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1.
Sci Rep ; 13(1): 4947, 2023 03 27.
Artículo en Inglés | MEDLINE | ID: mdl-36973299

RESUMEN

A- and B-antigens are present on red blood cells (RBCs) as well as other cells and secretions in Hominoidea including humans and apes such as chimpanzees and gibbons, whereas expression of these antigens on RBCs is subtle in monkeys such as Japanese macaques. Previous studies have indicated that H-antigen expression has not completely developed on RBCs in monkeys. Such antigen expression requires the presence of H-antigen and A- or B-transferase expression in cells of erythroid lineage, although whether or not ABO gene regulation is associated with the difference of A- or B-antigen expression between Hominoidea and monkeys has not been examined. Since it has been suggested that ABO expression on human erythrocytes is dependent upon an erythroid cell-specific regulatory region or the + 5.8-kb site in intron 1, we compared the sequences of ABO intron 1 among non-human primates, and demonstrated the presence of sites orthologous to the + 5.8-kb site in chimpanzees and gibbons, and their absence in Japanese macaques. In addition, luciferase assays revealed that the former orthologues enhanced promoter activity, whereas the corresponding site in the latter did not. These results suggested that the A- or B-antigens on RBCs might be ascribed to emergence of the + 5.8-kb site or the corresponding regions in ABO through genetic evolution.


Asunto(s)
Hylobates , Pan troglodytes , Animales , Intrones/genética , Pan troglodytes/genética , Hylobates/genética , Macaca fuscata , Sistema del Grupo Sanguíneo ABO/genética , Sistema del Grupo Sanguíneo ABO/metabolismo , Células Eritroides/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos , Eritrocitos/metabolismo , Primates/genética , Antígenos/metabolismo
2.
Genes (Basel) ; 14(2)2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36833167

RESUMEN

The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.


Asunto(s)
Hominidae , Hormona de Crecimiento Humana , Hombre de Neandertal , Animales , Femenino , Embarazo , Hominidae/genética , Pan troglodytes/genética , Gorilla gorilla/genética , Hylobates/genética , Hombre de Neandertal/genética , Secuencia de Bases , Filogenia , Placenta , Hormona del Crecimiento , Hormona de Crecimiento Humana/genética , Primates/genética , Pongo/genética
3.
J Hered ; 114(1): 35-43, 2023 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-36146896

RESUMEN

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.


Asunto(s)
Genoma , Hylobates , Animales , Hylobates/genética , Bosques , Especies en Peligro de Extinción , Indonesia
4.
Genome Res ; 32(10): 1941-1951, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36180231

RESUMEN

Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication-mediated NAHR only accounts for a small fraction of events. Several genomic features, including gene density and repeat (e.g., LINE-1) content, might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising more than 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbon diversification and speciation.


Asunto(s)
Hominidae , Hylobates , Animales , Hylobates/genética , Genoma , Primates/genética , Inversión Cromosómica/genética , Cromosomas , Hominidae/genética
6.
PLoS One ; 17(3): e0264519, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35358199

RESUMEN

Gibbons (Family Hylobatidae) are a suitable model for exploring hybridization in pair-living primates as several species form hybrid zones. In Khao Yai National Park, Thailand, white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) are distributed parapatrically and hybridize in a narrow zone. Their phenotypic characteristics suggest limited inter-species gene flow, although this has never been assessed. To uncover the history and degree of gene flow between the two species, we studied the genetic structure of gibbons in the hybrid zone by analyzing fecal DNA samples, phenotypic characteristics, vocalizations and individuals' social status. We determined eight autosomal single nucleotide variant (SNV) loci, and mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes of 72 gibbons. We compared these markers with reference types of wild pureblood white-handed gibbons (n = 12) in Kaeng Krachan National Park and pureblood pileated gibbons (n = 4) in Khao Soi Dao Wildlife Sanctuary. Autosomal genotypic analyses confirmed the various levels of mixed ancestry for several adult gibbons with or without atypical phenotypic traits in Khao Yai National Park. In some other adult gibbons, the mixed ancestry was not detected in either autosomal SNVs or their phenotypic traits but the mtDNA. Both male and female adult hybrids formed reproductive units mainly with a phenotypic pureblood partner and many of them produced offspring. Taken together, our results suggest that once hybridization occurs, white-handed-pileated-gibbon hybrids can reproduce with either parental species and that the backcrossing and thus introgression may occur in successive generations, with no drastic changes in phenotypic appearance.


Asunto(s)
Hylobates , Reproducción , Animales , ADN Mitocondrial/genética , Femenino , Hibridación Genética , Hylobates/genética , Masculino
7.
Primates ; 63(1): 51-63, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34716489

RESUMEN

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.


Asunto(s)
Hylobates , Parques Recreativos , Animales , Hibridación Genética , Hylobates/genética , Tailandia
8.
Dev Psychopathol ; 34(2): 689-703, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-34924087

RESUMEN

We expand upon prior work (Gibbons et al., ) relating childhood stressor effects, particularly harsh childhood environments, to risky behavior and ultimately physical health by adding longer-term outcomes - deoxyribonucleic acid (DNA) methylation-based measures of accelerated aging (DNAm-aging). Further, following work on the effects of early exposure to danger (McLaughlin et al., ), we also identify an additional pathway from harsh childhood environments to DNAm-aging that we label the danger/FKBP5 pathway, which includes early exposure to dangerous community conditions that are thought to impact glucocorticoid regulation and pro-inflammatory mechanisms. Because different DNAm-aging indices provide different windows on accelerated aging, we contrast effects on early indices of DNAm-aging based on chronological age with later indices that focused on predicting biological outcomes. We utilize data from Family and Community Health Study participants (N = 449) from age 10 to 29. We find that harshness influences parenting, which, in turn, influences accelerated DNAm-aging through the risky cognitions and substance use (i.e., behavioral) pathway outlined by Gibbons et al. (). Harshness is also associated with increased exposure to threat/danger, which, in turn, leads to accelerated DNAm-aging through effects on FKBP5 activity and enhanced pro-inflammatory tendencies (i.e., the danger/FKBP5 pathway).


Asunto(s)
Experiencias Adversas de la Infancia , Metilación de ADN , Animales , Humanos , Adulto Joven , Niño , Adolescente , Adulto , Hylobates/genética , Envejecimiento/genética , ADN , Epigénesis Genética
9.
Heredity (Edinb) ; 127(3): 312-322, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34188193

RESUMEN

Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.


Asunto(s)
Hominidae , Hylobates , Animales , Hibridación Genética , Hylobates/genética , Filogenia
10.
Mol Biol Evol ; 38(9): 3972-3992, 2021 08 23.
Artículo en Inglés | MEDLINE | ID: mdl-33983366

RESUMEN

Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.


Asunto(s)
Centrómero , Hylobates , Animales , Centrómero/genética , ADN Satélite/genética , Hylobates/genética , Hibridación Fluorescente in Situ , Retroelementos/genética
11.
Proc Natl Acad Sci U S A ; 117(32): 19328-19338, 2020 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-32690705

RESUMEN

Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.


Asunto(s)
Genoma , Hylobates/genética , Retroelementos , Animales , Cromatina/genética , Evolución Molecular , Regulación de la Expresión Génica , Hylobates/clasificación , Mutagénesis Insercional , Secuencias Reguladoras de Ácidos Nucleicos , Especificidad de la Especie
12.
Virus Genes ; 55(3): 421-424, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30877415

RESUMEN

A novel gamma-retroviral sequence (7912 bp), inclusive of both partial 5' and 3' long terminal repeat regions, was identified from the brain of a black flying-fox (Pteropus alecto), Queensland, Australia. The sequence was distinct from other retroviral sequences identified in bats and showed greater identity to Koala, Gibbon ape leukaemia, Melomys burtoni and Woolly monkey retroviruses, forming their own phylogenetic clade. This finding suggests that these retroviruses may have an unknown common ancestor and that further investigation into the diversity of gamma-retroviruses in Australian Pteropus species may elucidate their evolutionary origins.


Asunto(s)
Quirópteros/virología , Hylobates/virología , Phascolarctidae/virología , Retroviridae/genética , Animales , Australia , Quirópteros/genética , Hylobates/genética , Virus de la Leucemia del Gibón/genética , Phascolarctidae/genética , Filogenia , Virus del Sarcoma del Mono Lanudo/genética
13.
Am J Phys Anthropol ; 168(2): 364-369, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30575018

RESUMEN

OBJECTIVES: Semenogelin 1 and 2 (SEMG1 and SEMG2) are known as semen coagulating proteins in primates with a repetitive structure of 60-amino acids. The number of repeats varies among species and is hypothesized to be related to the level of primate sperm competition. Gibbons until recently were thought to be monogamous primates, but it is now known that gibbon social structure is flexible. Thus, hypotheses of the relationship between the SEMGs evolution and mating systems were tested. MATERIALS AND METHODS: The sequences of the exon 2 of the SEMG1 and SEMG2 were obtained from 50 captive gibbons comprising six species belonging to three genera (Hylobates, Symphalangus, and Nomascus). Then we quantified the levels of polymorphism and estimated rates of protein evolution by calculating d N /d S ratio. RESULTS: Several mutations that create a premature stop codon in the SEMG1 and a reduction in the repeats of the SEMG2 in the genus Hylobates were observed and may alter the coding properties for these proteins. We also found different level of nucleotide diversity in each gene and between genera. Strikingly, in Nomascus leucogenys we discovered a high d N /d S ratio in the SEMG1 and SEMG2. The Nomascus SEMG2 also showed significantly lower nucleotide diversity than the other two genera. DISCUSSION: These results are consistent with the presence of a strong positive selection in the Nomascus lineage even if the exact selective forces acting on these genes are not yet conclusively known. We were not able to demonstrate, among gibbons, unambiguous relationships between the SEMGs evolution and mating systems.


Asunto(s)
Evolución Molecular , Hylobates/genética , Reproducción/genética , Proteínas de Secreción de la Vesícula Seminal/genética , Animales , Antropología Física , Femenino , Masculino
14.
Gene ; 678: 318-323, 2018 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-30096459

RESUMEN

Retrogenes are a class of functional genes derived from the mRNA of various intron-containing genes. PIPSL was created through a unique mechanism, whereby distinct genes were assembled at the RNA level, and the resulting chimera was then reverse transcribed and integrated into the genome by the L1 retrotransposon. Expression of PIPSL RNA via its transcription start sites (TSSs) has been confirmed in the testes of humans and chimpanzee. Here, we demonstrated that PIPSL RNA is expressed in the testis of the white-handed gibbon. The 5'-end positions of gibbon RNAs were confined to a narrow range upstream of the PIPSL start codon and overlapped with those of orangutan and human, suggesting that PIPSL TSSs are similar among hominoid species. Reporter assays using a luciferase gene and the flanking sequences of human PIPSL showed that an upstream sequence exhibits weak promoter activity in human cells. Our findings suggest that PIPSL might have acquired a promoter at an early stage of hominoid evolution before the divergence of gibbons and ultimately retained similar TSSs in all of the lineages. Moreover, the upstream sequence derived from the phosphatidylinositol-4-phosphate 5-kinase, type I, alpha 5' untranslated region and/or neighboring repetitive sequences in the genome possibly exhibits promoter activity. Furthermore, we observed that a TATA-box-like sequence has emerged by nucleotide substitution in a lineage leading to humans, with this possibly responsible for a broader distribution of the human PIPSL TSSs.


Asunto(s)
Proteínas Portadoras/genética , Perfilación de la Expresión Génica/métodos , Hominidae/genética , Análisis de Secuencia de ARN/métodos , Testículo/química , Animales , Línea Celular , Evolución Molecular , Células Hep G2 , Humanos , Hylobates/genética , Masculino , Filogenia , Activación Transcripcional
15.
Am J Phys Anthropol ; 167(1): 61-71, 2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-29737526

RESUMEN

OBJECTIVES: It has long been recognized that in gibbons both sexes disperse from the natal group. However, the fate of dispersed individuals was rarely documented. Here we provide the first detailed information on sex differences in dispersal patterns by analyzing the spatial genetic structure of a well-known white-handed gibbon (Hylobates lar) population. MATERIALS AND METHODS: Mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes, and autosomal microsatellite genotypes were determined for individuals of the Mo Singto study site, Khao Yai National Park, Thailand. Mantel tests for the three genetic marker types were performed for 17 gibbon groups comprising 23 adult males and 18 adult females. RESULTS: Significant positive Mantel correlations were observed for spatial distance and both autosomal microsatellite-based as well as Y-chromosomal haplotype-based genetic distance among adult males. Neighboring adult males tended to be genetically related and share Y-chromosomal haplotypes. Conversely, no significant Mantel correlations were observed either in autosomal microsatellites or mtDNA among adult females. DISCUSSION: Our results confirm, at a genetic level, hypotheses from long-term demographic observations that white-handed gibbon males of the Mo Singto population primarily disperse into adjacent groups. Instead, females disperse more opportunistically either to adjacent or more distant groups. This sex-specific difference reflects an apparent greater tolerance between males than between females. The higher tolerance of adult males allows the formation of stable multimale groups and facilitates male dispersal into an adjacent group. Stable multifemale groups have never been documented for white-handed gibbons probably due to feeding competition between females.


Asunto(s)
ADN Mitocondrial/genética , Hylobates/genética , Cromosoma Y/genética , Animales , Antropología Física , Femenino , Hylobates/clasificación , Masculino , Repeticiones de Microsatélite/genética , Tailandia
16.
Zool Res ; 39(5): 356-363, 2018 09 18.
Artículo en Inglés | MEDLINE | ID: mdl-29616678

RESUMEN

Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.


Asunto(s)
Hylobates/genética , Animales , Animales de Zoológico , Núcleo Celular/genética , China , Especies en Peligro de Extinción , Genes/genética , Hylobates/clasificación , Hibridación Fluorescente in Situ , Cariotipo , Cariotipificación , Mitocondrias/genética , Reacción en Cadena de la Polimerasa
17.
Mol Biol Evol ; 35(1): 159-179, 2018 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-29087487

RESUMEN

The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species tree even in presence of excessive incomplete lineage sorting. Concatenation, mp-est and SVDQuartets were unreliable when the species tree contains very short internal branches. Likelihood ratio test of gene flow suggests a small amount of migration from Hylobates moloch to H. pileatus, while cross-genera migration is absent or rare. Our results highlight the utility of coalescent-based methods in addressing challenging species tree problems characterized by short internal branches and rampant gene tree-species tree discordance.


Asunto(s)
Hylobates/clasificación , Hylobates/genética , Análisis de Secuencia de ADN/métodos , Algoritmos , Animales , Teorema de Bayes , Simulación por Computador , Evolución Molecular , Especiación Genética , Genética de Población/métodos , Genómica/métodos , Modelos Genéticos , Filogenia
18.
Genome Biol Evol ; 9(8): 2037-2048, 2017 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-28633494

RESUMEN

Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes.


Asunto(s)
Encéfalo/embriología , Regulación del Desarrollo de la Expresión Génica , Hominidae/embriología , Hominidae/genética , Animales , Secuencia de Bases , Secuencia Conservada , Epigenómica/métodos , Evolución Molecular , Silenciador del Gen , Gorilla gorilla/genética , Humanos , Hylobates/genética , Pan troglodytes/genética , Pongo pygmaeus/genética , Secuencias Reguladoras de Ácidos Nucleicos
19.
Virus Genes ; 53(2): 165-172, 2017 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28220345

RESUMEN

Is the origin of gibbon ape leukemia virus (GALV) human after all? When GALV was discovered and found to cause neoplastic disease in gibbons, it stimulated a great deal of research including investigations into the origins of this virus. A number of publications have suggested that the GALV progenitor was a retrovirus present in one of several species of South East Asian rodents that had close contact with captive gibbons. However, there are no published retroviral sequences from any South East Asian species to support this view. Here we present an alternative hypothesis that the origin of GALV is a virus closely related to Melomys burtoni retrovirus, and that this virus infected human patients in Papua New Guinea from whom biological material was obtained or in some way contaminated these samples. This material we propose contained infectious MbRV-related virus that was then unwittingly introduced into gibbons which subsequently developed GALV infections.


Asunto(s)
Hylobates/virología , Virus de la Leucemia del Gibón/genética , ARN Viral/genética , Infecciones por Retroviridae/genética , Animales , Humanos , Hylobates/genética , Virus de la Leucemia del Gibón/patogenicidad , Filogenia , Retroviridae/genética , Retroviridae/patogenicidad , Infecciones por Retroviridae/virología , Roedores/virología
20.
Sci Rep ; 6: 38302, 2016 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-27922051

RESUMEN

Urate oxidase (Uox) catalyses the first reaction of oxidative uricolysis, a three-step enzymatic pathway that allows some animals to eliminate purine nitrogen through a water-soluble compound. Inactivation of the pathway in hominoids leads to elevated levels of sparingly soluble urate and puts humans at risk of hyperuricemia and gout. The uricolytic activities lost during evolution can be replaced by enzyme therapy. Here we report on the functional and structural characterization of Uox from zebrafish and the effects on the enzyme of the missense mutation (F216S) that preceded Uox pseudogenization in hominoids. Using a kinetic assay based on the enzymatic suppression of the spectroscopic interference of the Uox reaction product, we found that the F216S mutant has the same turnover number of the wild-type enzyme but a much-reduced affinity for the urate substrate and xanthine inhibitor. Our results indicate that the last functioning Uox in hominoid evolution had an increased Michaelis constant, possibly near to upper end of the normal range of urate in the human serum (~300 µM). Changes in the renal handling of urate during primate evolution can explain the genetic modification of uricolytic activities in the hominoid lineage without the need of assuming fixation of deleterious mutations.


Asunto(s)
Hiperuricemia/genética , Mutación Missense , Urato Oxidasa/química , Ácido Úrico/química , Pez Cebra/metabolismo , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Sitios de Unión , Biocatálisis , Evolución Biológica , Cristalografía por Rayos X , Expresión Génica , Humanos , Hylobates/genética , Hylobates/metabolismo , Hiperuricemia/enzimología , Hiperuricemia/patología , Cinética , Macaca fascicularis/genética , Macaca fascicularis/metabolismo , Modelos Moleculares , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Urato Oxidasa/metabolismo , Ácido Úrico/metabolismo , Pez Cebra/genética
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