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primate evolution

Jieyi Xiong, Jiang Xi, Angeliki Ditsiou, Yang Gao, Jing Sun, Elijah D Lowenstein, Shuyun Huang, Philipp Khaitovich
Although splicing is widespread and evolves rapidly among species, the mechanisms driving this evolution, as well as its functional implications, are not yet fully understood. We analyzed the evolution of splicing patterns based on transcriptome data from five tissues of humans, chimpanzees, rhesus macaques, and mice. In total, 1,526 exons and exon sets from 1,236 genes showed significant splicing differences among primates. More than 60% of these differences represent constitutive-to-alternative exon transitions while an additional 25% represent changes in exon inclusion frequency...
February 14, 2018: Human Molecular Genetics
Jasmine N Baker, Jerilyn A Walker, Michael W Denham, Charles D Loupe, Mark A Batzer
Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey ( Saimiri ), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups...
2018: Mobile DNA
Mikel Arlegi, Aida Gómez-Robles, Asier Gómez-Olivencia
OBJECTIVES: Although integration studies are important to understand the evolution of organisms' traits across phylogenies, vertebral integration in primates is still largely unexplored. Here we describe and quantify patterns of morphological integration and modularity in the subaxial cervical vertebrae (C3-C7) in extant hominines incorporating the potential influence of size. MATERIALS AND METHODS: Three-dimensional landmarks were digitized on 546 subaxial cervical vertebrae from 141 adult individuals of Gorilla gorilla, Pan troglodytes, and Homo sapiens...
February 15, 2018: American Journal of Physical Anthropology
Shohei Kitano, Hikaru Kurasawa, Yasunori Aizawa
Transposons are major drivers of mammalian genome evolution. To obtain new insights into the contribution of transposons to the regulation of protein translation, we here examined how transposons affected the genesis and function of upstream open reading frames (uORFs), which serve as cis-acting elements to regulate translation from annotated ORFs (anORFs) located downstream of the uORFs in eukaryotic mRNAs. Among 39,786 human uORFs, 3,992 had ATG trinucleotides of a transposon origin, termed "transposon-derived upstream ATGs" or TuATGs...
February 15, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Charles L Nunn, David R Samson
OBJECTIVES: Primates vary in their sleep durations and, remarkably, humans sleep the least per 24-hr period of the 30 primates that have been studied. Using phylogenetic methods that quantitatively situate human phenotypes within a broader primate comparative context, we investigated the evolution of human sleep architecture, focusing on: total sleep duration, rapid eye movement (REM) sleep duration, non-rapid eye movement (NREM) sleep duration, and proportion of sleep in REM. MATERIALS AND METHODS: We used two different Bayesian methods: phylogenetic prediction based on phylogenetic generalized least squares and a multistate Onrstein-Uhlenbeck (OU) evolutionary model of random drift and stabilizing selection...
February 14, 2018: American Journal of Physical Anthropology
Hanitriniaina Rakotonirina, Peter M Kappeler, Claudia Fichtel
BACKGROUND: Species recognition, i.e., the ability to distinguish conspecifics from heterospecifics, plays an essential role in reproduction. The role of facial cues for species recognition has been investigated in several non-human primate species except for lemurs. We therefore investigated the role of facial cues for species recognition in wild red-fronted lemurs (Eulemur rufifrons) at Kirindy Forest. We presented adult red-fronted lemurs pictures of male faces from five species including red-fronted lemurs, three closely related species, white-fronted lemurs (E...
February 13, 2018: BMC Evolutionary Biology
Dorothy L Cheney, Robert M Seyfarth
Vocalizations are a pervasive feature of nonhuman primate social life, yet we know surprisingly little about their function. We review studies supporting the hypothesis that many primate vocalizations function to facilitate social interactions by reducing uncertainty about the signaler's intentions and likely behavior. Such interactions help to establish and maintain the social bonds that increase reproductive success. Compared with humans, songbirds, and a few other mammals, primates have small vocal repertoires that show little acoustic modification during development...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Ping Feng, Rui-Jian Luo
Among the five basic tastes (umami, sweet, bitter, salty and sour), the perception of bitterness is believed to protect animals from digesting toxic and harmful substances, thus it is vital for animal survival. The taste of bitterness is triggered by the interaction between bitter substances and bitter taste receptors, which are encoded by Tas2rs. The gene numbers vary largely across species to meet different demands. So far, several ligands of bitter receptors have been identified in primates. They also discovered that the selective pressure of certain bitter taste receptor genes vary across taxa, genes or even different functional regions of the gene...
February 20, 2018: Yi Chuan, Hereditas
Breno Frederico de Carvalho Dominguez Souza, Alexander König, Andrea Rasche, Ianei de Oliveira Carneiro, Nora Stephan, Victor Max Corman, Pia Luise Roppert, Nora Goldmann, Ramona Kepper, Simon Franz Müller, Christof Völker, Alex Junior Souza de Souza, Michele Soares Gomes-Gouvêa, Andrés Moreira-Soto, Andreas Stöcker, Michael Nassal, Carlos Roberto Franke, João Renato Rebello Pinho, Manoel do Carmo Pereira Soares, Joachim Geyer, Philippe Lemey, Christian Drosten, Eduardo Martins Netto, Dieter Glebe, Jan Felix Drexler
BACKGROUND & AIMS: All known hepatitis B virus (HBV) genotypes occur in humans and hominoid Old World nonhuman primates (NHP). The divergent Woolly Monkey HBV (WMHBV) forms another orthohepadnavirus species. The evolutionary origins of HBV are unclear. METHODS: We analyzed sera from 124 Brazilian monkeys collected during 2012-2016 for hepadnaviruses using molecular and serological tools and conducted evolutionary analyses. RESULTS: We identified a novel orthohepadnavirus species in capuchin monkeys (CMHBV)...
February 8, 2018: Journal of Hepatology
Teesta Naskar, Mohammed Faruq, Priyajit Banerjee, Massarat Khan, Rashi Midha, Renu Kumari, Subhashree Devasenapathy, Bharat Prajapati, Sanghamitra Sengupta, Deepti Jain, Mitali Mukerji, Nandini Chatterjee Singh, Subrata Sinha
Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates...
January 9, 2018: EBioMedicine
Vance Powell, Borja Esteve-Altava, Julia Molnar, Brian Villmoare, Alesha Pettit, Rui Diogo
Network theory is increasingly being used to study morphological modularity and integration. Anatomical network analysis (AnNA) is a framework for quantitatively characterizing the topological organization of anatomical structures and providing an operational way to compare structural integration and modularity. Here we apply AnNA for the first time to study the macroevolution of the musculoskeletal system of the head and neck in primates and their closest living relatives, paying special attention to the evolution of structures associated with facial and vocal communication...
February 5, 2018: Scientific Reports
Peter Parham, Lisbeth A Guethlein
Natural killer (NK) cells have vital functions in human immunity and reproduction. In the innate and adaptive immune responses to infection, particularly by viruses, NK cells respond by secreting inflammatory cytokines and killing infected cells. In reproduction, NK cells are critical for genesis of the placenta, the organ that controls the supply of oxygen and nutrients to the growing fetus. Controlling NK cell functions are interactions of HLA class I with inhibitory NK cell receptors. First evolved was the conserved interaction of HLA-E with CD94:NKG2A; later established were diverse interactions of HLA-A, -B, -C with killer cell immunoglobulin-like receptors...
February 2, 2018: Annual Review of Immunology
Michèle Gerbault-Seureau, Lauriane Cacheux, Bernard Dutrillaux
Amongst Cercopithecidae, the species of the Cercopithecini tribe underwent a very active chromosome evolution, principally by fissions, which increased their chromosome number up to 72. In contrast, all the species of Papionini have fairly similar karyotypes with 42 chromosomes. In animals, nucleolus organizer regions (NORs) are generally considered as instable structures, which frequently vary in size, number, and location at both infra- and interspecific levels. Although in Cercopithecinae the NORs, involved in breaks, exchanges, and translocations, behave like fragile sites in somatic cells, their number and location appear to be very stable between species...
January 31, 2018: Cytogenetic and Genome Research
José Z Abramson, Mª Victoria Hernández-Lloreda, Lino García, Fernando Colmenares, Francisco Aboitiz, Josep Call
Vocal imitation is a hallmark of human spoken language, which, along with other advanced cognitive skills, has fuelled the evolution of human culture. Comparative evidence has revealed that although the ability to copy sounds from conspecifics is mostly uniquely human among primates, a few distantly related taxa of birds and mammals have also independently evolved this capacity. Remarkably, field observations of killer whales have documented the existence of group-differentiated vocal dialects that are often referred to as traditions or cultures and are hypothesized to be acquired non-genetically...
January 31, 2018: Proceedings. Biological Sciences
Jesse W Young, Liza J Shapiro
The importance of locomotion to evolutionary fitness has led to extensive study of primate locomotor behavior, morphology and ecology. Most previous research has focused on adult primates, but in the last few decades, increased attention to locomotor development has provided new insights toward our broader understanding of primate adaptation and evolution. Here, we review the contributions of this body of work from three basic perspectives. First, we assess possible determinants on the timing of locomotor independence, an important life history event...
January 2018: American Journal of Physical Anthropology
Susan C Antón, Ripan S Malhi, Agustín Fuentes
Biological Anthropology studies the variation and evolution of living humans, non-human primates, and extinct ancestors and for this reason the field should be in an ideal position to attract scientists from a variety of backgrounds who have different views and experiences. However, the origin and history of the discipline, anecdotal observations, self-reports, and recent surveys suggest the field has significant barriers to attracting scholars of color. For a variety of reasons, including quantitative research that demonstrates that diverse groups do better science, the discipline should strive to achieve a more diverse composition...
January 2018: American Journal of Physical Anthropology
Charles G Danko, Lauren A Choate, Brooke A Marks, Edward J Rice, Zhong Wang, Tinyi Chu, Andre L Martins, Noah Dukler, Scott A Coonrod, Elia D Tait Wojno, John T Lis, W Lee Kraus, Adam Siepel
How evolutionary changes at enhancers affect the transcription of target genes remains an important open question. Previous comparative studies of gene expression have largely measured the abundance of messenger RNA, which is affected by post-transcriptional regulatory processes, hence limiting inferences about the mechanisms underlying expression differences. Here, we directly measured nascent transcription in primate species, allowing us to separate transcription from post-transcriptional regulation. We used precision run-on and sequencing to map RNA polymerases in resting and activated CD4+ T cells in multiple human, chimpanzee and rhesus macaque individuals, with rodents as outgroups...
January 29, 2018: Nature Ecology & Evolution
Carlos G Schrago, Beatriz Mello, Anieli G Pereira, Carolina Furtado, Hector N Seuánez
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...
January 2018: Ecology and Evolution
Aida Gómez-Robles
Studies of brain evolution tend to focus on differences across species rather than on variation within species. A new study measures and compares intraspecific variation in macaque and human brain anatomy to explore the effect that short-term diversity has on long-term evolution.
January 17, 2018: Trends in Cognitive Sciences
Catalina I Villamil
Phenotypic integration and modularity represent important factors influencing evolutionary change. The mammalian cervical vertebral column is particularly interesting in regards to integration and modularity because it is highly constrained to seven elements, despite widely variable morphology. Previous research has found a common pattern of integration among quadrupedal mammals, but integration patterns also evolve in response to locomotor selective pressures like those associated with hominin bipedalism. Here, I test patterns of covariation in the cervical vertebrae of three hominoid primates (Hylobates, Pan, Homo) who engage in upright postures and locomotion...
January 23, 2018: Evolution; International Journal of Organic Evolution
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