Genomes reveal marked differences in the adaptive evolution between orangutan species

Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene

Neurodevelopmental and Epilepsy Phenotypes in Individuals With Missense Variants in the Voltage-Sensing and Pore Domains of KCNH5

Background and Objectives KCNH5 encodes the voltage-gated potassium channel EAG2/Kv10.2. We aimed to delineate the neurodevelopmental and epilepsy phenotypic spectrum associated with de novo KCNH5 variants.Methods We screened 893 individuals with developmental and epileptic encephalopathies for KCNH5 variants using targeted or exome sequencing. Additional individuals with KCNH5 variants were identified through an international collaboration. Clinical history, EEG, and imaging data were analyzed; seizure types and epilepsy syndromes were classified. We included 3 previously published individuals including additional phenotypic details.Results We report a cohort of 17 patients, including 9 with a recurrent de novo missense variant p.Arg327His, 4 with a recurrent missense variant p.Arg333His, and 4 additional novel missense variants. All variants were located in or near the functionally critical voltage-sensing or pore domains, absent in the general population, and classified as pathogenic or likely pathogenic using the American College of Medical Genetics and Genomics criteria. All individuals presented with epilepsy with a median seizure onset at 6 months. They had a wide range of seizure types, including focal and generalized seizures. Cognitive outcomes ranged from normal intellect to profound impairment. Individuals with the recurrent p.Arg333His variant had a self-limited drug-responsive focal or generalized epilepsy and normal intellect, whereas the recurrent p.Arg327His variant was associated with infantile-onset DEE. Two individuals with variants in the pore domain were more severely affected, with a neonatal-onset movement disorder, early-infantile DEE, profound disability, and childhood death.Discussion We describe a cohort of 17 individuals with pathogenic or likely pathogenic missense variants in the voltage-sensing and pore domains of Kv10.2, including 14 previously unreported individuals. We present evidence for a putative emerging genotype-phenotype correlation with a spectrum of epilepsy and cognitive outcomes. Overall, we expand the role of EAG proteins in human disease and establish KCNH5 as implicated in a spectrum of neurodevelopmental disorders and epilepsy.</p

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive

Evolutionary analysis of the genome load of loss-of-function variants and their contribution to immunodeficiencies

Human genomes have been found to harbor an unexpected number of ~100 loss-of-function (LoF) variants, with ~20 of them in an homozygous state, in most cases without a visible effect despite its potential truncation of proteins. This suggests that some of those variants should be neutral but also a fraction could be lethal alleles. In this work we study the implications of LoF variants in two different fields: in comparative genomics by exploring for the first time the mutational load of LoF variants segregating in 79 genomes belonging to six different great ape populations and its possible detrimental effects, and in medical genomics by its implication with other functional variants in 36 patients diagnosed with Common Variable Immunodeficiency, an heterogeneous disease with several genes implied in its etiology, using both monogenic and oligogenic models for this antibody deficiency.Recentment s'ha descobert que els genomes humans contenen unes inesperades ~100 variants que causen pèrdua de funció (LoF), ~20 de les quals es troben en homozigosi, sense causar cap efecte visible malgrat el seu potencial per esguerrar una proteïna. Això suggereix que algunes d'aquestes variants han de ser neutres, però també que una fracció podrien ser al·lels letals. En aquesta tesis estudiem les implicacions de les LoF variants en dos camps diferents: en la genòmica comparativa explorant per primer cop la carrega mutacional de les variants LoF segregant en 79 genomes que pertanyen a sis poblacions diferents de grans simis i els seus possibles efectes deleteris, i en el camp de la genòmica mèdica per la seva implicació, junt amb altres tipus de variants, en 36 pacients diagnosticats amb Immunodeficiència Comú Variable, una malaltia heterogènia amb varis gens implicats en la seva etiologia, utilitzant models monogènics i poligènics per estudiar aquesta deficiència d'anticossos

Evolutionary analysis of the genome load of loss-of-function variants and their contribution to immunodeficiencies

Human genomes have been found to harbor an unexpected number of ~100 loss-of-function (LoF) variants, with ~20 of them in an homozygous state, in most cases without a visible effect despite its potential truncation of proteins. This suggests that some of those variants should be neutral but also a fraction could be lethal alleles. In this work we study the implications of LoF variants in two different fields: in comparative genomics by exploring for the first time the mutational load of LoF variants segregating in 79 genomes belonging to six different great ape populations and its possible detrimental effects, and in medical genomics by its implication with other functional variants in 36 patients diagnosed with Common Variable Immunodeficiency, an heterogeneous disease with several genes implied in its etiology, using both monogenic and oligogenic models for this antibody deficiency.Recentment s'ha descobert que els genomes humans contenen unes inesperades ~100 variants que causen pèrdua de funció (LoF), ~20 de les quals es troben en homozigosi, sense causar cap efecte visible malgrat el seu potencial per esguerrar una proteïna. Això suggereix que algunes d'aquestes variants han de ser neutres, però també que una fracció podrien ser al·lels letals. En aquesta tesis estudiem les implicacions de les LoF variants en dos camps diferents: en la genòmica comparativa explorant per primer cop la carrega mutacional de les variants LoF segregant en 79 genomes que pertanyen a sis poblacions diferents de grans simis i els seus possibles efectes deleteris, i en el camp de la genòmica mèdica per la seva implicació, junt amb altres tipus de variants, en 36 pacients diagnosticats amb Immunodeficiència Comú Variable, una malaltia heterogènia amb varis gens implicats en la seva etiologia, utilitzant models monogènics i poligènics per estudiar aquesta deficiència d'anticossos

Non-Hodgkin lymphoma in pediatric patients with common variable immunodeficiency

Piquer Gibert, Monica et al.Common variable immunodeficiency (CVID) is a heterogeneous primary immunodeficiency associated with an increased risk of malignancy in adulthood, with lymphoma as one of the major causes of death. The aim of this study is to describe those malignancies detected in our cohort of pediatric CVID patients. We reviewed the clinical and laboratory data and the treatments and their outcomes in all pediatric CVID patients from our institution that developed a neoplasia. Four malignancies were diagnosed in three out of 27 pediatric CVID patients. Three malignancies were non-Hodgkin lymphoma (NHL) of B cell origin (mean age at diagnosis: 8 years old), and the remaining was a low-grade astrocytoma. Among NHL, two were mucosa-associated lymphoid tissue (MALT) lymphomas and one was associated with Epstein-Barr virus infection. NHL developed before CVID diagnosis in two patients. CVID patients showed different clinical phenotypes and belonged to different groups according Euroclass and Pediatric classification criteria.We gratefully acknowledge Ferran Casals for the genetic analyses supported by SAF2012-35025 grant from the Spanish Ministerio de Economía y Competitividad.Peer reviewe

Mutational load and loss of function variant diversity in great apes

Trabajo presentado en la XIII Jornada de Biologia Evolutiva, celebrada en Barcelona el 2 de julio de 2013.Humans have been recently shown to harbor an unexpectedly high number of polymorphic stop gain or loss codon mutations, frameshift indels and large deletions. Loss of function (LoF) variants are predicted to disrupt gene function, and these results suggest an important level of pathway robustness and gene redundancy in the human genome. We have analyzed the mutational load and performed a systematic research based on human gene annotations of the LoF variants in the Great Ape Genome Diversity Project dataset, including 73 whole-genome sequences from chimpanzee, bonobo, gorilla and orangutan populations. The site frequency spectrum (SFS) shows differences across the primate species, since it is shaped by the particular demographic history of each population. One common pattern of SFS, also seen in humans, is that missense variants are enriched relative to synonymous variants at the lower frequencies, because of the action of purifying selection. However the relative amount of nonsynonymous compared to synonymous variants shows differences across the different populations, related to the different efficiency of natural selection to remove detrimental mutations in each population as a consequence of more efficient purifying selection at larger population sizes. After applying stringent filters on mapping, sequence quality and gene annotation, we observed that the total number of polymorphic LoF variants per individual varies from similar estimates to the one hundred reported in humans up to two or three fold across primate species. Homozygous variants potentially producing a complete lack of function also follow this tendency. Because of their functional impact LoF variants accumulate at low frequencies, and the proportion of LoF to synonymous variants per individual correlates negatively with the Ne, concordant with the same findings on the overall mutational load. This high and seemingly excessive individual mutational load is found to proportionally increase with diversity and effective population size, suggesting that a fraction of LoF variants may not have an important functional effect. Enrichment analysis of genes with polymorphic LoF variants did not detect an accumulation of mutations in particular pathways and functional categories, and we found little sharing both at the gene, pathway or functional levels across ape species.N

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

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

Genomes reveal marked differences in the adaptive evolution between orangutan species

Abstract Background Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene. Results Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities. Conclusions We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies