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https://www.readbyqxmd.com/read/29290090/rates-of-gut-microbiome-divergence-in-mammals
#1
Alex H Nishida, Howard Ochman
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet...
December 31, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29285965/admixture-and-ancestry-inference-from-ancient-and-modern-samples-through-measures-of-population-genetic-drift
#2
Alexandre M Harris, Michael DeGiorgio
Methods that leverage the information about population history contained within the increasingly abundant genetic sequences of extant and extinct hominid populations are diverse in form and versatile in application. Here, we review key methods recently developed to detect and quantify admixture and ancestry in modern human populations. We begin with an overview of the f- and D-statistics, covering their conceptual principles and important applications, as well as any extensions developed for them. We then cover a combination of more recent and more complex methods for admixture and ancestry inference, discussing tests for direct ancestry between two populations, quantification of admixture in large data sets, and determination of admixture dates...
January 2017: Human Biology
https://www.readbyqxmd.com/read/29282311/a-cellular-microrna-facilitates-regulatory-t-lymphocyte-development-by-targeting-the-foxp3-promoter-tata-box-motif
#3
Yiwen Zhang, Weiwei Liu, Yingshi Chen, Jun Liu, Kang Wu, Lishi Su, Wanying Zhang, Yawen Jiang, Xu Zhang, Yijun Zhang, Chao Liu, Liang Tao, Bingfeng Liu, Hui Zhang
The CD4+CD25+FOXP3+ regulatory T cells (Tregs) mediate immunological self-tolerance and suppress various immune responses. FOXP3 is a key transcriptional factor for the generation and development of Tregs. Its expression is regulated by various cytokines including TGF-β, IL-2, and IL-10. It is important to further identify the regulatory factors for Tregs. Given that many microRNAs (miRNAs) could specifically interact with the core promoter region and specifically enhance the transcription of many target genes, we searched for any possible miRNA(s) targeting the core promoter region of the FOXP3 gene...
December 27, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29246655/the-c-305del3-in-il-2-gene-in-homonoidea-theoretically-affects-il-2-il-2r%C3%AE-interaction-as-well-as-lymphocyte-homeostasis
#4
Hamed Hosseinian, Karim Mahnam, Mostafa Shakhsi-Niaei
Interleukin-2 (IL-2) is a well-known monomeric T-cell growth factor that is produced primarily by activated CD4+ T cells following exposure to antigen. IL-2 structural analysis among primates showed a few polymorphisms as well as a 3-nucleotide deletion (c.305del3) in Hominoidea superfamily including Homo sapiens. On the other hand, the interaction of IL-2 with its alpha subunit of the receptor (IL-2Rα) is the first step for assembly of the whole IL-2R and considered as a species-specific phase. Four models of human IL-2, IL-2Rα, and their ancestral forms were made and were used for molecular dynamics (MD) simulation...
December 12, 2017: Cytokine
https://www.readbyqxmd.com/read/29187630/evolutionary-history-of-enigmatic-bears-in-the-tibetan-plateau-himalaya-region-and-the-identity-of-the-yeti
#5
Tianying Lan, Stephanie Gill, Eva Bellemain, Richard Bischof, Muhammad Ali Nawaz, Charlotte Lindqvist
Although anecdotally associated with local bears (Ursus arctos and U. thibetanus), the exact identity of 'hominid'-like creatures important to folklore and mythology in the Tibetan Plateau-Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region...
December 13, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29169316/coevolution-of-siglec-11-and-siglec-16-via-gene-conversion-in-primates
#6
Toshiyuki Hayakawa, Zahra Khedri, Flavio Schwarz, Corinna Landig, Suh-Yuen Liang, Hai Yu, Xi Chen, Naoko T Fujito, Yoko Satta, Ajit Varki, Takashi Angata
BACKGROUND: Siglecs-11 and -16 are members of the sialic acid recognizing Ig-like lectin family, and expressed in same cells. Siglec-11 functions as an inhibitory receptor, whereas Siglec-16 exhibits activating properties. In humans, SIGLEC11 and SIGLEC16 gene sequences are extremely similar in the region encoding the extracellular domain due to gene conversions. Human SIGLEC11 was converted by the nonfunctional SIGLEC16P allele, and the converted SIGLEC11 allele became fixed in humans, possibly because it provides novel neuroprotective functions in brain microglia...
November 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29163252/the-paradox-of-isochrony-in-the-evolution-of-human-rhythm
#7
Andrea Ravignani, Guy Madison
Isochrony is crucial to the rhythm of human music. Some neural, behavioral and anatomical traits underlying rhythm perception and production are shared with a broad range of species. These may either have a common evolutionary origin, or have evolved into similar traits under different evolutionary pressures. Other traits underlying rhythm are rare across species, only found in humans and few other animals. Isochrony, or stable periodicity, is common to most human music, but isochronous behaviors are also found in many species...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/29148040/the-endocranial-shape-of-australopithecus-africanus-surface-analysis-of-the-endocasts-of-sts-5-and-sts-60
#8
Amélie Beaudet, Jean Dumoncel, Frikkie de Beer, Stanley Durrleman, Emmanuel Gilissen, Anna Oettlé, Gérard Subsol, John Francis Thackeray, José Braga
Assessment of global endocranial morphology and regional neuroanatomical changes in early hominins is critical for the reconstruction of evolutionary trajectories of cerebral regions in the human lineage. Early evidence of cortical reorganization in specific local areas (e.g. visual cortex, inferior frontal gyrus) is perceptible in the non-human South African hominin fossil record. However, to date, little information is available regarding potential global changes in the early hominin brain. The introduction of non-invasive imaging techniques opens up new perspectives for the study of hominin brain evolution...
November 16, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29126115/hominid-a-framework-for-identifying-associations-between-host-genetic-variation-and-microbiome-composition
#9
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances. Using simulated data we show that HOMINID has accuracy in identifying associated SNPs, and performs better compared to existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs...
November 8, 2017: GigaScience
https://www.readbyqxmd.com/read/29109249/hominid-butchers-and-biting-crocodiles-in-the-african-plio-pleistocene
#10
Yonatan Sahle, Sireen El Zaatari, Tim D White
Zooarchaeologists have long relied on linear traces and pits found on the surfaces of ancient bones to infer ancient hominid behaviors such as slicing, chopping, and percussive actions during butchery of mammal carcasses. However, such claims about Plio-Pleistocene hominids rely mostly on very small assemblages of bony remains. Furthermore, recent experiments on trampling animals and biting crocodiles have shown each to be capable of producing mimics of such marks. This equifinality-the creation of similar products by different processes-makes deciphering early archaeological bone assemblages difficult...
November 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29103940/morphometric-behavioral-and-genomic-evidence-for-a-new-orangutan-species
#11
Alexander Nater, Maja P Mattle-Greminger, Anton Nurcahyo, Matthew G Nowak, Marc de Manuel, Tariq Desai, Colin Groves, Marc Pybus, Tugce Bilgin Sonay, Christian Roos, Adriano R Lameira, Serge A Wich, James Askew, Marina Davila-Ross, Gabriella Fredriksson, Guillem de Valles, Ferran Casals, Javier Prado-Martinez, Benoit Goossens, Ernst J Verschoor, Kristin S Warren, Ian Singleton, David A Marques, Joko Pamungkas, Dyah Perwitasari-Farajallah, Puji Rianti, Augustine Tuuga, Ivo G Gut, Marta Gut, Pablo Orozco-terWengel, Carel P van Schaik, Jaume Bertranpetit, Maria Anisimova, Aylwyn Scally, Tomas Marques-Bonet, Erik Meijaard, Michael Krützen
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...
November 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29043294/integrating-networks-and-comparative-genomics-reveals-retroelement-proliferation-dynamics-in-hominid-genomes
#12
Orr Levy, Binyamin A Knisbacher, Erez Y Levanon, Shlomo Havlin
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29032037/ecocultural-range-expansion-scenarios-for-the-replacement-or-assimilation-of-neanderthals-by-modern-humans
#13
Joe Yuichiro Wakano, William Gilpin, Seiji Kadowaki, Marcus W Feldman, Kenichi Aoki
Recent archaeological records no longer support a simple dichotomous characterization of the cultures/behaviors of Neanderthals and modern humans, but indicate much cultural/behavioral variability over time and space. Thus, in modeling the replacement or assimilation of Neanderthals by modern humans, it is of interest to consider cultural dynamics and its relation to demographic change. The ecocultural framework for the competition between hominid species allows their carrying capacities to depend on some measure of the levels of culture they possess...
October 12, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/29027198/shape-analysis-of-spatial-relationships-between-orbito-ocular-and-endocranial-structures-in-modern-humans-and-fossil-hominids
#14
Ana Sofia Pereira-Pedro, Michael Masters, Emiliano Bruner
The orbits and eyes of modern humans are situated directly below the frontal lobes and anterior to the temporal lobes. Contiguity between these orbital and cerebral elements could generate spatial constraints, and potentially lead to deformation of the eye and reduced visual acuity during development. In this shape analysis we evaluate whether and to what extent covariation exists between ocular morphology and the size and spatial position of the frontal and temporal areas in adult modern humans. Magnetic resonance imaging (MRI) was used to investigate patterns of variation among the brain and eyes, while computed tomography (CT) was used to compare cranial morphology in this anatomical region among modern humans, extinct hominids and chimpanzees...
December 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29026075/evidence-of-a-chimpanzee-sized-ancestor-of-humans-but-a-gibbon-sized-ancestor-of-apes
#15
Mark Grabowski, William L Jungers
Body mass directly affects how an animal relates to its environment and has a wide range of biological implications. However, little is known about the mass of the last common ancestor (LCA) of humans and chimpanzees, hominids (great apes and humans), or hominoids (all apes and humans), which is needed to evaluate numerous paleobiological hypotheses at and prior to the root of our lineage. Here we use phylogenetic comparative methods and data from primates including humans, fossil hominins, and a wide sample of fossil primates including Miocene apes from Africa, Europe, and Asia to test alternative hypotheses of body mass evolution...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29022796/aural-exostoses-surfer-s-ear-provide-vital-fossil-evidence-of-an-aquatic-phase-in-man-s-early-evolution
#16
P H Rhys Evans, M Cameron
For over a century, otolaryngologists have recognised the condition of aural exostoses, but their significance and aetiology remains obscure, although they tend to be associated with frequent swimming and cold water immersion of the auditory canal. The fact that this condition is usually bilateral is predictable since both ears are immersed in water. However, why do exostoses only grow in swimmers and why do they grow in the deep bony meatus at two or three constant sites? Furthermore, from an evolutionary point of view, what is or was the purpose and function of these rather incongruous protrusions? In recent decades, paleoanthropological evidence has challenged ideas about early hominid evolution...
September 15, 2017: Annals of the Royal College of Surgeons of England
https://www.readbyqxmd.com/read/28976033/photonic-microhand-with-autonomous-action
#17
Daniele Martella, Sara Nocentini, Dmitry Nuzhdin, Camilla Parmeggiani, Diederik S Wiersma
Grabbing and holding objects at the microscale is a complex function, even for microscopic living animals. Inspired by the hominid-type hand, a microscopic equivalent able to catch microelements is engineered. This microhand is light sensitive and can be either remotely controlled by optical illumination or can act autonomously and grab small particles on the basis of their optical properties. Since the energy is delivered optically, without the need for wires or batteries, the artificial hand can be shrunk down to the micrometer scale...
October 4, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28976008/the-genes-of-life-and-death-a-potential-role-for-placental-specific-genes-in-cancer-active-retrotransposons-in-the-placenta-encode-unique-functional-genes-that-may-also-be-used-by-cancer-cells-to-promote-malignancy
#18
REVIEW
Erin C Macaulay, Aniruddha Chatterjee, Xi Cheng, Bruce C Baguley, Michael R Eccles, Ian M Morison
The placenta invades the adjacent uterus and controls the maternal immune system, like a cancer invades surrounding organs and suppresses the local immune response. Intriguingly, placental and cancer cells are globally hypomethylated and share an epigenetic phenomenon that is not well understood - they fail to silence repetitive DNA sequences (retrotransposons) that are silenced (methylated) in healthy somatic cells. In the placenta, hypomethylation of retrotransposons has facilitated the evolution of new genes essential for placental function...
November 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28947156/bidding-evidence-for-primate-vocal-learning-and-the-cultural-substrates-for-speech-evolution
#19
REVIEW
Adriano R Lameira
Speech evolution seems to defy scientific explanation. Progress on this front has been jammed in an entrenched orthodoxy about what great apes can and (mostly) cannot do vocally, an idea epitomized by the Kuypers/Jürgens hypothesis. Findings by great ape researchers paint, however, starkly different and more optimistic landscapes for speech evolution. Over twenty studies qualify as positive evidence for primate vocal (production) learning following accepted terminology. Additionally, the Kuypers/Jürgens hypothesis shows low etymological, empirical, and theoretical soundness...
September 22, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28855259/the-mobile-element-locator-tool-melt-population-scale-mobile-element-discovery-and-biology
#20
Eugene J Gardner, Vincent K Lam, Daniel N Harris, Nelson T Chuang, Emma C Scott, W Stephen Pittard, Ryan E Mills, Scott E Devine
Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale...
November 2017: Genome Research
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