A Molecular Phylogeny of Living Primates

Perelman, Polina L.; Johnson, Warren E.; Roos, Christian; Seuánez, Héctor N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody E.; Rumpler, Y.; Schneider, Maria Paula Cruz; Silva, Artur M. S.; O’Brien, Stephen J.; Pecon-Slattery, Jill

doi:10.1371/journal.pgen.1001342

Cited by 1,206 publications

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References 77 publications

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“…From this it was proposed that LCVs have coevolved with the host, but some evidence of interspecies virus transfer was also apparent (63,64). The extensive differences between ma-EBNA1 and hu-EBNA1 (outside of the Cterminal domain) suggest that EBNA1 has undergone subfunctionalisation since the separation of Old and New World primates 43 MYA.…”

Section: Discussionmentioning

confidence: 99%

Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1

2014

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Abstract:Epstein-Barr virus (EBV) is a clinically important human virus associated with several cancers and is the etiologic agent of infectious mononucleosis. The viral nuclear antigen-1 (EBNA1) is central to the replication and propagation of the viral genome and likely contributes to tumourigenesis. We have compared EBNA1 homologues from other primate lymphocryptoviruses (LCV) and found that the central glycine/alanine repeat (GAr) domain, as well as predicted cellular protein (USP7 and CK2) binding sites are present in homologues in the Old World primates, but not the marmoset; suggesting that these motifs may have co-evolved. Using the resolved structure of the C-terminal one third of EBNA1 (homodimerisation and DNA binding domain), we have gone on to develop monomeric and dimeric models in silico of the full length protein.The C-terminal domain is predicted to be structurally highly similar between homologues, indicating conserved function. Zinc could be stably incorporated into the model, bonding with two N-terminal cysteines predicted to facilitate multimerisation. The GAr contains secondary structural elements in the models, while the protein binding regions are unstructured, irrespective of the prediction approach used and sequence origin. These intrinsically disordered regions may facilitate the diversity observed in partner interactions. We hypothsise that the structured GAr could mask the disordered regions, thereby protecting the protein from default degradation. In the dimer conformation, the C-terminal tails of each monomer wrap around a proline-rich protruding loop of the partner monomer, providing dimer stability, a feature which could be exploited in therapeutic design. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation EBV-B95-8 hu-EBNA1CyEBV-TsBB6 cy-EBNA1 CeHV15 rh-EBNA1CeHV12 ba-EBNA1 CalHV3 ma EBNA1Modelling the structure of full length Epstein-Barr Virus Nuclear Antigen Figure S2. EBNA1 model comparison.The EBV B95-8 EBNA1 sequence was input to I-TASSER, which selected the EBNA1 C-terminal domain crystal structure (1B3T) and several fragment templates comprising: yeast fatty acid synthetase (2PFF), a-L-fucosidase (2Z8X), photosynthetic reaction centre (1C51), type A collagen (1YOF) and dimeric 6-phosphoglucouronate dehydrogenase (2ZYD). The 1B3T template was also used to generate models in MOE. EBNA1 models constructed using I-TASSER and MOE (and the composite of these two generated in Modeller9v8 (shown above), were assessed for structural plausibility using Molprobity and QMEAN score servers (table S1). Models were superimposed over the template (1B3T) and RMSD was estimated for each. The qualitative model energy analysis, normalised (QMEANnorm) score of a protein structural model provides a composite scoring function based on several geometrical aspects, both global (for the entire structure) and local (per residue), enabling the discrimination of good and bad models. The human and other primate LCV EBNA1 protein structure models (as indicated) were ...

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Section: Discussionmentioning

confidence: 99%

Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1

2014

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“…In earlier analyses of morphological and molecular data, all supported that the African colobine forms a monophyletic clade [1,12,19], grouping Piliocolobus, Procolobus, and Colobus together [17][18][19][24][25][26]29,30] (Figure 3). Interestingly, a recent phylogenetic analyses of 83 mobile elements from Roos et al [19] indicated a closer association of the Procolobus/Piliocolobus clade to Asian colobines than to Colobus, a relationship that was not rejected by nuclear sequence data in their study, leading them to propose African colobines paraphyly hypothesis ( Figure 3(e)).…”

Section: Phylogeny Of African Colobinaementioning

confidence: 88%

“…In comparison, Figure 3 Hypotheses of phylogenetic relationships among Colobine genera. Trees were reconstructed based on (a) 12 protein-coding mt genes (10 kb) [17]; (b) fragment of X-chromosome (4.3 kb) [26] and 54 nuclear genes (35 kb) [18]; (c) complete cytb gene (1.8 kb) [30] and 7 mt genes (6.1 kb) [29]; (d) 15 mt genes and 43 nuclear genes (42 kb) [25], 44 nuclear non-coding genes (23 kb) [31]; (e) 83 mobile elements [19]; (f) nuclear genes (13 kb) [19]; (g) complete mt genomes (16.5 kb) [31].…”

Section: Phylogeny Of Asian Presbytinamentioning

confidence: 99%

“…Understanding the true evolutionary history of the colobine monkeys, therefore, becomes an important field and has received special attention. However, due to the fact that nearly all the extant colobine genera diversify from one another within a four-million-year window [17][18][19], attempts to clarify relationships among these colobine genera have encountered challenges.…”

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Summary of phylogeny in subfamily Colobinae (Primate: Cercopithecidae)

Wang

Zhang

2013

Chin. Sci. Bull.

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The phylogeny of the colobine monkeys has a complex evolutionary history, evolving several distinct radiations and owned a wide range of forest and woodland habits in tropical Africa and in southern and eastern Asia. Understanding the true evolutionary history of the colobine monkeys becomes an important field and has received special attention. In this article, we review phylogeny of Colobinae based on previous fossil, cytological, morphological and molecular evidence and indicate the phylogenetic controversies. This review is expected to guide the future research of Colobinae phylogeny, and also provide theoretic evidence for the conservation of these highly endangered and unique primates. Colobinae, phylogeny, Asian presbytina, African colobinae Citation:Wang X P, Zhang Y P, Yu L. Summary of phylogeny in subfamily Colobinae (Primate: Cercopithecidae).

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“…Conversely, the chromosome complement of Neotropical primates (NP) underwent a dramatic karyotypic shuffling during the evolutionary divergence of these species (Stanyon et al., 2008), which took approximately 40 million years (Perelman et al., 2011; Schrago, 2007). Differently from hominids, chromosome diploid number varies sharply in NP, ranging from 16 in Callicebus lugens (Bonvicino et al., 2003) to 62 in Brachyteles arachnoides and Lagothrix lagotricha .…”

Section: Introductionmentioning

confidence: 99%

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

Schrago

Mello

Pereira

et al. 2017

Ecology and Evolution

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Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.

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A Molecular Phylogeny of Living Primates

Cited by 1,206 publications

References 77 publications

Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1

Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1

Summary of phylogeny in subfamily Colobinae (Primate: Cercopithecidae)

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

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