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https://www.readbyqxmd.com/read/29103940/morphometric-behavioral-and-genomic-evidence-for-a-new-orangutan-species
#1
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/29101448/discovery-of-gorilla-mhc-c-expressing-c1-ligand-for-kir
#2
Jörg B Hans, Linda Vigilant
In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic sequence data for a reassessment of allelic diversity at Gogo-C, the gorilla orthologue of HLA-C. Through the combination of long-range amplifications and long-read sequencing technology, we obtained, among the 35 gorillas reanalyzed, three novel full-length genomic sequences including a coding region sequence that has not been previously described...
November 3, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28959963/parental-influence-on-human-germline-de-novo-mutations-in-1-548-trios-from-iceland
#3
Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson, Lucas D Ward, Gudny A Arnadottir, Einar A Helgason, Hannes Helgason, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Thorunn Rafnar, Mike Frigge, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
The characterization of mutational processes that generate sequence diversity in the human genome is of paramount importance both to medical genetics and to evolutionary studies. To understand how the age and sex of transmitting parents affect de novo mutations, here we sequence 1,548 Icelanders, their parents, and, for a subset of 225, at least one child, to 35× genome-wide coverage. We find 108,778 de novo mutations, both single nucleotide polymorphisms and indels, and determine the parent of origin of 42,961...
September 28, 2017: Nature
https://www.readbyqxmd.com/read/28675688/whole-mitochondrial-genome-capture-from-faecal-samples-and-museum-preserved-specimens
#4
Tom van der Valk, Frida Lona Durazo, Love Dalén, Katerina Guschanski
Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
July 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28672035/modern-day-siv-viral-diversity-generated-by-extensive-recombination-and-cross-species-transmission
#5
Sidney M Bell, Trevor Bedford
Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-noncoding-sequences-on-embryonic-brain-development
#6
Morteza Mahmoudi Saber, Naruya Saitou
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...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28419279/primates-lice-and-bacteria-speciation-and-genome-evolution-in-the-symbionts-of-hominid-lice
#7
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zachary S Quicksall, Tandy Warnow, Lawrence Mugisha, Kevin P Johnson, David L Reed
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement...
July 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28348269/bonobos-maintain-immune-system-diversity-with-three-functional-types-of-mhc-b
#8
COMPARATIVE STUDY
Emily E Wroblewski, Lisbeth A Guethlein, Paul J Norman, Yingying Li, Christiana M Shaw, Alex S Han, Jean-Bosco N Ndjango, Steve Ahuka-Mundeke, Alexander V Georgiev, Martine Peeters, Beatrice H Hahn, Peter Parham
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein...
May 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28332079/gorilla-mhc-class-i-gene-and-sequence-variation-in-a-comparative-context
#9
COMPARATIVE STUDY
Jörg B Hans, Richard A Bergl, Linda Vigilant
Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans' closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (Gogo). Here, we combined long-range amplifications and long-read sequencing technology to analyze full-length MHC class I genes in 35 gorillas. We obtained 50 full-length genomic sequences corresponding to 15 Gogo-A alleles, 4 Gogo-Oko alleles, 21 Gogo-B alleles, and 10 Gogo-C alleles including 19 novel coding region sequences...
May 2017: Immunogenetics
https://www.readbyqxmd.com/read/28324014/variation-in-the-insulin-like-growth-factor-1-gene-in-primates
#10
Peter Rotwein
Insulin-like growth factor 1 (IGF1) is a multifunctional peptide that is involved in a wide range of physiological and pathophysiological processes in many animal species, ranging from somatic growth in children to metabolism and tissue regeneration and repair in adults. The IGF1 gene is under multifactorial regulation in the few species in which it has been studied, with major control being exerted by growth hormone through a gene expression pathway involving inducible binding of the STAT5b transcription factor to dispersed enhancer elements...
April 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28265767/the-y-chromosomes-of-the-great-apes
#11
REVIEW
Pille Hallast, Mark A Jobling
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28010125/proposed-association-between-the-hexanucleotide-repeat-of-c9orf72-and-opposability-index-of-the-thumb
#12
Zhongbo Chen, Kuang Lin, Jeffrey D Macklis, Ammar Al-Chalabi
OBJECTIVE: Amyotrophic lateral sclerosis (ALS) is a fatal disease caused by motor neuron and sub-cerebral projection neuron degeneration. We sought to explore the particular susceptibility of humans to neurodegeneration and whether any characteristic human features might predispose to selective vulnerability of the critical motor circuitry in ALS. The pathophysiology of the C9orf72 repeat is not yet understood, despite its role as a common cause of ALS and frontotemporal dementia. METHODS: We examined the development of the monosynaptic cortico-motoneuronal system, key to skilled hand movements, measured by the thumb opposability index, and its relationship to the C9orf72 hexanucleotide repeat expansion, a strong predisposing factor for neurodegeneration, using the genomic tool BLAST...
May 2017: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
https://www.readbyqxmd.com/read/27716526/evolution-and-demography-of-the-great-apes
#13
REVIEW
Martin Kuhlwilm, Marc de Manuel, Alexander Nater, Maja P Greminger, Michael Krützen, Tomas Marques-Bonet
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics...
December 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27607836/bacillus-cereus-biovar-anthracis-causing-anthrax-in-sub-saharan-africa-chromosomal-monophyly-and-broad-geographic-distribution
#14
Kym S Antonation, Kim Grützmacher, Susann Dupke, Philip Mabon, Fee Zimmermann, Felix Lankester, Tianna Peller, Anna Feistner, Angelique Todd, Ilka Herbinger, Hélène M de Nys, Jean-Jacques Muyembe-Tamfun, Stomy Karhemere, Roman M Wittig, Emmanuel Couacy-Hymann, Roland Grunow, Sébastien Calvignac-Spencer, Cindi R Corbett, Silke R Klee, Fabian H Leendertz
Through full genome analyses of four atypical Bacillus cereus isolates, designated B. cereus biovar anthracis, we describe a distinct clade within the B. cereus group that presents with anthrax-like disease, carrying virulence plasmids similar to those of classic Bacillus anthracis. We have isolated members of this clade from different mammals (wild chimpanzees, gorillas, an elephant and goats) in West and Central Africa (Côte d'Ivoire, Cameroon, Central African Republic and Democratic Republic of Congo). The isolates shared several phenotypic features of both B...
September 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27601674/variation-in-the-molecular-clock-of-primates
#15
Priya Moorjani, Carlos Eduardo G Amorim, Peter F Arndt, Molly Przeworski
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27463672/cospeciation-of-gut-microbiota-with-hominids
#16
Andrew H Moeller, Alejandro Caro-Quintero, Deus Mjungu, Alexander V Georgiev, Elizabeth V Lonsdorf, Martin N Muller, Anne E Pusey, Martine Peeters, Beatrice H Hahn, Howard Ochman
The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations...
July 22, 2016: Science
https://www.readbyqxmd.com/read/27435933/in-silico-phylogenomics-using-complete-genomes-a-case-study-on-the-evolution-of-hominoids
#17
Igor Rodrigues Costa, Francisco Prosdocimi, W Bryan Jennings
The increasing availability of complete genome data is facilitating the acquisition of phylogenomic data sets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments remains piecemeal and arduous. We designed software that performs these tasks and outputs anonymous loci (AL) or anchored enrichment/ultraconserved element loci (AE/UCE) data sets in ready-to-analyze formats. We demonstrate our program by applying it to the hominoids. Starting with human, chimpanzee, gorilla, and orangutan genomes, our software generated an exhaustive data set of 292 ALs (∼1 kb each) in ∼3 h...
September 2016: Genome Research
https://www.readbyqxmd.com/read/27381764/out-of-africa-origins-and-evolution-of-the-human-malaria-parasites-plasmodium-falciparum-and-plasmodium-vivax
#18
REVIEW
Dorothy E Loy, Weimin Liu, Yingying Li, Gerald H Learn, Lindsey J Plenderleith, Sesh A Sundararaman, Paul M Sharp, Beatrice H Hahn
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque...
February 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/27289102/multigenomic-delineation-of-plasmodium-species-of-the-laverania-subgenus-infecting-wild-living-chimpanzees-and-gorillas
#19
Weimin Liu, Sesh A Sundararaman, Dorothy E Loy, Gerald H Learn, Yingying Li, Lindsey J Plenderleith, Jean-Bosco N Ndjango, Sheri Speede, Rebeca Atencia, Debby Cox, George M Shaw, Ahidjo Ayouba, Martine Peeters, Julian C Rayner, Beatrice H Hahn, Paul M Sharp
Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA...
July 2, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27105073/functional-implications-of-human-specific-changes-in-great-ape-micrornas
#20
Alicia Gallego, Marta Melé, Ingrid Balcells, Eva García-Ramallo, Ignasi Torruella-Loran, Hugo Fernández-Bellon, Teresa Abelló, Ivanela Kondova, Ronald Bontrop, Christina Hvilsom, Arcadi Navarro, Tomàs Marquès-Bonet, Yolanda Espinosa-Parrilla
microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans...
2016: PloS One
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