1, Sironi M. 1

1 Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy

Arenaviruses can be divided into two groups, New world (NW) and Old World (OW) arenaviruses. OWA include Lassa virus (LASV), which causes human hemorragic fevers, and lymphocytic choriomeningitis virus (LCMV), an agent of acute central nervous system disease and congenital malformations. Arenaviruses have a bisegmented negative-stranded RNA genome, which encodes four viral proteins with multiple functions. GP (glycoprotein) and NP (nucleoprotein) are encoded by the Small segment, L (polymerase) and Z (zinc finger) by the Large segment. We used branch-site tests to investigate the evolutionary history of these proteins (excluding the small Z protein) in a large subset of OW strains and species, selected to represent viruses sampled during distinct outbreaks. Data indicated that the L protein was a major selection target during OWA speciation, whereas NP was targeted by episodic positive selection during the speciation events that separated LCMV from the other OWA. Because a positive relation between LASV pathogenicity and codon adaptation index (CAI) was previously proposed, we also analyzed CAI (normalized to human CAI accounting for GC content and amino acid composition, nCAI) in OWA. Results showed that in all OWA the highest nCAI values are observed for L, the lowest for GP. Comparison among LASV strains sampled in different geographic locations (in turn possibly associated with varying virulence) and from distinct hosts (rodents and humans) were not suggestive of an association between CAI and disease severity. Moreover, non-pathogenic arenaviruses did not show lower nCAI values compared to LASV and LCMV. Our data suggest that CAI has little role in determine virulence in OWA and that, in analogy to other RNA viruses, non-structural proteins represent major targets of adaptive evolution.

Identification of selective sweeps in domesticated apple (Malus x domestica Borkh.)

Kerschbamer E., Bianco L., Cestaro A., Feurtey A., Giraud T., Troggio M., Micheletti D.1

1Fondazione Edmund Mach

Domesticated apple is one of the most genetically polymorphic agricultural species. Studying the genetic diversity of the apple germplasm could provide important hints about the domestication process as giving a valuable resource for high resolution genetic mapping, QTL analysis and breeding programs. The availability of a chromosome scale genome assembly and the reduced costs of DNA sequencing have now made high resolution genetic characterization of crop germplasm feasible. In apple, the availability of whole genome re-sequencing (WGS) data, has allowed the study the genome-wide genetic variability patterns and the identifications of genomic regions that may have been selected during the process of plant domestication. For this study more than 70 apple cultivars representative of the European germplasm diversity and about ten wild Malus accessions were resequenced at high coverage (Illumina paired ends sequencing) and variant calling was performed. The identified SNPs (over 15 millions) were filtered for quality and to avoid repeated and paralogous regions. Additional filters (minor allele frequency and Hardy-Weinberg equilibrium) were applied to discard variants derived from genotyping errors. The SNPs that passed all quality filters were used to study the population structure and the genetic diversity. A weak stratification of the analyzed population emerged. This analysis also showed the presence of a high level of admixture. Two different approaches were used to identify selective sweeps. The first is based on site frequency spectrum as been implemented in SweeD. The second based on linkage disequilibrium patterns and the omega statistic as been implemented in OmegaPlus. Regions identified by both software were merged and used as candidate regions for positive selection.

Functional genomic analysis of adaptations to local environments

Moyerbrailean G., Isherwood J., Findley A., Pique-Regi R., Luca F.1

1Wayne State University

Polygenic variation in binding sites for distinct classes of transcription factors (TF) is suspected to have been a major target of evolutionary forces contributing to complex trait variation and local adaptations in humans. To test this hypothesis, we are still missing a complete catalog of regulatory variants in TF binding sites (TFBS) active across diverse tissues and environments. We predicted regulatory (r) SNPs in TFBS for 1,363 TFs and 653 tissues (ENCODE, RoadMap Epigenome). We intersected these annotations with gene expression response from RNA-seq data that we collected across 250 cellular environments. rSNPs were enriched for rare variants and depleted in core promoters, suggesting that rSNPs in these regions have a major impact on regulatory processes shared across tissues. Accordingly, rSNPs were 1.38-fold depleted in TFBS active in >50 tissues. Using a test similar to McDonald-Kreitman test we found evidence of positive selection in TFBS for 84 TFs, including TFs that regulate neuro-developmental processes. rSNPs in TFBS for 67 TFs were enriched for signals of adaption to local environments, in particular to Humid Tropical Ecoregion, Foraging Subsistence, and Solar Radiation. TFs with selection signals for 9 environments were also predictive of cellular response to environmental perturbations; for example, TFs with selection signals for Solar Radiation (Nhp6a and E2L1) predicted gene expression response to Vitamin D. These results suggest that adaptations occurred at TFBS, particularly for TFs that modulate response to environmental selective pressures, and resulted in changes of the gene expression and possibly organismal responses to environmental perturbations. Indeed, ATF factors were enriched for both selection signals related to plant/cereals based diets and for SNPs associated with blood cholesterol levels.

Towards understanding the genetic basis of mouth asymmetry in Perissodus microlepis

Raffini F.1, Fruciano C., Franchini P., Meyer A.

1University of Konstanz

A textbook example of adaptive evolution is mouth asymmetry in the scale-eating cichlid Perissodus microlepis, where individuals with left- and right-bending mouth are found in sympatry in approximately equal frequencies. Its morphological polymorphism is accompanied by lateralized foraging behavior, where left-bending fish preferentially feed on the scales of the right side of its prey fish, while the opposite is true for the right morph. This asymmetry has been proposed to be maintained by negative frequency-dependent selection. However, to clarify if this is the case, the genetic basis underlying this trait, which remains elusive, should be understood. To address this issue, we analyzed wild-caught fish using high-throughput DNA sequencing data (ddRAD and PoolSeq). We obtained more than 155,000 SNPs using ddRADseq, and 3,900,000 SNPs with PoolSeq. Among these, we identified one (ddRAD) SNP, and 38 or 378 (PoolSeq) windows whose allele frequency are statistically different between the left and right morph. This allowed us to uncover candidates genomic regions that potentially contain genes for this trait. Interestingly, we identified genes related to immunity, ion transporters and cell adhesion proteins. Immunity genes are known to be potent drivers of lineages differentiation in fish; the other genes are at the basis of the mechanism determining the early establishment of the left-right patterning during embryogenesis. Particularly, protocadherins are involved in neuronal network formation; they may play a central role in the formation of P. microlepis asymmetry, especially in behavioral lateralization. Our results suggest that mouth asymmetry in P. microlepis is likely to be influenced by multiple loci. These outcomes will contribute to understand the evolutionary processes driving adaptation and maintaining stable polymorphisms.

High resolution populations genomics reveals an extremely complex dynamics of early speciation in Afrotropical malaria vectors

Bottà G.1, Miles A. 2, Harding N.2, Caputo B.1, della Torre A.1, Kwiatkowski D.2 and the Anopheles Gambiae 1000 Genomes Consortium.

1Department of Public Health and Infectious Diseases, University of Rome La Sapienza
2Wellcome Trust Centre for Human Genetics, University of Oxford

The Anopheles gambiae complex is an established model system to study evolutionary dynamics between recently diverged species. The Anopheles gambiae 1000 Genomes Consortium made recently available an extraordinary genomic data resource consisting of 765 genomes sequenced at high coverage from 8 countries spanning Sub-Saharan Africa of the main malaria vectors An. gambiae and An. coluzzii. Here we report at a very fine scale level complex dynamics of early speciation forging the genomes in contrasting way, leading to various levels of reproductive isolation and to the establishment of two new hybrid forms at the opposite edges of the species range. One hybrid form was found in Guinea bissau and is characterised by prominent An. coluzzii ancestry and almost absent signatures of admixture on the autosomes, while displaying linked genomic blocks mostly of An. gambiae ancestry on the highly divergent centromeric region of the sexual chromosome X. The second hybrid form was unexpectedly found on the East coast, where only An. gambiae have been previously reported. We virtually described all possible directions a geographically non-homogenised early speciation process can take: i) local genomic divergence surrounded by homogeneity due to gene flow, ii) adaptive introgression events followed by the reestablishment of reproductive barriers, iii) reinforcement of reproductive barriers in sympatry, iv) origins of hybrid forms with local complete replacement of pure individuals.

analysis applied to time series of ancient genotype data reveals how medieval religious reform shaped the genomes of modern chickens.

Loog L.

University of Oxford

A number of statistical approaches have been developed in recent years to detect and quantify the strength of natural selection using modern genomic data. However, these approaches all have poor temporal resolution and limited power to detect selection acting on standing genetic variation. Ancient DNA allele frequency data provides the most direct and sensitive alternative for detecting selection at specific loci, and offers the possibility of resolving temporal variation in selection strength. However, ancient DNA sample sizes are typically small, and samples tend to be sparsely and unevenly distributed in space and time. In addition, all approaches are sensitive to confounding effects of demography. Here we present a Bayesian framework for reconstruction allele frequency trajectories through time from ancient allele frequency data that can explicitly accommodate the confounding effects of gene flow between populations and uncertainty in sample ages. We applied this method to ancient European domestic chicken genotype data from TSHR locus, which has been argued to be under strong and recent selection in domestic chickens. We find that the hypothesized sweep allele shows a pattern of strong selection starting 1100 years ago, coinciding with a European-wide known shift in poultry management between the mid-ninth to mid-eleventh century. This shift is associated with religious but also a legal rule that required people to abstain from quadruped meat, brought in as part of the Benedictine reform. This work directly highlights the importance of ancient DNA and statistical modeling for understanding how cultural practices in the past have shaped modern domesticated species.

Patterns of selection and introgression at protective wing colour pattern loci in
Heliconius butterflies

Moest M.1, Simon M. Martin H., Salazar C., D. Jiggins C.

1Institute of Ecology, University of Innsbruck

The tropical radiation of Heliconius butterflies has been intensively studied over many decades, in particular in the context of mimicry, speciation and adaptive introgression. These butterflies are Müllerian mimics and they signal their unpalatability to predators via conspicuous wing colour patterns. Recent evidence from a few case studies suggests that those protective colour patterns are also promiscuously shared among closely related Heliconius species and novel studies have identified regulatory elements underlying the different colour patterns. In my current project, I have prepared a dataset comprising targeted sequence capture and whole genome data for ca. 500 individuals to investigate the evolutionary history of the different colour pattern alleles, characterize selection on the non-coding element s regulating colour pattern variation, and test scenarios of adaptive introgression and hybrid trait speciation across the melpomene-clade. During this meeting, I aim to discuss and better understand appropriate methods to detect the, in some cases ancient and therefore subtle, signals of selection on these regulatory regions and their interpretation in the context of gene flow between species.

Sex dependent dominance et a single locus maintains variation in age at maturity in salmon.

Barson NJ1, Aykanat T, Hindar K, Baranski M, Bolstad GH, Fiske P, Jacq C, Jensen AJ, Johnston SE, Karlsson S, Kent M, Moen T, Niemelä E, Nome T, Næsje TF, Orell P, Romakkaniemi A, Sægrov H, Urdal K, Erkinaro J, Lien S, Primmer CR.

1Norwegian University of Life Sciences

The importance of balancing selection in maintaining variation in fitness-related traits, which are expected to be under strong selection, is a long-standing question in evolutionary biology. Males and females share many traits that have a common genetic basis, however, selection on these traits often differs between the sexes leading to sexual conflict and balancing selection. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, the specific loci underlying sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic diversity. We have identified a large effect locus controlling age at maturity in Atlantic salmon, an important fitness trait in which selection favours earlier maturation in males than females, and show it is a clear example of sex-dependent dominance reducing intralocus sexual conflict and maintaining adaptive variation in wild populations. Our results provide the first empirical example of dominance reversal permitting greater optimisation of phenotypes within each sex, contributing to the resolution of sexual conflict in a major and widespread evolutionary trade-off between age and size at maturity. Additionally, this knowledge will contribute to population management of Atlantic salmon, which has experienced reductions in age at maturity over much of its range, and potentially other exploited species where similar trends have been observed.

Adaptation and drift in the deep sea

Rus Hoelzel A.1, Gaither M. & Gkafas G.

1Biosciences, Durham University, South Road, Durham, DH1 3LE, UK

Species that live in deep water experience environmental variation in both horizontal and vertical dimensions. This study focused on multiple species in the genus Coryphaenoides, a deep water demersal lineage (the ‘grenadiers’) distributed in most oceans and living at depths ranging from ~500 to 5000m. We used genomic analyses to compare species within the genus and individuals along a depth gradient within a focal species, C. rupestris. We consider two potential habitat boundaries in the vertical dimension. The first is around 1 km depth, the base of the mesopelagic zone and where the thermocline ends in temperate regions, salinity levels off, and oxygen is at a minimum. We compared 60 C. rupestris genomes, one sequenced at 120X depth and annotated, and the rest sequenced at ~6X. Samples compared were distributed over a transect ranging from 800 to 1800m depth at the same geographic location. This revealed signals for selection correlated with depth, and the implications of fixed non-synonymous changes were investigated. The second boundary was across 4 km depth, the division between the bathypelagic zone and the abyss. For this we compared genomes from 14 species, 7 bathypelagic and 7 abyssal. We discuss results in the broader context of variation by both genetic drift and selection for these and related species in the deep sea.

genomics reveals environmental associated adaptive genetic variation in Atlantic salmon (
Salmo salar)

Barson N., Jacq C., Wang J., Sandve S.,, Karlsson S., Moen T., Kent M., Hindar K., Lien S.

Genotype-environment associations (GEA) are a potentially powerful way to identify adaptive genetic variation and have been increasingly applied to understand the genetics of adaptation in non-model organisms. We applied two Bayesian methods of GEA detection to genome-wide data from Atlantic salmon (LFMM and BayesEnv) that differ in their sensitivity to demographic structure and history and which control for population structure either simultaneously or consecutively to environmental association. We compared these results to a haplotype-based outlier approach for detecting loci under selection that controls for population structure using the relatedness tree (HapFLK). Atlantic salmon recolonised the Norwegian coast following the retreat of the glacial ice sheet. The resulting populations show a typical salmonid structure with a mixture of isolation-by-distance and strong population structuring that is historically and habitat contingent. Sampling was conducted to create pairs of populations inhabiting divergent environments across the latitudinal range of the sampling, such a design is predicted to maximise power to detect associations given the demographic history. Genotype-environment associations were conducted using a suite of variables from the world clim dataset and some salmon specific habitat features, such as flow rate and length of riverine migration. Our results are consistent with major signalling pathways and transcription factors being major targets of local adaptation in Atlantic salmon.

Adaptive regulatory evolution after whole genome duplication

Gareth G.1, Rohlfs R.2, SandveS.R. 1 and Hvidsten T.R.1

1Norwegian University of Life Sciences, Norway.
2San Francisco State University, USA,

The common ancestor of salmonid fish underwent an autotetraploidization event 80 Mya, making salmonids an excellent model system for studying the regulatory fate of gene duplicates after whole genome duplication. In the recently published Atlantic salmon genome paper, we used a tissue expression atlas to quantify expression divergence in approximately 8000 salmon duplicates and their non-duplicated orthologs in Northern pike. By utilizing comparable expression data from pike as a proxy for the ancestral state of pre-duplication tissue expression, we estimated that 28% of the salmon duplicates had undergone regulatory neofunctionalization compared to only 23 (<1%) cases of subfunctionalization. Relying only on the data from the genome paper, it was not possible to estimate the proportions of the regulatory neofunctionalization that was simply due to neutral drift (i.e. the beginning of pseudogenization) or adaptive regulatory evolution. To address this knowledge gap, we have now collected expression data for two additional diploid outgroups (Zebrafish and Medaka) and five additional duplicated salmonid species. These datasets offer the opportunity to analyse the evolution of gene expression in a phylogenetic context. To this end, we have used the EVE program to detect shifts in liver gene expression between each salmon duplicate and their orthologs in the phylogenetic tree. EVE estimates a likelihood ratio test statistic for expression shifts, allowing us to identify genes with significantly diverged expression. Preliminary results indicate that 17% of salmon duplicates contain one gene that has undergone an expression shift in liver, with up- and down-regulation being approximately equally likely (55% versus 45%, respectively). We are now aiming to consolidate our previous approach, based on correlation across tissues, with the phylogenetic approach, based on expression level changes (shifts), generalizing the phylogenetic approach to tissue atlas-type data.

Identifying selection and local adaptation in spatially structured populations

Siska V.1, Eriksson A., Manica A.

1University of Cambridge

The availability of large­scale, dense genomic data has facilitated the development of\nvarious statistical methods to detect signals of recent natural selection in the genome. However, selection scans using different methods and datasets often generate lists that have very few candidate regions in common, questioning whether many hits are false\npositives. Neutral demographic processes can leave signatures which are hard to distinguish from those of local selection, and might be a major confounding factor limiting\nour ability to detect selected loci. In this project, we use a spatially explicit model informed\nby past climate to reconstruct past population sizes, local movements, and range\nexpansions of Anatomically Modern Humans, and thus provide a realistic null demographic model against which the signature of geographically­localised selection can be detected. We parameterise our spatial model using patterns of genetic variation in modern human populations and ancient genomic data, and then use its predictions to how different methods behave on neutral markers, as well as under various modes of selection under such realistic complex demographies.