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https://www.readbyqxmd.com/read/29222464/the-irish-dna-atlas-revealing-fine-scale-population-structure-and-history-within-ireland
#1
Edmund Gilbert, Seamus O'Reilly, Michael Merrigan, Darren McGettigan, Anne M Molloy, Lawrence C Brody, Walter Bodmer, Katarzyna Hutnik, Sean Ennis, Daniel J Lawson, James F Wilson, Gianpiero L Cavalleri
The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the 'Irish DNA Atlas', a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of 'Gaelic' Irish ancestry, and three of shared Irish-British ancestry...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221753/pura-the-gene-encoding-pur-alpha-member-of-an-ancient-nucleic-acid-binding-protein-family-with-mammalian-neurological-functions
#2
REVIEW
Dianne C Daniel, Edward M Johnson
The PURA gene encodes Pur-alpha, a 322 amino acid protein with repeated nucleic acid binding domains that are highly conserved from bacteria through humans. PUR genes with a single copy of this domain have been detected so far in spirochetes and bacteroides. Lower eukaryotes possess one copy of the PUR gene, whereas chordates possess 1-4 PUR family members. Human PUR genes encode Pur-alpha (Pura), Pur-beta (Purb) and two forms of Pur-gamma (Purg). Pur-alpha is a protein that binds specific DNA and RNA sequence elements...
December 5, 2017: Gene
https://www.readbyqxmd.com/read/29221677/epigenetic-regulation-of-biological-rhythms-an-evolutionary-ancient-molecular-timer
#3
REVIEW
Tyler J Stevenson
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms...
December 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29219264/-identification-of-y-chromosomal-genetic-types-for-the-soldier-s-remains-from-huaihai-campaign
#4
C Z Wang, S Q Wen, M S Shi, X E Yu, X J Wang, Y L Pan, Y F Zhang, H Li, J Z Tan
OBJECTIVES: To identify the Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign, and to offer a clue for search of their paternal relatives. METHODS: DNA of the remains were extracted by the ancient DNA extraction method. Yfiler kit was used for the multiplex amplification of 17 Y-STR loci. The haplogroups of the samples were speculated. Detailed genotyping of the selected Y-SNP was performed based on the latest Y-chromosome phylogenetic tree...
August 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29216758/iron-age-italic-population-genetics-the-piceni-from-novilara-8th-7th-century-bc
#5
P Serventi, C Panicucci, R Bodega, S De Fanti, S Sarno, M Fondevila Alvarez, F Brisighelli, B Trombetta, P Anagnostou, G Ferri, A Vazzana, C Delpino, G Gruppioni, D Luiselli, E Cilli
BACKGROUND: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis...
December 7, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/29213275/dynamic-changes-in-host-gene-expression-following-in-vitro-viral-mimic-stimulation-in-crocodile-cells
#6
Subir Sarker, Yinan Wang, Brenden Warren-Smith, Karla J Helbig
The initial control of viral infection in a host is dominated by a very well orchestrated early innate immune system; however, very little is known about the ability of a host to control viral infection outside of mammals. The reptiles offer an evolutionary bridge between the fish and mammals, with the crocodile having evolved from the archosauria clade that included the dinosaurs, and being the largest living reptile species. Using an RNA-seq approach, we have defined the dynamic changes of a passaged primary crocodile cell line to stimulation with both RNA and DNA viral mimics...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29213053/the-conserved-ancient-role-of-chordate-pias-as-a-multilevel-repressor-of-the-nf-%C3%AE%C2%BAb-pathway
#7
Ruihua Wang, Shengfeng Huang, Xianan Fu, Guangrui Huang, Xinyu Yan, Zirui Yue, Shangwu Chen, Yingqiu Li, Anlong Xu
In vertebrates, PIAS genes encode versatile cellular regulators, with functions extremely complex and redundant. Here we try to understand their functions from an evolutionary perspective. we evaluate the sequences, expression and molecular functions of amphioxus PIAS genes and compare them with their vertebrate counterparts. Phylogenetic analysis suggests a single PIAS gene in ancestral chordates, which has been duplicated into four families (PIAS1-4) in vertebrates by 2R-WGD but remained single in a basal chordate (amphioxus)...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29202706/ancient-dna-reveals-genetic-connections-between-early-di-qiang-and-han-chinese
#8
Jiawei Li, Wen Zeng, Ye Zhang, Albert Min-Shan Ko, Chunxiang Li, Hong Zhu, Qiaomei Fu, Hui Zhou
BACKGROUND: Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese...
December 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29193490/the-eastern-side-of-the-westernmost-europeans-insights-from-subclades-within-y-chromosome-haplogroup-j-m304
#9
Licínio Manco, Joana Albuquerque, Maria Francisca Sousa, Rui Martiniano, Ricardo Costa de Oliveira, Sofia Marques, Verónica Gomes, António Amorim, Luís Alvarez, Maria João Prata
OBJECTIVES: We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. METHODS: A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci...
November 29, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/29187630/evolutionary-history-of-enigmatic-bears-in-the-tibetan-plateau-himalaya-region-and-the-identity-of-the-yeti
#10
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/29177730/type-ia-dna-topoisomerases-a-universal-core-and-multiple-activities
#11
Florence Garnier, Hélène Debat, Marc Nadal
All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29167511/transcription-factor-nf-%C3%AE%C2%BAb-is-modulated-by-symbiotic-status-in-a-sea-anemone-model-of-cnidarian-bleaching
#12
Katelyn M Mansfield, Nicole M Carter, Linda Nguyen, Phillip A Cleves, Anar Alshanbayeva, Leah M Williams, Camerron Crowder, Ashley R Penvose, John R Finnerty, Virginia M Weis, Trevor W Siggers, Thomas D Gilmore
Transcription factor NF-κB plays a central role in immunity from fruit flies to humans, and NF-κB activity is altered in many human diseases. To investigate a role for NF-κB in immunity and disease on a broader evolutionary scale we have characterized NF-κB in a sea anemone (Exaiptasia pallida; called Aiptasia herein) model for cnidarian symbiosis and dysbiosis (i.e., "bleaching"). We show that the DNA-binding site specificity of Aiptasia NF-κB is similar to NF-κB proteins from a broad expanse of organisms...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29167281/polytene-chromosome-structure-and-somatic-genome-instability
#13
Allan C Spradling
Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all Drosophila larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of Drosophila polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29167200/assessing-the-relationship-of-ancient-and-modern-populations
#14
Joshua G Schraiber
Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error and post-mortem damage by analyzing raw read from multiple ancient individuals simultaneously...
November 22, 2017: Genetics
https://www.readbyqxmd.com/read/29166859/divergent-clades-or-cryptic-species-mito-nuclear-discordance-in-a-daphnia-species-complex
#15
Anne Thielsch, Alexis Knell, Ali Mohammadyari, Adam Petrusek, Klaus Schwenk
BACKGROUND: Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D...
November 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29165562/the-diversity-of-recent-and-ancient-human-dream-a-new-microarray-for-genetic-anthropology-and-genealogy-forensics-and-personalized-medicine
#16
Eran Elhaik, Leeban Yusuf, Ainan I J Anderson, Mehdi Pirooznia, Dimitrios Arnellos, Gregory Vilshansky, Gunes Ercal, Yontao Lu, Teresa Webster, Michael L Baird, Umberto Esposito
The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation (CNVs), drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. While many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity...
November 20, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29162904/whole-y-chromosome-sequences-reveal-an-extremely-recent-origin-of-the-most-common-north-african-paternal-lineage-e-m183-m81
#17
Neus Solé-Morata, Carla García-Fernández, Vadim Urasin, Asmahan Bekada, Karima Fadhlaoui-Zid, Pierre Zalloua, David Comas, Francesc Calafell
E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29151852/ancient-oncogenesis-infection-and-human-evolution
#18
REVIEW
Riaan F Rifkin, Marnie Potgieter, Jean-Baptiste Ramond, Don A Cowan
The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA...
December 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29144465/parallel-palaeogenomic-transects-reveal-complex-genetic-history-of-early-european-farmers
#19
Mark Lipson, Anna Szécsényi-Nagy, Swapan Mallick, Annamária Pósa, Balázs Stégmár, Victoria Keerl, Nadin Rohland, Kristin Stewardson, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Eadaoin Harney, Susanne Nordenfelt, Bastien Llamas, Balázs Gusztáv Mende, Kitti Köhler, Krisztián Oross, Mária Bondár, Tibor Marton, Anett Osztás, János Jakucs, Tibor Paluch, Ferenc Horváth, Piroska Csengeri, Judit Koós, Katalin Sebők, Alexandra Anders, Pál Raczky, Judit Regenye, Judit P Barna, Szilvia Fábián, Gábor Serlegi, Zoltán Toldi, Emese Gyöngyvér Nagy, János Dani, Erika Molnár, György Pálfi, László Márk, Béla Melegh, Zsolt Bánfai, László Domboróczki, Javier Fernández-Eraso, José Antonio Mujika-Alustiza, Carmen Alonso Fernández, Javier Jiménez Echevarría, Ruth Bollongino, Jörg Orschiedt, Kerstin Schierhold, Harald Meller, Alan Cooper, Joachim Burger, Eszter Bánffy, Kurt W Alt, Carles Lalueza-Fox, Wolfgang Haak, David Reich
Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38)...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29144219/trypanosoma-sp-diversity-in-amazonian-bats-chiroptera-mammalia-from-acre-state-brazil
#20
Francisco C B Dos Santos, Cristiane V Lisboa, Samanta C C Xavier, Maria A Dario, Rair de S Verde, Armando M Calouro, André Luiz R Roque, Ana M Jansen
Bats are ancient hosts of Trypanosoma species and their flying ability, longevity and adaptability to distinct environments indicate that they are efficient dispersers of parasites. Bats from Acre state (Amazon Biome) were collected in four expeditions conducted in an urban forest (Parque Zoobotânico) and one relatively more preserved area (Seringal Cahoeira) in Rio Branco and Xapuri municipalities. Trypanosoma sp. infection was detected by hemoculture and fresh blood examination. Isolated parasite species were identified by the similarity of the obtained DNA sequence from 18S rDNA polymerase chain reaction and reference strains...
November 16, 2017: Parasitology
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