Publications

Heterogeneity of dN/dS Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny

Journal of Molecular Evolution (2016)

Authors: B.D. Bitarello, R.S. Francisco, D. Meyer

Tags: allelic lineages antigen recognition site balancing selection dN/dS molecular evolution divergent allele advantage phylogenetics immunogenetics

The classical class I HLA loci of humans show an excess of nonsynonymous with respect to synonymous substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. Additionally, high polymporphism, linkage disequilibrium, and disease associations suggest that one or more balancing selection regimes have acted upon these genes. However, several questions about these selective regimes remain open. First, it is unclear if stronger evidence for selection on deep timescales is due to changes in the intensity of selection over time or to a lack of power of most methods to detect selection on recent timescales. Another question concerns the functional entities which define the selected phenotype. While most analyses focus on selection acting on individual alleles, it is also plausible that phylogenetically defined groups of alleles (“lineages”) are targets of selection. To address these questions, we analyzed how dN/dS ($ømega$) varies with respect to divergence times between alleles and phylogenetic placement (position of branches). We find that $ømega$ for ARS codons of class I HLA genes increases with divergence time and is higher for inter-lineage branches. Throughout our analyses, we used non-selected codons to control for possible effects of inflation of $ømega$ associated to intra-specific analysis, and showed that our results are not artifactual. Our findings indicate the importance of considering the timescale effect when analysing $ømega$ over a wide spectrum of divergences. Finally, our results support the divergent allele advantage model, whereby heterozygotes with more divergent alleles have higher fitness than those carrying similar alleles.

Publication

Mapping bias overestimates reference allele frequencies at the HLA genes in the 1000 genomes project phase I data

G3: Genes, Genomes, Genetics (2015)

Authors: D.Y.C. Brandt, V.R.C. Aguiar, B.D. Bitarello, K. Nunes, J. Goudet, D. Meyer

Tags: 1000 Genomes HLA mapping bias NGS immunogenetics

© 2015 Brandt et al.Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity.

Publication

Kiwi genome provides insights into evolution of a nocturnal lifestyle

Genome Biology (2015)

Authors: D. Le Duc, G. Renaud, A. Krishnan, M.S. Almén, L. Huynen, S.J. Prohaska, M. Ongyerth, B.D. Bitarello, H.B. Schiöth, M. Hofreiter, P.F. Stadler, K. Prüfer, D. Lambert, J. Kelso, T. Schöneberg

Tags: genome assembly comparative genomics adaptation dN/dS molecular evolution

Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.

Publication

HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms

Immunogenetics (2015)

Authors: R. dos Santos Francisco, S. Buhler, J.M. Nunes, B.D. Bitarello, G.S. França, D. Meyer, A. Sanchez-Mazas

Tags: adaptation HLA human populations natural selection immunogenetics balancing selection

Supertypes are groups of human leukocyte antigen (HLA) alleles which bind overlapping sets of peptides due to sharing specific residues at the anchor positions—the B and F pockets—of the peptide-binding region (PBR). HLA alleles within the same supertype are expected to be functionally similar, while those from different supertypes are expected to be functionally distinct, presenting different sets of peptides. In this study, we applied the supertype classification to the HLA-A and HLA-B data of 55 worldwide populations in order to investigate the effect of natural selection on supertype rather than allelic variation at these loci. We compared the nucleotide diversity of the B and F pockets with that of the other PBR regions through a resampling procedure and compared the patterns of within-population heterozygosity (He) and between-population differentiation (GST) observed when using the supertype definition to those estimated when using randomized groups of alleles. At HLA-A, low levels of variation are observed at B and F pockets and randomized He and GST do not differ from the observed data. By contrast, HLA-B concentrates most of the differences between supertypes, the B pocket showing a particularly high level of variation. Moreover, at HLA-B, the reassignment of alleles into random groups does not reproduce the patterns of population differentiation observed with supertypes. We thus conclude that differently from HLA-A, for which supertype and allelic variation show similar patterns of nucleotide diversity within and between populations, HLA-B has likely evolved through specific adaptations of its B pocket to local pathogens.

Publication

Projeto Genográfico e as Implicações da Popularização dos Estudos de Genealogia Gênica

Revista da Biologia (2009)

Authors: Bárbara Domingues Bitarello

Tags: dna genealogia gênica genográfico português

O Projeto Genográfico busca caracterizar a variabilidade genética da população mundial, baseando-se majoritariamente em dados genéticos de grupos indígenas isolados e, em menor escala, na participação voluntária de indivíduos interessados em entender suas origens. No entanto, as implicações deste conhecimento merecem ressalva, assim como é importante avaliar o grau de ilusão que está sendo gerado entre os leigos que buscam conhecer sua ancestralidade genética.