In silico peptide-binding predictions of MHC class I reveal similarities across distantly related songbird species, suggesting convergence on the level of protein function
Author(s): Westerdahl, H, Follin, E, Karlsson, M, Drews, A, Lundegaard, C, Nielsen, M, Wallin, S, Paulsson, K
Many songbirds have a large number of transcribed MHC class I genes compared to most mammals. To elucidate the reasons for this large number of genes and to search for non-classical MHC genes in songbirds, we compared songbird MHC class I alleles (α1-α3 domains). By applying phylogenetic analysis, homology modelling and in silico peptide-binding predictions, we could compare both functional and genetic relationships among transcribed genes. We found more pronounced clustering of the MHC class I allomorphs (allele-specific proteins) in regard to their protein function (peptide-binding specificities) compared to their genetic relationships (amino acid sequences), indicating that the high number of alleles is of functional significance.
The MHC class I allomorphs from house sparrow and tree sparrow, species that diverged ten MYA, had overlapping peptide-binding specificities. These similarities across species were also confirmed in phylogenetic analyses, and were similar for genes that we interpret as classical and non-classical. Remarkably, there were also overlapping peptide-binding specificities in the allomorphs from house sparrows and great reed warblers, although these species diverged about 30 MYA. This overlap was not found in a tree based on amino acid sequences. Our interpretation is that convergent evolution on the level of the protein function, possibly driven by selection from shared pathogens, has resulted in allomorphs with similar peptide-binding repertoires, although trans-species evolution in combination with gene conversion cannot be excluded.
Institute of Environmental Sciences
Evolution of MHC gene number: optimality hypothesis and beyond
Author(s): Radwan, J
MHC genes code for proteins involved in recognition of pathogens. Their extreme polymorphism, thought to be driven primarily by selection from parasites, has been subject of much theoretical and empirical work. In addition to allelic diversity, MHC genes are often multiplicated, but the evolution of the MHC copy number received relatively less attention. Optimality hypothesis (Nowak et al. 1992) poses that an increase in parasite recognition capabilities with increased number of MHC molecules expressed is traded off against higher rate of deletion of auto-reactive lymphocytes, thus some intermediate individual MHC diversity should be favoured. Empirical tests of this hypothesis have been hampered by technical difficulties associated with the typing of multi-locus genotypes, but this has now been overcome by new generation sequencing methods. I will review the recent empirical studies of the optimality hypothesis. The presence of multiple MHC genes in the genome may also facilitate creation of new alleles via inter-genic recombination (Ohta 1991). The results of simulations of host-parasite coevolution showed that such newly created alleles are very likely to be retained in populations. This opens the possibility for haplotypes with a high number of MHC copies to hitch-hike with positively selected alleles.
Centro de Biologia Ambiental
Evolution of olfaction in tubenose seabirds
Author(s): Silva, MC, Su, Q, Daugherty, S, Coelho, M, Silva, JC
The sense of olfaction is one of the most ancient senses with which vertebrates collect information about their surroundings, playing a critical role in survival and reproduction. We are extending the understanding of the evolution of the olfactory receptor (OR) genes in the avian group, by focusing on Procellariiform seabirds. This group has one of the largest relative olfactory bulb sizes among extant birds, and other anatomical features correlated with high olfactory capability. We built a cosmid library of Cory’s Shearwater (Calonectris diomedea) gDNA, which was screened with partial shearwater OR genes. 96 positive clones were sequenced with a combination of Sanger (cosmid ends), Illumina and 454 sequencing technologies. The resulting hybrid assembly has a cumulative length of 7.4Mb, including 399 unique scaffolds (2.6Mb), and ~ 21K degenerate scaffolds. A total of 144 ORFs (> 75 amino acids) have a significant similarity to OR genes, as determined with HMMs built from bird OR genes. Many are full length OR genes, and provide the basis for a comprehensive study of OR evolution in a lineage that relies extensively on olfaction. Preliminary phylogenetic analyses of shearwater, chicken, zebra finch and lizard OR genes revealed at least three distinct clades in Cory’s Shearwater. A few genes clustered with those of the remaining species in a clade, gamma, that predates the divergence of birds. However, most of the sampled shearwater genes belong to the avian-specific gamma-c clade, within which sequences cluster by species, consistent with a scenario of ubiquitous, lineage-specific expansions and/or the action of concerted evolution. Ongoing analyses will address the evolutionary history and genomic context of OR genes in this avian clade, namely the possible genomic association with MHC genes, as well as sequence diversity within and between clades, in particular in putative ligand-binding pockets encoded by shearwater-specific OR lineages.
Institut des sciences de l'évolution de Montpellier
Evolution of two multigene families involved in subspecies recognition and sexual isolation in the house mouse: insights from a transcriptomic and genomic perspective
Author(s): Loire, E, Boursot, P, Smadja, C
The two subspecies of the house mouse Mus musculus musculus and M. m. domesticus have evolved in allopatry for half a million years before meeting secondarily in Europe 5000 years ago, forming a narrow hybrid zone with unfit hybrids. Previous studies have shown that these incipient species recognise each other through signals present in urine and mate assortatively in the contact zone. This suggests a reinforcement process in this zone where prezygotic isolation would evolve as a response to selection against hybridisation. Our study addresses the genetic basis of sexual isolation between these two subspecies by analyzing divergence of two large multigene families involved in chemosensory recognition. On the signaling side, we focused on the Major Urinary Proteins (MUP), a cluster of more than 21 duplicated genes known to act as pheromones in the house mouse. On the reception side, we focused on their potential receptors, the vomeronasal receptors (VR), a very large multigene family composed of more than 200 genes, expressed in the vomeronasal organ of the mouse and known to be involved in pheromone recognition. Since assortative mating is displayed in the hybrid zone, we predicted strong sign of divergence between the two subspecies at our candidate families provided that they are involved in sexual isolation. Moreover, if reinforcing selection is acting on the mate recognition system in the hybrid zone, we expected a stronger signature of selection in the genomic regions baring VR and MUP genes in individuals of the hybrid zone as compared to individuals residing in allopatric zones of the distribution range. By combining several high-throughput genomic methods such as RNA-seq and exome sequencing, we tested these predictions and explored divergence affecting the VR and MUP gene families at the sequence, expression and structural levels.
Department of Pathology
Gene co-evolution in action: how genomic organisation impacts evolution of the adaptive immune system of jawed vertebrates
Author(s): Kaufman, J
A crucial part of the adaptive immune system of jawed vertebrates is recognition by T lymphocytes of pathogen components presented by molecules of the major histocompatibility complex (MHC). MHC genes often have high levels of allelic polymorphism and sequence diversity, thought to be due to an on-going arms race with pathogens. However, the strong genetic associations of humans are with autoimmune disease. Starting with the chicken MHC as a model, we have found that key features of the MHC genomic organisation and subsequent function differ between typical mammals and many (if not most) non-mammalian vertebrates. In particular, the chicken MHC is organised differently than typical mammals, which leads to haplotypes of polymorphic interacting genes, which in turn leads to single dominantly-expressed MHC class I and class II molecules, which finally leads to strong genetic associations with resistance and susceptibility to infectious pathogens. The salient features discovered for the chicken MHC are shared with many non-mammalian vertebrates and are likely ancestral, with the organisation of the typical mammalian MHC arising from an inversion. However, among jawed vertebrates there are at least two other functional strategies for the MHC which have arisen independently, and still others (like passerine birds) not well understood. The co-evolution between antigen processing and antigen presenting genes should mean that evolution is slower in chickens than in mammals, so we have tried to understand the molecular basis for function in an historic recombinant, and have screened many commercial chickens and other populations for such recombinants.
Evolutionary Ecology of Marine Fishes
Genetic signature of local adaptation of MHC genes to varying parasite pressures
Author(s): Eizaguirre, C, Lenz, TL, Kalbe, M, Milinski, M
Although crucial for the understanding of adaptive evolution, genetically resolved examples of local adaptation are rare. To maximize survival and reproduction in their local environment, hosts should resist their local parasites and pathogens. The major histocompatibility complex (MHC) with its key function in parasite resistance represents an ideal candidate to investigate parasite-mediated local adaptation. Using replicated field mesocosms, stocked with second-generation lab-bred three-spined stickleback hybrids of a lake and a river population, we show local adaptation of MHC genotypes to population-specific parasites, independently of the genetic background. Furthermore, the multi-locus specificity of MHC genes revealed that increased individual allele divergence of lake MHC genotypes allows lake fish to fight the broad range of lake parasites, whereas more specific river genotypes confer selective advantages against the less diverse river parasites. Such results demonstrate that not only the presence of given alleles is important for local adaptation but also that the combinations of alleles on the different duplicated loci are crucial for host-parasite coevolution.
Department of Systematics and Evolution
Genetic structure, selection and duplication in European eels MHC class II genes
Author(s): Wirth, T, Galan, M, Delgado, SF, Gilabert, A
Understanding adaptation and selection in populations facing environmental changes is a major concern. Our project aims to understand the adaptation and resilience of endangered catadromous European eel to increasing parasitic pressure. Anguilla anguilla has encountered successive waves of exotic invasive parasites, namely, the swimbladder nematode Anguillicoloides crassus. Infested individuals have high swimming performance costs; and might fail to complete the reproductive migration back to the Sargasso Sea. Prevalence of such parasites is much higher in the naive European populations compared to native Japanese hosts. However, the nature of the ongoing adaptation and impact on eel’s biology remain largely unknown. Given the role of Major Histocompatibility Complex (MHC) genes in host–parasite interactions, we designed specific primers to sequence 2 class II exons. Using NGS, we sampled alleles from 12 European populations (N = 120) collected throughout the species distribution range, as well as from one American population (N=10). Additional historical samples (1874) from Charente were included. Our results indicate success in isolating relevant MHC class II genes; we identified respectively 149 and 154 DAA and DAB MHC class II alleles. The multiple copy nature of the MHC loci was confirmed, with at least 4 and 5 gene copies for DAA and DAB loci, respectively. European and American eels were found to share the same allelic pool, a result in sharp contrast with microsatellite data, suggesting that balancing selection is acting on these genes while ancient polymorphisms is retained within the Atlantic lineages. There was no evidence for temporally fluctuating selection pressure. Finally, the eel MHC class II exons appeared to be under positive selection and at the upper range of rho and omega values in teleosts. These results suggest that recent duplications occurred in the genus that might have facilitated inter-locus recombination and high allelic diversity.
Comparative and Computational Genomics
Interplay of gene conversion and crossover in the molecular evolution of multigene families
Author(s): Hartasanchez, DA, Valles-Codina, O, Navarro, A
Multigene families are part of the pervasive Structural Variation (SV) present in eukaryotic genomes. In humans, regions with SV have been associated to disease and have been shown to participate in evolutionary innovation. Despite its widespread abundance and functional relevance, an accurate description of the underlying forces shaping the evolution of these regions is still lacking. In particular, the proper characterization of the interplay between mutation, crossover and gene conversion in multigene families is fundamental. We have developed a forward-time simulation program that incorporates duplications and focuses on the effect of concerted evolution (the non-independent evolution of duplicated regions). By means of simulations, we have explored a wide range of parameters, gaining insight into the evolution of regions under concerted evolution such as the MHC. First, we observe that neutral concerted evolution can confound scans for selection by mimicking the effects of both weak purifying selection or weak positive selection. These effects can be more pronounced if duplicated regions are collapsed, as is frequent in low-quality genome assemblies. Additionally, we explore the effects of crossover hotspots in duplicated regions that present gene conversion activity. Our results show that multigene-family evolution is highly dependent on the spatial distribution of crossover and gene conversion events and their rates, even under neutrality.
Animal and Plant Sciences
Linking chemosensory multigene-family evolution with speciation in the pea aphid (Acyrthosiphon pisum)
Author(s): Duvaux, L, Smadja, C, Ferrari, J, Zhou, J, Butlin, RK
Ludovic DUvaux, Carole Smadja, Julia Ferrari, Within and between species, multigene families (MF) are known to be highly diverse in terms of both Copy Number Variation (CNV) and allelic diversity. Accordingly, within and between population diversities of MF have a strong potential to result from, or to fuel, local adaptation – and possibly speciation. However, these diversities have seldom been contrasted and their relative evolutionary dynamics remain poorly understood. The host-plant races of the pea aphid provide an excellent system to understand these dynamics in the context of speciation with gene flow. Notably, Chemosensory MF (CMF) – e.g. Olfactory Receptors (OR), Gustatory Receptors (GR), Odorant Binding Proteins (OBP) – are critically important for specific host plant recognition, i.e. putatively a main cause of reproductive isolation. We sequenced 120 individuals from 8 races using a target enrichment protocol and Solexa sequencing – guaranteeing a median coverage of 150X. In doing so, we assessed CNV and nucleotidic diversity at about 3000 exons (from CMF, other MF and control genes) and 650 promoters of CMF genes. Preliminary results show CNV is widespread, as it occurs in 65% of all exons (even surprisingly up to 57% for control exons). As with SNPs in single copy genes, most CNV in non CMF genes is shared among races. In contrast, for targets linked to chemosensory genes – notably GR exons and promoters – CNV tends to structure by race. Also, the rate of duplication appears higher for CMF: OR, OBP and promoters show significantly more CNV than other MF. Together, these results suggest that many CMF genes may evolve under positive selection and contribute to adaptation to host plants. In order to better understand the genetic basis of adaptation, work is ongoing to link patterns of CNV (i) to the history of gene flow between races; and (ii) to observed differences in gene expression within and between races across native and non-native host plants.
Department of Integrative Ecology
Low genetic diversity in MHC loci in the critically endangered Iberian lynx
Author(s): Marmesat-Bertoli, E, Mazzoni, C, Soriano, L, Sommer, S, Godoy, JA
A central premise in Conservation Genetics is that genetic erosion occurring in declining populations reduces adaptive potential and compromises viability. However, functional variation is seldom assessed in endangered populations. Here we use the Major Histocompatibility Complex class I and II-DRB loci (MHC) as functional model loci to study the impact of the decline on Iberian lynx genetic variation, a species for which previous genetic studies have shown a strong decline in the neutral variation and concomitant fitness reductions.
We genotyped the most variable exon of MHC I and II-DRB genes in 300 individuals from the two extant wild and the captive populations using a 454 platform and a new pipeline analysis. We used transcriptomic and genomic data for primer design and expression analysis. Captive individuals, having a well-established pedigree, allowed us to infer composite haplotypes and to analyse segregation. We found a total of 13 and 6 alleles probably corresponding to 7 and 3 loci for MHCI and MHCII, respectively. One allele shows signals of pseudogenization and not all other alleles were confirmed to be expressed. In the case of MHCII, most individuals in the smallest and less diverse Doñana population show a three-allele profile, consistent with homozygosity at all three loci. Additionally global diversity levels for MCH_I and II are low compared to other felid species.
Our results suggest that the immune response in remnant Iberian lynx populations may be compromised and that the severe reduction and fragmentation may have eroded not only the neutral, but also the functional genomic diversity, thus compromising the evolutionary adaptive potential of the species.