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Catharine Wang, Tiernan J Cahill, Andrew Parlato, Blake Wertz, Qiankun Zhong, Tricia Norkunas Cunningham, James J Cummings
BACKGROUND: With the availability of raw DNA generated from direct-to-consumer (DTC) testing companies, there has been a proliferation of third-party online services that are available to interpret the raw data for both genealogy and/or health purposes. This study examines the current landscape and downstream clinical implications of consumer use of third-party services. METHODS: Study participants were recruited online from social media platforms. A total of 321 survey respondents reported using third-party services for raw DNA interpretation...
January 2018: Molecular Genetics & Genomic Medicine
F O Bussiman, B C Perez, R V Ventura, M G C D Peixoto, R A Curi, J C C Balieiro
Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares...
February 22, 2018: Animal: An International Journal of Animal Bioscience
Erik M Volz, Xavier Didelot
Non-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history...
February 7, 2018: Systematic Biology
Melissa M Marr, Selina Brace, Danielle C Schreve, Ian Barnes
Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses...
February 9, 2018: Scientific Reports
Richard McMahon
A recently blossoming historiographical literature recognizes that physical anthropologists allied with scholars of diverse aspects of society and history to racially classify European peoples over a period of about a hundred years. They created three successive race classification coalitions - ethnology, from around 1840; anthropology, from the 1850s; and interwar raciology - each of which successively disintegrated. The present genealogical study argues that representing these coalitions as 'transdisciplinary' can enrich our understanding of challenges to disciplinary specialization...
February 8, 2018: British Journal for the History of Science
Guohong Albert Wu, Javier Terol, Victoria Ibanez, Antonio López-García, Estela Pérez-Román, Carles Borredá, Concha Domingo, Francisco R Tadeo, Jose Carbonell-Caballero, Roberto Alonso, Franck Curk, Dongliang Du, Patrick Ollitrault, Mikeal L Roose, Joaquin Dopazo, Frederick G Gmitter, Daniel S Rokhsar, Manuel Talon
The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch...
February 7, 2018: Nature
Eric Tzyy Jiann Chong, Joveen Wan Fen Neoh, Tiek Ying Lau, Yvonne Ai-Lian Lim, Kek Heng Chua, Ping-Chin Lee
Malaria is a notorious disease which causes major global morbidity and mortality. This study aims to investigate the genetic and haplotype differences of Plasmodium knowlesi (P. knowlesi) isolates in Malaysian Borneo and Peninsular Malaysia based on the molecular analysis of the cytochrome b (cyt b) gene. The cyt b gene of 49 P. knowlesi isolates collected from Sabah, Malaysian Borneo and Peninsular Malaysia was amplified using PCR, cloned into a commercialized vector and sequenced. In addition, 45 cyt b sequences were retrieved from humans and macaques bringing to a total of 94 cyt b gene nucleotide sequences for phylogenetic analysis...
February 1, 2018: Acta Tropica
Diying Huang, Gustavo Hormiga, Chenyang Cai, Yitong Su, Zongjun Yin, Fangyuan Xia, Gonzalo Giribet
Understanding the genealogical relationships among the arachnid orders is an onerous task, but fossils have aided in anchoring some branches of the arachnid tree of life. The discovery of Palaeozoic fossils with characters found in both extant spiders and other arachnids provided evidence for a series of extinctions of what was thought to be a grade, Uraraneida, that led to modern spiders. Here, we report two extraordinarily well-preserved Mesozoic members of Uraraneida with a segmented abdomen, multi-articulate spinnerets with well-defined spigots, modified male palps, spider-like chelicerae and a uropygid-like telson...
February 5, 2018: Nature Ecology & Evolution
Stephanie A Zlatic, Alysia Vrailas-Mortimer, Avanti Gokhale, Lucas J Carey, Elizabeth Scott, Reid Burch, Morgan M McCall, Samantha Rudin-Rush, John Bowen Davis, Cortnie Hartwig, Erica Werner, Lian Li, Michael Petris, Victor Faundez
Rare neurological diseases shed light onto universal neurobiological processes. However, molecular mechanisms connecting genetic defects to their disease phenotypes are elusive. Here, we obtain mechanistic information by comparing proteomes of cells from individuals with rare disorders with proteomes from their disease-free consanguineous relatives. We use triple-SILAC mass spectrometry to quantify proteomes from human pedigrees affected by mutations in ATP7A, which cause Menkes disease, a rare neurodegenerative and neurodevelopmental disorder stemming from systemic copper depletion...
January 30, 2018: Cell Systems
Y-T Huang, M Kolařík, M T Kasson, J Hulcr
Species of Geosmithia are cosmopolitan but understudied fungi, and most are associated with phloem-feeding bark beetles on various woody hosts. We surveyed 207 bark and ambrosia beetles from 37 species in the eastern USA for associated fungi. The community is dominated by species in the G. pallida species complex (GPSC) and included several Geosmithia isolates that appear to be new to science. The new Geosmithia isolates exhibited the characteristic brownish-colored colonies typical for the G. pallida species complex and were phylogenetically resolved as two genealogically exclusive lineages based on a concatenated multilocus data set based on the internal transcribed spacers (ITS) of the nuc rDNA (ITS1-5...
December 4, 2017: Mycologia
F S S Raidan, L R Porto-Neto, Y Li, S A Lehnert, A Reverter
A combined matrix that exploits genealogy together with marker based information could improve the selection of elite individuals in breeding programs. We present genetic parameters for adaptive and growth traits in beef cattle by exploring linear combinations of pedigree-based (A) and marker-based (G) relationship matrices. We use a dataset with 2,111 Brahman (BB) and 2,550 Tropical Composite cattle (TC) with genotypes for 729,068 single nucleotide polymorphism (SNP), and phenotypes for five traits. A weighted relationship matrix (WRM) combining G and A was constructed as yij=Xβ+Zu+eij...
January 27, 2018: Journal of Animal Science
Orr Levy, Isak Nethanël Gath
We investigate the spread from ancestors to descendants, under a model of sexual reproduction, of hereditary elements distinguishing individuals from their fellow human beings. These hereditary elements, termed labels, are either symbolic, implying a socio-cultural or ethnic self-determined category, or biological, i.e. a DNA sequence (for example founder mutations). The impact of various modes of preferential (assortative) mating on the dissemination of a known ancestral label was studied for both kinds of labels, the symbolic and the biological...
January 27, 2018: Journal of Theoretical Biology
Kittisak Buddhachat, Chatmongkon Suwannapoom
Taxonomic uncertainty of the Asian tree frog Polypedates leucomystax complex presents the challenging task of inferring its biogeographical history. Here, we describe its dispersion and the genetic relationships among different populations in Thailand, where we connect the population of the P. leucomystax complex of the Sunda Islands to the Indochina (mainland) population based on analyses of 266 sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp...
2018: PeerJ
Sofie Claerhout, Michiel Vandenbosch, Kelly Nivelle, Leen Gruyters, Anke Peeters, Maarten H D Larmuseau, Ronny Decorte
Knowledge of Y-chromosomal short tandem repeat (Y-STR) mutation rates is essential to determine the most recent common ancestor (MRCA) in familial searching or genealogy research. Up to now, locus-specific mutation rates have been extensively examined especially for commercially available forensic Y-STRs, while haplogroup specific mutation rates have not yet been investigated in detail. Through 450 patrilineally related namesakes distributed over 212 deep-rooting genealogies, the individual mutation rates of 42 Y-STR loci were determined, including 27 forensic Y-STR loci from the Yfiler® Plus kit and 15 additional Y-STR loci (DYS388, DYS426, DYS442, DYS447, DYS454, DYS455, DYS459a/b, DYS549, DYS607, DYS643, DYS724a/b and YCAIIa/b)...
January 17, 2018: Forensic Science International. Genetics
Sarra Elkamel, Sami Boussetta, Houssein Khodjet-El-Khil, Amel Benammar Elgaaied, Lotfi Cherni
OBJECTIVES: Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS: A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions...
January 23, 2018: American Journal of Human Biology: the Official Journal of the Human Biology Council
Vanessa Riffet, Gilles Frison, Guy Bouchoux
The two first steps of the Strecker synthesis of glycine, namely (a) addition of ammonia to formaldehyde to give aminomethanol and (b) its dehydration leading to methaneimine, is studied using high level quantum chemistry computations (G3B3). Water solvation is modeled by considering the effect of adding a discrete number of active or passive molecules of water (up to four) and by immersing the identified water-solute complexes in a conductor-like polarizable continuum solvent model. Activation of the reactants by protonation is also examined...
January 22, 2018: Journal of Physical Chemistry. A
Niamh Reilly
The recent unprecedented focus on ending impunity for conflict-related sexual violence (CRSV) is positive in many respects. However, it has narrowed the scope of Security Council Resolution 1325 and the women, peace, and security (WPS) agenda it established in 2000. Through a critical discursive genealogy of the interrelation of two UN agendas-protection of civilians in armed conflict and women, peace, and security-the author traces how CRSV emerged as the defining issue of the latter while the transformative imperative of making women's participation central to every UN endeavor for peace and security has failed to gain traction...
June 1, 2017: Violence Against Women
Elena Voskoboeva, Alla Semyachkina, Maria Yablonskaya, Ekaterina Nikolaeva
We present the results of the 45-year clinical observation of 27 Russian homocystinuria patients. We made a mutation analysis of the CBS gene for thirteen patients from eleven unrelated genealogies. All patients except for the two were compound heterozygotes for the mutations detected. The most frequent mutation in the cohort investigated was splice mutation IVS11-2a->c. We detected one new nonsense mutation, one new missense-mutation and three novel small deletions. We also report the clinical case of the B6-responsive patient genotyped as Ile278Thr/Cys109Arg...
March 2018: Molecular Genetics and Metabolism Reports
Vahideh Rafiei, Ziaeddin Banihashemi, Laura S Bautista-Jalon, María Del Mar Jiménez-Gasco, Gillian Turgeon, Michael G Milgroom
Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, SNPs and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, all but four isolates were assigned to lineage 2B824; four isolates were assigned to lineage 4B...
January 10, 2018: Phytopathology
Darryl Leroux
Relying on a populace well-educated in family history based in ancestral genealogy, a robust national genomics sector has developed in Québec over the past decade-and-a-half. The same period roughly coincides with a fourfold increase in the number of individuals and organizations in the region self-identifying with a mixed-race form of indigeneity that is counter to existing Indigenous understandings of kinship and citizenship. This paper examines how recent efforts by genetic scientists, working on a multi-year research project on the 'diversity' of the Québec gene pool, intervene in complex settler-Indigenous relations by redefining indigeneity according to the logics of 'Native American DNA'...
January 1, 2018: Social Studies of Science
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