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https://www.readbyqxmd.com/read/28202101/berber-genealogy-and-the-politics-of-prehistoric-archaeology-and-craniology-in-french-algeria-1860s-1880s
#1
Bonnie Effros
Following the conquest of Algiers and its surrounding territory by the French army in 1830, officers noted an abundance of standing stones in this region of North Africa. Although they attracted considerably less attention among their cohort than more familiar Roman monuments such as triumphal arches and bridges, these prehistoric remains were similar to formations found in Brittany and other parts of France. The first effort to document these remains occurred in 1863, when Laurent-Charles Féraud, a French army interpreter, recorded thousands of dolmens and stone formations south-west of Constantine...
February 16, 2017: British Journal for the History of Science
https://www.readbyqxmd.com/read/28196347/disentangling-life-darwin-selectionism-and-the-postgenomic-return-of-the-environment
#2
Maurizio Meloni
In this paper, I analyze the disruptive impact of Darwinian selectionism for the century-long tradition in which the environment had a direct causative role in shaping an organism's traits. In the case of humans, the surrounding environment often determined not only the physical, but also the mental and moral features of individuals and whole populations. With its apparatus of indirect effects, random variations, and a much less harmonious view of nature and adaptation, Darwinian selectionism severed the deep imbrication of organism and milieu posited by these traditional environmentalist models...
February 11, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28194930/representation-archaeology-and-genealogy-three-spatial-metaphors-for-inquiring-into-nursing-phenomena-with%C3%A2-foucauldian-discourse-analysis
#3
Michael E Clinton, Rusla Anne Springer
Foucault used the "Quadrilateral of Language" metaphor to describe how language functioned in what the French called the Classic Age, roughly 1650 to 1800, the period from Descartes to Kant. His purpose was to show how the functions of language changed radically with the arrival of the Modern Age (~1800). Foucault developed his archaeological methods to investigate the impact of this change, but later revised his methods to introduce genealogical strategies to conduct "histories of the present". Our purpose in this paper is to clarify Foucault's thinking about ruptures in the functions of language and to show their implications for analyzing nursing discourse...
February 14, 2017: Nursing Philosophy: An International Journal for Healthcare Professionals
https://www.readbyqxmd.com/read/28192145/population-based-familial-aggregation-of-eosinophilic-esophagitis-suggests-a-genetic-contribution
#4
Kristina Allen-Brady, Rafael Firszt, John C Fang, Jathine Wong, Ken R Smith, Kathryn A Peterson
BACKGROUND: Prior familial clustering studies have observed an increased risk of eosinophilic esophagitis (EoE) mostly among first-degree relatives suggesting a genetic contribution to EoE, and twin studies have suggested a powerful contribution from environmental factors. OBJECTIVE: Clarify the contribution of genetic factors to EoE through estimation of familial aggregation and risk of EoE in extended relatives. METHODS: The Utah Population Database, a population-based genealogy resource linked to electronic medical records for healthcare systems across the state of Utah, was used to identify EoE cases and age, sex and birthplace-matched controls at a 5:1 ratio...
February 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28188662/population-genetics-of-reef-coral-endosymbionts-symbiodinium-dinophyceae
#5
D J Thornhill, E J Howells, D C Wham, T D Steury, S R Santos
Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broad-scale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations...
February 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#6
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28186915/a-novel-variable-precision-reduction-approach-to-comprehensive-knowledge-systems
#7
Chao Yang, Hongbo Liu, Sean McLoone, C L Philip Chen, Xindong Wu
A comprehensive knowledge system reveals the intangible insights hidden in an information system by integrating information from multiple data sources in a synthetical manner. In this paper, we present a variable precision reduction theory, underpinned by two new concepts: 1) distribution tables and 2) genealogical binary trees. Sufficient and necessary conditions to extract comprehensive knowledge from a given information system are also presented and proven. A complete variable precision reduction algorithm is proposed, in which we introduce four important strategies, namely, distribution table abstracting, attribute rank dynamic updating, hierarchical binary classifying, and genealogical tree pruning...
February 8, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28183358/genetic-diversity-and-population-structure-of-the-primary-malaria-vector-anopheles-sinensis-diptera-culicidae-in-china-inferred-by-cox1-gene
#8
Xinyu Feng, Libin Huang, Lin Lin, Manni Yang, Yajun Ma
BACKGROUND: Anopheles sinensis is a primary vector for Plasmodium vivax malaria in most regions of China. A comprehensive understanding of genetic variation and structure of the mosquito would be of benefit to the vector control and in a further attempt to contribute to malaria elimination in China. However, there is only inadequate population genetic data pertaining to An. sinensis currently. METHODS: Genetic variations and structure among populations of An. sinensis was examined and analyzed based on the nucleotide sequences of a 662 nt variable region of the mitochondrial cox1 gene among 15 populations from 20 collection sites in China...
February 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28169989/clustering-of-770-000-genomes-reveals-post-colonial-population-structure-of-north-america
#9
Eunjung Han, Peter Carbonetto, Ross E Curtis, Yong Wang, Julie M Granka, Jake Byrnes, Keith Noto, Amir R Kermany, Natalie M Myres, Mathew J Barber, Kristin A Rand, Shiya Song, Theodore Roman, Erin Battat, Eyal Elyashiv, Harendra Guturu, Eurie L Hong, Kenneth G Chahine, Catherine A Ball
Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records...
February 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28168122/catchments-catch-all-in-south-african-coastal-lowlands-topography-and-palaeoclimate-restricted-gene-flow-in-nymania-capensis-meliaceae-a-multilocus-phylogeographic-and-distribution-modelling-approach
#10
Alastair J Potts
BACKGROUND: This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots). METHODS: A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM)...
2017: PeerJ
https://www.readbyqxmd.com/read/28164382/performance-of-genomic-selection-under-a-single-step-approach-in-autochthonous-spanish-beef-cattle-populations
#11
E-F Mouresan, J Altarriba, C Moreno, S Munilla, A González-Rodríguez, L Varona
This study evaluated different strategies for implementing a single-step genomic selection programme in two autochthonous Spanish beef cattle populations (Pirenaica-Pi and Rubia Gallega-RG). The strategies were compared in terms of accuracy attained under different scenarios by simulating genomic data over the known genealogy. Several genotyping approaches were tested, as well as, other factors like marker density, effective population size, mutation rate and heritability of the trait. The results obtained showed gains in accuracy with respect to pedigree BLUP evaluation in all cases...
February 6, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28161998/paternal-genetic-structure-in-contemporary-mennonite-communities-from-the-american-midwest
#12
Kristine G Beaty, M J Mosher, Michael H Crawford, Phillip Melton
Over the last 35 years, researchers from the Laboratory of Biological Anthropology at the University of Kansas have been working with Mennonite communities to better understand evolutionary patterns of fission-fusion in relationship to their genetic history and population structure. In this study, short tandem repeat (STR) markers from the nonrecombining region of the Y chromosome (NRY) provided increased resolution of the molecular population structure for these groups. NRY is known to be informative for determining paternal genetic ancestral patterns in recently derived human populations...
April 2016: Human Biology
https://www.readbyqxmd.com/read/28161911/cryptic-diversity-and-discordance-in-single-locus-species-delimitation-methods-within-horned-lizards-phrynosomatidae-phrynosoma
#13
Christopher Blair, Robert W Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data...
February 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28156254/population-based-description-of-familial-clustering-of-chiari-malformation-type-i
#14
Diana Abbott, Douglas Brockmeyer, Deborah W Neklason, Craig Teerlink, Lisa A Cannon-Albright
OBJECTIVE A population-based genealogical resource with linked medical data was used to define the observed familial clustering of Chiari malformation Type I (CM-I). METHODS All patients with CM-I were identified from the 2 largest health care providers in Utah; those patients with linked genealogical data were used to test hypotheses regarding familial clustering. Relative risks (RRs) in first-, second-, and third-degree relatives were estimated using internal cohort-specific CM-I rates; the Genealogical Index of Familiality (GIF) test was used to test for an excess of relationships between all patients with CM-I compared with the expected distribution of relationships for matched control sets randomly selected from the resource...
February 3, 2017: Journal of Neurosurgery
https://www.readbyqxmd.com/read/28143695/population-structure-and-coalescence-in-pedigrees-comparisons-to-the-structured-coalescent-and-a-framework-for-inference
#15
Peter R Wilton, Pierre Baduel, Matthieu M Landon, John Wakeley
Contrary to what is often assumed in population genetics, independently segregating loci do not have completely independent ancestries, since all loci are inherited through a single, shared population pedigree. Previous work has shown that the non-independence between gene genealogies of independently segregating loci created by the population pedigree is weak in panmictic populations, and predictions made from standard coalescent theory are accurate for populations that are at least moderately sized. Here, we investigate patterns of coalescence in pedigrees of structured populations...
January 28, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28133576/the-impact-of-parental-investment-on-lifetime-reproductive-success-in-iceland
#16
Robert F Lynch, Emily C Lynch
BACKGROUND: Demonstrating the impact that parents have on the fitness of their children is a crucial step towards understanding how parental investment has affected human evolution. Parents not only transfer genes to their children, they also influence their environments. By analyzing reproductive patterns within and between different categories of close relatives, this study provides insight into the genetic and environmental effects that parents have on the fitness of their offspring...
2017: PeerJ
https://www.readbyqxmd.com/read/28133437/genome-scale-metabolic-modeling-of-archaea-lends-insight-into-diversity-of-metabolic-function
#17
REVIEW
ShengShee Thor, Joseph R Peterson, Zaida Luthey-Schulten
Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28105797/a-new-species-of-genus-fejervarya-anura-dicroglossidae-from-northern-thailand
#18
Chatmongkon Suwannapoom, Zhi-Yong Yuan, Nikolay A Poyarkov, Fang Yan, Somboon Kamtaeja, Robert W Murphy, Jing Che
We describe a new species of frog in the dicroglossid genus Fejervarya from Ban Monjong, Omkoi District, Chiang Mai Province, northern Thailand. Analysis of DNA sequence data from the mitochondrial gene 16S, advertisement calls, and morphological distinctiveness support recognition of the new species. Matrilineal genealogy suggests that the new population from Chiang Mai is a sister taxon to the South Asian clade that includes F. syhadrensis, F. granosa, and F. pierrei. The new species, Fejervarya chiangmaiensissp...
18, 2016: Zool Res
https://www.readbyqxmd.com/read/28088402/historical-relationships-of-three-enigmatic-phasianid-genera-aves-galliformes-inferred-using-phylogenomic-and-mitogenomic-data
#19
Ning Wang, Peter A Hosner, Bin Liang, Edward L Braun, Rebecca T Kimball
The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred...
January 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28077772/phylogenomics-provides-new-insight-into-evolutionary-relationships-and-genealogical-discordance-in-the-reef-building-coral-genus-acropora
#20
Natalie L Rosser, Luke Thomas, Sean Stankowski, Zoe T Richards, W Jason Kennington, Michael S Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts...
January 11, 2017: Proceedings. Biological Sciences
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