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https://www.readbyqxmd.com/read/28654647/ancient-female-philopatry-asymmetric-male-gene-flow-and-synchronous-population-expansion-support-the-influence-of-climatic-oscillations-on-the-evolution-of-south-american-sea-lion-otaria-flavescens
#1
Larissa Rosa de Oliveira, Marcelo C M Gehara, Lúcia D Fraga, Fernando Lopes, Juan Ignacio Túnez, Marcelo H Cassini, Patricia Majluf, Susana Cárdenas-Alayza, Héctor J Pavés, Enrique Alberto Crespo, Nestor García, Rocío Loizaga de Castro, A Rus Hoelzel, Maritza Sepúlveda, Carlos Olavarría, Victor Hugo Valiati, Renato Quiñones, Maria Jose Pérez-Alvarez, Paulo Henrique Ott, Sandro L Bonatto
The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species...
2017: PloS One
https://www.readbyqxmd.com/read/28653997/type-w-human-endogenous-retrovirus-herv-w-integrations-and-their-mobilization-by-l1-machinery-contribution-to-the-human-transcriptome-and-impact-on-the-host-physiopathology
#2
REVIEW
Nicole Grandi, Enzo Tramontano
Human Endogenous Retroviruses (HERVs) are ancient infection relics constituting ~8% of our DNA. While HERVs' genomic characterization is still ongoing, impressive amounts of data have been obtained regarding their general expression across tissues. Among HERVs, one of the most studied is the W group, which is the sole HERV group specifically mobilized by the long interspersed element-1 (LINE-1) machinery, providing a source of novel insertions by retrotransposition of HERV-W processed pseudogenes, and comprising a member encoding a functional envelope protein coopted for human placentation...
June 27, 2017: Viruses
https://www.readbyqxmd.com/read/28652321/nonenzymatic-gluconeogenesis-like-formation-of-fructose-1-6-bisphosphate-in-ice
#3
Christoph B Messner, Paul C Driscoll, Gabriel Piedrafita, Michael F L De Volder, Markus Ralser
The evolutionary origins of metabolism, in particular the emergence of the sugar phosphates that constitute glycolysis, the pentose phosphate pathway, and the RNA and DNA backbone, are largely unknown. In cells, a major source of glucose and the large sugar phosphates is gluconeogenesis. This ancient anabolic pathway (re-)builds carbon bonds as cleaved in glycolysis in an aldol condensation of the unstable catabolites glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, forming the much more stable fructose 1,6-bisphosphate...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28649358/postglacial-dispersal-patterns-and-mitochondrial-genetic-structure-of-the-pyrenean-desman-galemys-pyrenaicus-in-the-northwestern-region-of-the-iberian-peninsula
#4
Marina Querejeta, Angel Fernández-González, Rafael Romero, Jose Castresana
The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman (Galemys pyrenaicus) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649256/evolutionary-insights-based-on-snp-haplotypes-of-red-pericarp-grain-size-and-starch-synthase-genes-in-wild-and-cultivated-rice
#5
Nisha Singh, Balwant Singh, Vandna Rai, Sukhjeet Sidhu, Ashok K Singh, Nagendra K Singh
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28635635/identifying-bird-remains-using-ancient-dna-barcoding
#6
Love Dalén, Vendela K Lagerholm, Johan A A Nylander, Nick Barton, Zbigniew M Bochenski, Teresa Tomek, David Rudling, Per G P Ericson, Martin Irestedt, John R Stewart
Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#7
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#8
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28632161/endogenous-retroviral-insertions-indicate-a-secondary-introduction-of-domestic-sheep-lineages-to-the-caucasus-and-central-asia-between-the-bronze-and-iron-age
#9
Oskar Schroeder, Norbert Benecke, Kai Frölich, Zuogang Peng, Kai Kaniuth, Leonid Sverchkov, Sabine Reinhold, Andrey Belinskiy, Arne Ludwig
Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds suggests that over the course of millennia, successive introductions of improved lineages and selection for wool quality occurred in the Mediterranean region and most of Asia. Here we present a novel ancient DNA approach using data of endogenous retroviral insertions in Bronze and Iron Age domestic sheep from the Caucasus and Pamir mountain areas...
June 20, 2017: Genes
https://www.readbyqxmd.com/read/28625158/a-minimally-invasive-method-for-sampling-human-petrous-bones-from-the-cranial-base-for-ancient-dna-analysis
#10
Kendra A Sirak, Daniel M Fernandes, Olivia Cheronet, Mario Novak, Beatriz Gamarra, Tímea Balassa, Zsolt Bernert, Andrea Cséki, János Dani, József Zsolt Gallina, Gábor Kocsis-Buruzs, Ivett Kővári, Orsolya László, Ildikó Pap, Róbert Patay, Zsolt Petkes, Gergely Szenthe, Tamás Szeniczey, Tamás Hajdu, Ron Pinhasi
Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28625153/stories-in-ancient-dna
#11
Nathan Blow
Technology developments are leading to rapid advances in ancient DNA analysis. Nathan Blow talks to researchers peering into the past through ancient DNA.
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28615043/-like-sugar-in-milk-reconstructing-the-genetic-history-of-the-parsi-population
#12
Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi, Kurush Dalal, Shagufta Khaliq, Syed Qasim Mehdi, Lalji Singh, Mait Metspalu, Toomas Kivisild, Chris Tyler-Smith, Richard Villems, Kumarasamy Thangaraj
BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28613039/sex-estimation-standards-for-medieval-and-contemporary-croats
#13
Željana Bašić, Ivana Kružić, Ivan Jerković, Deny Anđelinović, Šimun Anđelinović
AIM: To develop discriminant functions for sex estimation on medieval Croatian population and test their application on contemporary Croatian population. METHODS: From a total of 519 skeletons, we chose 84 adult excellently preserved skeletons free of antemortem or postmortem changes and took all standard measurements. Sex was estimated/determined using standard anthropological procedures and ancient DNA (amelogenin analysis) where pelvis was insufficiently preserved or where sex morphological indicators were not consistent...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28610170/integration-of-molecular-bioacoustical-and-morphological-data-reveals-two-new-cryptic-species-of-i-pelodytes-i-anura-pelodytidae-from-the-iberian-peninsula
#14
Jesús Díaz-Rodríguez, Marcelo Gehara, Rafael Márquez, Miguel Vences, Helena Gonçalves, Fernando Sequeira, Iñigo Martínez-Solano, Miguel Tejedo
Parsley frogs (Pelodytes) comprise the only genus in the family Pelodytidae, an ancient anuran lineage that split from their closest relatives over 140 million years ago. Pelodytes is a Palearctic group restricted to Western Eurasia including three extant species: the eastern species P. caucasicus, endemic to the Caucasus area, and two closely related species inhabiting Western Europe: the Iberian endemic P. ibericus and the more widespread P. punctatus. Previous studies based on mitochondrial and nuclear DNA markers have revealed the existence of two additional lineages of Parsley frogs in the Iberian Peninsula, which have been flagged as candidate species...
March 13, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#15
Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Background.: Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. Findings.: We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains...
June 13, 2017: GigaScience
https://www.readbyqxmd.com/read/28609451/anti-cancer-agents-in-saudi-arabian-herbals-revealed-by-automated-high-content-imaging
#16
Dina Hajjar, Stephan Kremb, Salim Sioud, Abdul-Hamid Emwas, Christian R Voolstra, Timothy Ravasi
Natural products have been used for medical applications since ancient times. Commonly, natural products are structurally complex chemical compounds that efficiently interact with their biological targets, making them useful drug candidates in cancer therapy. Here, we used cell-based phenotypic profiling and image-based high-content screening to study the mode of action and potential cellular targets of plants historically used in Saudi Arabia's traditional medicine. We compared the cytological profiles of fractions taken from Juniperus phoenicea (Arar), Anastatica hierochuntica (Kaff Maryam), and Citrullus colocynthis (Hanzal) with a set of reference compounds with established modes of action...
2017: PloS One
https://www.readbyqxmd.com/read/28604700/excess-of-non-conservative-amino-acid-changes-in-marine-bacterioplankton-lineages-with-reduced-genomes
#17
Haiwei Luo, Yongjie Huang, Ramunas Stepanauskas, Jijun Tang
Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed...
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28604332/microbacterium-tumbae-sp-nov-an-actinobacterium-isolated-from-the-stone-chamber-of-ancient-tumulus
#18
Miyuki Nishijima, Nozomi Tazato, Yutaka Handa, Nao Umekawa, Rika Kigawa, Chie Sano, Junta Sugiyama
Eight strains characterised as Gram-stain-positive, non-spore-forming and non-motile rods were isolated from samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli in Asuka village, Nara Prefecture, Japan. Among them, one strain, T7528-3-6bT, was shown to form a novel lineage within the genus Microbacterium. The most closely phylogenetically related species to T7528-3-6bT was Microbacterium panaciterrae, with 97.8 % sequence similarity. The major isoprenoid quinones of T7528-3-6bT were MK-12, MK-13 and MK-11...
June 13, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28593700/the-one-past-health-workshop-connecting-ancient-dna-and-zoonosis-research
#19
Sébastien Calvignac-Spencer, Tobias L Lenz
No abstract text is available yet for this article.
June 8, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28588137/the-real-significance-of-ancient-dna
#20
Laura Parducci, K D Bennett
No abstract text is available yet for this article.
June 6, 2017: American Journal of Botany
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