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https://www.readbyqxmd.com/read/28543951/determination-of-genetic-relatedness-from-low-coverage-human-genome-sequences-using-pedigree-simulations
#1
Michael D Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin
We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate, and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination, and sequencing error...
May 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28539931/characterization-and-phylogenetic-analysis-of-ancient-italian-landraces-of-pear
#2
Nicoletta Ferradini, Hovirag Lancioni, Renzo Torricelli, Luigi Russi, Isabella Dalla Ragione, Irene Cardinali, Gianpiero Marconi, Mauro Gramaccia, Luciano Concezzi, Alessandro Achilli, Fabio Veronesi, Emidio Albertini
Pear is one of the oldest fruit tree crops and the third most important temperate fruit species. Its domestication took place independently in the Far East (China) and in the Caucasus region. While the origin of Eastern Asian cultivars is clear, that of European cultivars is still in doubt. Italy has a wealth of local varieties and genetic resources safeguarded by several public and private collections to face the erosion caused by the introduction of improved varieties in specialized orchards. The objectives of the present study were: (i) to characterize the existing germplasm through nuclear (SSR) and (ii) to clarify the genetic divergence between local and cultivated populations through chloroplast DNA (cpDNA) markers in order to provide insights into phylogenetic relationships of Pyrus spp...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539631/phylogeography-of-the-tyrrhenian-red-deer-cervus-elaphus-corsicanus-resolved-using-ancient-dna-of-radiocarbon-dated-subfossils
#3
K Doan, F E Zachos, B Wilkens, J-D Vigne, N Piotrowska, A Stanković, B Jędrzejewska, K Stefaniak, M Niedziałkowska
We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526291/direct-radiocarbon-dating-and-dna-analysis-of-the-darra-i-kur-afghanistan-human-temporal-bone
#4
Katerina Douka, Viviane Slon, Chris Stringer, Richard Potts, Alexander Hübner, Matthias Meyer, Fred Spoor, Svante Pääbo, Tom Higham
The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type...
June 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#5
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28510184/footprint-of-the-eastern-euroasian-past-in-italian-populations-of-cryptotaenia-thomasii-ten-dc
#6
Anna Maria Palermo, Liliana Bernardo, Domenico Gargano, Giuseppe Pellegrino
BACKGROUND: The knowledge of the genetic architecture of closely related species and/or populations of a single species can be very useful to shed light on the processes that led to their current distributions. The present study provides a preliminary evaluation of the conservation status of the populations of Cryptotaenia thomasii, a very narrow endemic species occurring in southern Italy. Previous studies showed that C. thomasii was phylogenetically closely related to C. flahaultii, endemic species of Caucasus, and to evaluate its conservation status and the genetic variability of plant species the internal transcribed spacers (ITSs) of nuclear ribosomal DNA were sequenced and the SNPs were analyzed...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28502003/microsatellite-analysis-for-identification-of-individuals-using-bone-from-the-extinct-steller-s-sea-cow-hydrodamalis-gigas
#7
Jeffery F Warner, Michael G Harpole, Lorelei D Crerar
Microsatellite DNA can provide more detailed population genetic information than mitochondrial DNA which is normally used to research ancient bone. The methods detailed in this chapter can be utilized for any type of bone. However, for this example, four microsatellite loci were isolated from Steller's sea cow (Hydrodamalis gigas) using published primers for manatee and dugong microsatellites. The primers DduC05 (Broderick et al., Mol Ecol Notes 6:1275-1277, 2007), Tmakb60, TmaSC5 (Pause et al., Mol Ecol Notes 6: 1073-1076, 2007), and TmaE11 (Garcia-Rodriguez et al...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28502002/pcr-identification-of-genetic-polymorphisms
#8
Amanda M Harbison, Jenny Ngoc Tran Nguyen
Polymerase chain reaction (PCR) enables the amplification of a specific sequence of deoxyribonucleic acid (DNA) through the process of three main steps: template DNA denaturation, annealing of the primers to complementary sequences, and primer extension to synthesize DNA strands. By using this method, the target sequence will be copied and amplified at an exponential rate. PCR provides a qualitative method for identifying DNA from fresh or dried cells/body fluids, formalin-fixed archival tissue specimens, and ancient specimens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28493321/local-genes-for-local-bacteria-evidence-of-allopatry-in-the-genomes-of-transatlantic-campylobacter-populations
#9
Ben Pascoe, Guillaume Méric, Koji Yahara, Helen Wimalarathna, Susan Murray, Matthew D Hitchings, Emma L Sproston, Catherine D Carrillo, Eduardo N Taboada, Kerry K Cooper, Steven Huynh, Alison J Cody, Keith A Jolley, Martin C J Maiden, Noel D McCarthy, Xavier Didelot, Craig T Parker, Samuel K Sheppard
The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin...
May 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28486705/a-new-model-for-ancient-dna-decay-based-on-paleogenomic-meta-analysis
#10
Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins, Robin G Allaby
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28480140/high-diversity-and-suggested-endemicity-of-culturable-actinobacteria-in-an-extremely-oligotrophic-desert-oasis
#11
Hector Fernando Arocha-Garza, Ricardo Canales-Del Castillo, Luis E Eguiarte, Valeria Souza, Susana De la Torre-Zavala
The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media...
2017: PeerJ
https://www.readbyqxmd.com/read/28478763/molecular-phylogeny-of-anopheles-hyrcanus-group-diptera-culicidae-based-on-mtdna-coi
#12
Yuan Fang, Wen-Qi Shi, Yi Zhang
BACKGROUND: The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy. METHODS: Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range...
May 8, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28469152/lineage-specific-snps-for-genotyping-of-mycobacterium-tuberculosis-clinical-isolates
#13
Horng-Yunn Dou, Chien-Hsing Lin, Yih-Yuan Chen, Shiu-Ju Yang, Jia-Ru Chang, Keh-Ming Wu, Ying-Tsong Chen, Pei-Ju Chin, Yen-Ming Liu, Ih-Jen Su, Shih-Feng Tsai
Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolates based on the DNA sequences of the divergent lineages of MTB infecting human populations. Here, we identified single nucleotide polymorphisms (SNPs) of six representative strains from Taiwan by whole-genome sequencing and comparing the results to the sequence of the H37Rv reference strain...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28460080/a-genomic-landscape-of-mitochondrial-dna-insertions-in-the-pig-nuclear-genome-provides-evolutionary-signatures-of-interspecies-admixture
#14
Giuseppina Schiavo, Orsolya Ivett Hoffmann, Anisa Ribani, Valerio Joe Utzeri, Marco Ciro Ghionda, Francesca Bertolini, Claudia Geraci, Samuele Bovo, Luca Fontanesi
Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0...
April 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28455625/toward-a-consensus-on-snp-and-str-mutation-rates-on-the-human-y-chromosome
#15
REVIEW
O Balanovsky
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate...
May 2017: Human Genetics
https://www.readbyqxmd.com/read/28453634/recent-sex-chromosome-divergence-despite-ancient-dioecy-in-the-willow-salix-viminalis
#16
Pascal Pucholt, Alison E Wright, Lei Liu Conze, Judith E Mank, Sofia Berlin
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes...
April 27, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28452089/congruent-population-structure-across-paralogous-and-non-paralogous-loci-in-salish-sea-chum-salmon-oncorhynchus-keta
#17
R K Waples, J E Seeb, L W Seeb
Whole genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently paralogs are often excluded from studies. The effects of an ancient whole genome duplication (approximately 88MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing (RADseq) on ten collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and re-diploidized regions of the genome...
April 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28450643/ancient-genomic-changes-associated-with-domestication-of-the-horse
#18
Pablo Librado, Cristina Gamba, Charleen Gaunitz, Clio Der Sarkissian, Mélanie Pruvost, Anders Albrechtsen, Antoine Fages, Naveed Khan, Mikkel Schubert, Vidhya Jagannathan, Aitor Serres-Armero, Lukas F K Kuderna, Inna S Povolotskaya, Andaine Seguin-Orlando, Sébastien Lepetz, Markus Neuditschko, Catherine Thèves, Saleh Alquraishi, Ahmed H Alfarhan, Khaled Al-Rasheid, Stefan Rieder, Zainolla Samashev, Henri-Paul Francfort, Norbert Benecke, Michael Hofreiter, Arne Ludwig, Christine Keyser, Tomas Marques-Bonet, Bertrand Ludes, Eric Crubézy, Tosso Leeb, Eske Willerslev, Ludovic Orlando
The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage...
April 28, 2017: Science
https://www.readbyqxmd.com/read/28450591/dna-from-cave-soil-reveals-ancient-human-occupants
#19
Lizzie Wade
No abstract text is available yet for this article.
April 28, 2017: Science
https://www.readbyqxmd.com/read/28450384/neandertal-and-denisovan-dna-from-pleistocene-sediments
#20
Viviane Slon, Charlotte Hopfe, Clemens L Weiß, Fabrizio Mafessoni, Marco de la Rasilla, Carles Lalueza-Fox, Antonio Rosas, Marie Soressi, Monika V Knul, Rebecca Miller, John R Stewart, Anatoly P Derevianko, Zenobia Jacobs, Bo Li, Richard G Roberts, Michael V Shunkov, Henry de Lumley, Christian Perrenoud, Ivan Gušić, Željko Kućan, Pavao Rudan, Ayinuer Aximu-Petri, Elena Essel, Sarah Nagel, Birgit Nickel, Anna Schmidt, Kay Prüfer, Janet Kelso, Hernán A Burbano, Svante Pääbo, Matthias Meyer
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia...
May 12, 2017: Science
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