Great ape genomics : diversity and evolution

Els grans simis són els nostres parents evolutius més propers i com a tals són la millor eina per entendre els nostres orígens més recents. Mitjançant la genòmica comparativa ara podem estudiar en profunditat aquesta qüestió, però la manca de genomes de grans simis no ha permès una anàlisi completa d’aquesta i d’altres qüestions relacionades amb la família Hominidae. En el context de la revolució de la seqüenciació, en aquesta tesi presento les meves contribucions en l’estudi de la genòmica de grans simis. Començant des de l’estudi de genomes individualment, faig un resum de les troballes més importants del panell més complet de genomes de grans simis, on vam incloure totes les espècies i la majoria de subespècies d’aquesta família i vam proporcionar una visió sense precedents en diversitat genètica, demografia i estructura de la població. També discuteixo les implicacions més rellevants d’aquest treball i com aquest pot ser una eina important en la conservació dels grans simis.Great apes are our closest relatives and as such they are our best resource to understand our recent origins. Through comparative genomics we can fully investigate this question, but the lack of great ape genomes have precluded to have a complete view on this and many other questions related to the Hominidae family. In the context of the current sequencing revolution, herein I present the contributions I have made in the study of great ape genomes. Starting from studies studying single genomes and following with the analysis of diversity in multiple great ape genomes, I summarize the findings in the most complete dataset of great ape genomes, covering all great ape species and most subspecies, providing an unprecedented view on diversity, demography and population structure in great apes. I finally discuss the most relevant implications of this work and how this can boost the conservation efforts in the protection of great apes

Labyrinthopeptins exert broad-spectrum antiviral activity through lipid-binding-mediated virolysis

To counteract the serious health threat posed by known and novel viral pathogens, drugs that target a variety of viruses through a common mechanism have attracted recent attention due to their potential in treating (re-)emerging infections, for which direct acting antivirals are not available. We found that labyrinthopeptins A1 and A2, the prototype congeners of carbacyclic lanthipeptides, inhibit the proliferation of diverse enveloped viruses, including Dengue virus, Zika virus, West Nile virus, Hepatitis C virus, Chikungunya virus, Karposi's Sarcoma-associated Herpes virus, Cytomegalovirus, and Herpes Simplex virus, in the low μM to nM range. Mechanistic studies on viral particles revealed that labyrinthopeptins induce a virolytic effect through binding to the viral membrane lipid phosphatidylethanolamine (PE). These effects are enhanced by a combined equimolar application of both labyrinthopeptins, and a clear synergism was observed across a concentration range corresponding to IC10-IC90 values of the compounds. Time-resolved experiments with large unilamellar vesicles (LUVs) reveal that membrane lipid raft compositions (PC/PE/Chol/SM (17:10:33:40)) are particularly sensitive to labyrinthopeptins compared to PC/PE (90:10) LUVs, even though the overall PE-amount remains constant. Labyrinthopeptins exhibited low cytotoxicity and had favorable pharmacokinetic properties in mice (t1/2= 10.0 h), which designates them as promising antiviral compounds acting by an unusual viral lipid targeting mechanism.Importance For many viral infections, current treatment options are insufficient. Because the development of each antiviral drug is time-consuming and expensive, the prospect of finding broad-spectrum antivirals that can fight multiple, diverse viruses - well-known as well as (re-)emerging species - has gained attention, especially for the treatment of viral co-infections. While most known broad spectrum agents address processes in the host cell, we found that targeting lipids of the free virus outside the host cell with the natural products labyrinthopeptin A1 and A2 is a viable strategy to inhibit the proliferation of a broad range of viruses from different families, including Chikungunya virus, Dengue virus, Zika virus, Karposi's Sarcoma-associated Herpes virus, or Cytomegalovirus. Labyrinthopeptins bind to viral phosphatidylethanolamine and induce virolysis without exerting cytotoxicity to host cells. This represents a novel and unusual mechanism to tackle medically relevant viral infections.Andreas Meyerhans and Javier P. Martinez were supported by a grant from the Spanish Ministry of Economy, Industry and Competitiveness and FEDER grant no. SAF2016-75505-R (AEI/MINEIC/FEDER, UE). Mark Brönstrup, Andreas Meyerhans and Javier P. Martinez would like to acknowledge a networking contribution from the COST Action CM1407 “Challenging organic syntheses inspired by nature – from natural products chemistry to drug discovery”. Martin Messerle and Thomas F. Schulz were supported by funding from DZIF (project 07.802 TTU IICH). Christine Goffinet, Thomas Pietschmann and Mark Brönstrup were supported by a grant provided by “Innovationsfonds der Helmholtz-Zentren”. Christine Goffinet was supported by a DFG grant within German African Cooperation Projects in Infectiology (GO2153/3-1) and by funding of the Helmholtz Center for Infection Research (HZI) and of Berlin Institute of Health (BIH). Sergej Franz was supported by the Infection Biology international PhD program of Hannover Biomedical Research Schoo

Characterization of nuclear mitochondrial insertions in the whole genomes of primates

The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various cellular pathways. Many previous studies have explored the impact of these insertions, referred to as NumtS, but have focused primarily on older events that have become fixed and are therefore present in all individual genomes for a given species. We previously developed an approach to identify novel Numt polymorphisms from next-generation sequence data and applied it to thousands of human genomes. Here, we extend this analysis to 79 individuals of other great ape species including chimpanzee, bonobo, gorilla, orang-utan and also an old world monkey, macaque. We show that recent Numt insertions are prevalent in each species though at different apparent rates, with chimpanzees exhibiting a significant increase in both polymorphic and fixed Numt sequences as compared to other great apes. We further assessed positional effects in each species in terms of evolutionary time and rate of insertion and identified putative hotspots on chromosome 5 for Numt integration, providing insight into both recent polymorphic and older fixed reference NumtS in great apes in comparison to human events.Funding: National Institutes of Health (1R01HG007068-01A1 to R.E.M). T.M.B is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880

Genetic load of loss-of-function polymorphic variants in great apes

Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species.The authors thank funding to F.C. by grant SAF2012-35025 from the Ministerio de Economía y Competitividad (Spain) and FEDER and by Direcció General de Recerca, Generalitat de Catalunya (2014SGR-866). T.M.B. is supported by EMBO YIP 2013, MINECO BFU2011-28549, BFU2014-55090-P (FEDER), BFU2015-7116-ERC and BFU2015-6215-ERC (www.mecd.gob.es), NIH U01 MH106874 grant and Fundació Zoo Barcelona

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.Supported by Royal Society grant RG130105 (A.S.), Wellcome Trust grants 098051 (Q.A., Y.C., V.N., L.P., M.A.Q., M.S., C.T.-S., Y.X., B.Y.) and 099769/Z/12/Z (V.N.), NIH grant HG002385 (E.E.E.), a European Research Council Starting Grant (260372), and Ministerio de Ciencia e Innovacion grant BFU2011-28549 (T.M.-B.

The interplay between DNA methylation and sequence divergence in recent human evolution

Despite the increasing knowledge about DNA methylation, the understanding of human epigenome evolution is in its infancy. Using whole genome bisulfite sequencing we identified hundreds of differentially methylated regions (DMRs) in humans compared to non-human primates and estimated that ∼25% of these regions were detectable throughout several human tissues. Human DMRs were enriched for specific histone modifications and the majority were located distal to transcription start sites, highlighting the importance of regions outside the direct regulatory context. We also found a significant excess of endogenous retrovirus elements in human-specific hypomethylated.We reported for the first time a close interplay between inter-species genetic and epigenetic variation in regions of incomplete lineage sorting, transcription factor binding sites and human differentially hypermethylated regions. Specifically, we observed an excess of human-specific substitutions in transcription factor binding sites located within human DMRs, suggesting that alteration of regulatory motifs underlies some human-specific methylation patterns. We also found that the acquisition of DNA hypermethylation in the human lineage is frequently coupled with a rapid evolution at nucleotide level in the neighborhood of these CpG sites. Taken together, our results reveal new insights into the mechanistic basis of human-specific DNA methylation patterns and the interpretation of inter-species non-coding variation.We acknowledge support from AGAUR (Generalitat de Catlunya, Spain) and the Barcelona Zoo (Ajuntament de Barcelona) for an award to I.H.H. H.H. is a Miguel Servet (CP14/00229) researcher funded by the Spanish Institute of Health Carlos III (ISCIII).T.M.B. and M.E. are ICREA Research Professors. Funding for open access charge: European Research Council (ERC), grant EPINORC, under agreement No. 268626; MICINN Projects—SAF2011-22803 and BFU2011-28549; Cellex Foundation; European Community's Seventh Framework Programme (FP7/2007-2013), grant HEALTH-F5-2011-282510—BLUEPRINT, and the Health and Science Departments of the Generalitat de Catalunya

Dynamics of DNA methylation in recent human and great ape evolution

DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified 800 genes with significantly altered methylation patterns among the great apes, including 170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics.TMB is supported by the European Research Council (ERC Starting Grant, StG_20091118) and the Spanish Government (BFU2011-28549). AJS is supported by NIH grants 1R01DA033660, 1R01HG006696, and a grant from the Alzheimer’s Association (2012ALZNIRG69983). IHH is supported by the European Social Fund, AGAUR (Generalitat de Catalunya, Spain) and the Spanish National Research Council (CSIC). We also thank the Spanish Government for the grant BFU2009-13409-C02-02 to AN and the Barcelona Zoo (Ajuntament de Barcelona) for an award to JPM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

Evolution and diversity of copy number variation in the great ape lineage

Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed 97 deeply sequenced great ape and human genomes and estimate 16% (469 Mb) of the hominid genome has been affected by recent CNV. We identify a comprehensive set of fixed gene deletions (n = 340) and duplications (n = 405) as well as >13.5 Mb of sequence that has been specifically lost on the human lineage. We compared the diversity and rates of copy number and single nucleotide variation across the hominid phylogeny. We find that CNV diversity partially correlates with single nucleotide diversity (r2 = 0.5) and recapitulates the phylogeny of apes with few exceptions. Duplications significantly outpace deletions (2.8-fold). The load of segregating duplications remains significantly higher in bonobos, Western chimpanzees, and Sumatran orangutans—populations that have experienced recent genetic bottlenecks (P = 0.0014, 0.02, and 0.0088, respectively). The rate of fixed deletion has been more clocklike with the exception of the chimpanzee lineage, where we observe a twofold increase in the chimpanzee–bonobo ancestor (P = 4.79 × 10−9) and increased deletion load among Western chimpanzees (P = 0.002). The latter includes the first genomic disorder in a chimpanzee with features resembling Smith-Magenis syndrome mediated by a chimpanzee-specific increase in segmental duplication complexity. We hypothesize that demographic effects, such as bottlenecks, have contributed to larger and more gene-rich segments being deleted in the chimpanzee lineage and that this effect, more generally, may account for episodic bursts in CNV during hominid evolution.P.H.S. is supported by a Howard Hughes International Student Fellowship.T.M.B. is supported by an ERC Starting Grant (260372). T.M.B. is an ICREA Research Investigator (Institut Catala d’Estudis i Recerca Avancats de la Generalitat de Catalunya). This work was supported, in part, by U.S. National Institutes of Health (NIH) grant HG002385 to E.E.E., BFU2009-13409-C02-02 to J.P.M., and MICINN (Spain) BFU2011-28549 to T.M.B. E.E.E. is an investigator of the Howard Hughes Medical Institut

Evolution and diversity of copy number variation in the great ape lineage

Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed 97 deeply sequenced great ape and human genomes and estimate 16% (469 Mb) of the hominid genome has been affected by recent CNV. We identify a comprehensive set of fixed gene deletions (n = 340) and duplications (n = 405) as well as >13.5 Mb of sequence that has been specifically lost on the human lineage. We compared the diversity and rates of copy number and single nucleotide variation across the hominid phylogeny. We find that CNV diversity partially correlates with single nucleotide diversity (r2 = 0.5) and recapitulates the phylogeny of apes with few exceptions. Duplications significantly outpace deletions (2.8-fold). The load of segregating duplications remains significantly higher in bonobos, Western chimpanzees, and Sumatran orangutans—populations that have experienced recent genetic bottlenecks (P = 0.0014, 0.02, and 0.0088, respectively). The rate of fixed deletion has been more clocklike with the exception of the chimpanzee lineage, where we observe a twofold increase in the chimpanzee–bonobo ancestor (P = 4.79 × 10−9) and increased deletion load among Western chimpanzees (P = 0.002). The latter includes the first genomic disorder in a chimpanzee with features resembling Smith-Magenis syndrome mediated by a chimpanzee-specific increase in segmental duplication complexity. We hypothesize that demographic effects, such as bottlenecks, have contributed to larger and more gene-rich segments being deleted in the chimpanzee lineage and that this effect, more generally, may account for episodic bursts in CNV during hominid evolution.P.H.S. is supported by a Howard Hughes International Student Fellowship.T.M.B. is supported by an ERC Starting Grant (260372). T.M.B. is an ICREA Research Investigator (Institut Catala d’Estudis i Recerca Avancats de la Generalitat de Catalunya). This work was supported, in part, by U.S. National Institutes of Health (NIH) grant HG002385 to E.E.E., BFU2009-13409-C02-02 to J.P.M., and MICINN (Spain) BFU2011-28549 to T.M.B. E.E.E. is an investigator of the Howard Hughes Medical Institut

Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions

The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.T.M-B is supported by ICREA (www.icrea.cat), EMBO YIP (www.embo.org) 2013, MINECO BFU2014-55090-P (FEDER), BFU2015-7116-ERC and BFU2015-6215-ERCU01 MH106874 grant, Fundacio Zoo Barcelona and Secretaria d'Universitats i Recerca del Departament d'Economia i/nConeixement de la Generalitat de Catalunya. S.T. was supported by the Young Researcher Fellowship (51000 Year 2010 and Unicredit 2013 Funds) from the University of Ferrar