scholarly journals Circumpolar peoples and their languages: lexical and genomic data suggest ancient Chukotko-Kamchatkan–Nivkh and Yukaghir-Samoyedic connections

2021 ◽  
Author(s):  
George Starostin ◽  
N. Ezgi Altınışık ◽  
Mikhail Zhivlov ◽  
Piya Changmai ◽  
Olga Flegontova ◽  
...  
Keyword(s):  
Model Comparison ◽  
Historical Linguistics ◽  
Permutation Test ◽  
Long Distance ◽  
Common Descent ◽  
Genome Wide ◽  
Comparison Approach ◽  
Show Evidence ◽  
Basic Vocabulary ◽  
Linguistic Methods

Relationships between universally recognized language families represent a hotly debated topic in historical linguistics, and the same is true for correlation between signals of genetic and linguistic relatedness. We developed a weighted permutation test and applied it on basic vocabularies for 31 pairs of languages and reconstructed proto-languages to show that three groups of circumpolar language families in the Northern Hemisphere show evidence of relationship though borrowing in the basic vocabulary or common descent: [Chukotko-Kamchatkan and Nivkh]; [Yukaghir and Samoyedic]; [Yeniseian, Na-Dene, and Burushaski]. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows. For finding the genetic signals we used genome-wide genetic data for present-day groups and a bootstrapping model comparison approach for admixture graphs or, alternatively, haplotype sharing statistics. Our findings further support some hypotheses on long-distance language relationship put forward based on the linguistic methods but lacking universal acceptance.

scholarly journals A Bayesian model comparison approach to test the specificity of visual integration impairment in schizophrenia or psychosis

2018 ◽  
Vol 265 ◽  
pp. 271-278 ◽  
Author(s):  
Tyler B. Grove ◽  
Beier Yao ◽  
Savanna A. Mueller ◽  
Merranda McLaughlin ◽  
Vicki L. Ellingrod ◽  
...  
Keyword(s):  
Bayesian Model ◽  
Model Comparison ◽  
Visual Integration ◽  
Bayesian Model Comparison ◽  
Comparison Approach

Long-distance wh-movement and long-distance wh-movement avoidance in L2 English: Evidence from French and Bulgarian speakers

2014 ◽  
Vol 31 (2) ◽  
pp. 179-210 ◽  
Author(s):  
Nikolay Slavkov
Keyword(s):  
Second Language ◽  
Second Language Acquisition ◽  
Language Acquisition ◽  
First Language ◽  
Processing Load ◽  
Long Distance ◽  
Canadian French ◽  
Equivalent Length ◽  
Show Evidence ◽  
L1 Acquisition

This article investigates spoken productions of complex questions with long-distance wh-movement in the L2 English of speakers whose first language is (Canadian) French or Bulgarian. Long-distance wh-movement is of interest as it can be argued that it poses difficulty in acquisition due to its syntactic complexity and related high processing load. Adopting the derivational complexity hypothesis, which has so far been applied to long-distance (LD) wh-movement in L1 acquisition and child second language acquisition, I argue that adult L2 learners also show evidence that questions with LD wh-movement are often replaced by alternative utterances with lower derivational complexity. I propose that such utterances, which are sometimes of equivalent length and with similar meaning to the targeted LD wh-structures, are avoidance strategies used by the learners as an intermediate acquisition resource. That is, such strategies are used as an escape-hatch from the derivational complexity of LD wh-movement. Overall, the results of this research indicate that the link between the number and complexity of derivational steps in a given structure is a fruitful area with strong potential in the second language acquisition field.

Association of Interleukin 23 Receptor Variants with Psoriatic Arthritis

2009 ◽  
Vol 36 (1) ◽  
pp. 137-140 ◽  
Author(s):  
PROTON RAHMAN ◽  
ROBERT D. INMAN ◽  
WALTER P. MAKSYMOWYCH ◽  
JEFF P. REEVE ◽  
LYNETTE PEDDLE ◽  
...  
Keyword(s):  
Psoriatic Arthritis ◽  
Permutation Test ◽  
Psoriatic Skin ◽  
Nucleotide Polymorphisms ◽  
Marker Haplotype ◽  
Sliding Windows ◽  
Genome Wide ◽  
Canadian Population ◽  
Interleukin 23 ◽  
Coding Snp

Objective.A recent genome-wide pooling study noted a significant association of interleukin 23 receptor (IL-23R) and psoriasis. Overxpression of IL-23 has been detected in lesional psoriatic skin, and induces epidermal proliferation. Given the interplay between psoriasis and PsA, we examined the association of IL-23R variants in 2 independent Canadian Caucasian cohorts of patients with psoriatic arthritis (PsA).Methods.We examined 496 PsA probands and 476 controls. Cases and controls were genotyped for a panel of 11 single-nucleotide polymorphisms (SNP) in IL-23R. Allele and haplotype associations were calculated using WHAP software. P values for haplotype associations were calculated using a permutation test.Results.The 381Gln allele of the coding SNP Arg381Gln (rs11209026) was found to be protective in the Canadian population (p = 0.004; corrected p = 0.044).A 2-marker haplotype from SNP rs7530511 and rs11209026 was associated with PsA (p = 0.011). All 3-marker sliding windows containing SNP rs11209026 were associated with PsA (p = 0.02 for all 3 windows). The magnitude of effect of IL-23R association in PsA appears to be similar to that reported in uncomplicated psoriasis.Conclusion.Significant associations between Arg381Gln SNP and haplotypes encoding this variant were noted in PsA. It remains to be determined what contribution of this association, if any, is specifically due to the inflammatory arthritis (PsA) rather than psoriasis.

scholarly journals Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality

2019 ◽  
Author(s):  
Anton Levitan ◽  
Andrew N. Gale ◽  
Emma K. Dallon ◽  
Darby W. Kozan ◽  
Kyle W. Cunningham ◽  
...  
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Yeast Species ◽  
Transposon Mutagenesis ◽  
Learning Approach ◽  
Long Distance ◽  
Gene Essentiality ◽  
Genome Wide ◽  
Machine Learning Approach

ABSTRACTIn vivo transposon mutagenesis, coupled with deep sequencing, enables large-scale genome-wide mutant screens for genes essential in different growth conditions. We analyzed six large-scale studies performed on haploid strains of three yeast species (Saccharomyces cerevisiae, Schizosaccaromyces pombe, and Candida albicans), each mutagenized with two of three different heterologous transposons (AcDs, Hermes, and PiggyBac). Using a machine-learning approach, we evaluated the ability of the data to predict gene essentiality. Important data features included sufficient numbers and distribution of independent insertion events. All transposons showed some bias in insertion site preference because of jackpot events, and preferences for specific insertion sequences and short-distance vs long-distance insertions. For PiggyBac, a stringent target sequence limited the ability to predict essentiality in genes with few or no target sequences. The machine learning approach also robustly predicted gene function in less well-studied species by leveraging cross-species orthologs. Finally, comparisons of isogenic diploid versus haploid S. cerevisiae isolates identified several genes that are haplo-insufficient, while most essential genes, as expected, were recessive. We provide recommendations for the choice of transposons and the inference of gene essentiality in genome-wide studies of eukaryotic haploid microbes such as yeasts, including species that have been less amenable to classical genetic studies.

scholarly journals Capturing Ordinal Theoretical Constraint in Psychological Science

2018 ◽  
Author(s):  
Julia M. Haaf ◽  
Fayette Klaassen ◽  
Jeffrey Rouder
Keyword(s):  
Social Sciences ◽  
Linear Model ◽  
Bayesian Model ◽  
Model Comparison ◽  
Social Scientists ◽  
Psychological Science ◽  
Bayesian Model Comparison ◽  
Comparison Approach ◽  
The Social ◽  
Ordinal Level

Most theories in the social sciences are verbal and provide ordinal-level predictions for data. For example, a theory might predict that performance is better in one condition than another, but not by how much. One way of gaining additional specificity is to posit many ordinal constraints that hold simultaneously. For example a theory might predict an effect in one condition, a larger effect in another, and none in a third. We show how common theoretical positions naturally lead to multiple ordinal constraints. To assess whether multiple ordinal constraints hold in data, we adopt a Bayesian model comparison approach. The result is an inferential system that is custom-tuned for the way social scientists conceptualize theory, and that is more intuitive and informative than current linear-model approaches.

scholarly journals Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of fruit trees in the Mediterranean

2021 ◽  
Author(s):  
Alex Baumel ◽  
Gonzalo Nieto Feliner ◽  
Frederic Medail ◽  
Stefano La Malfa ◽  
Mario Diguardo ◽  
...  
Keyword(s):  
Eastern Mediterranean ◽  
Ex Situ ◽  
Plant Domestication ◽  
Mediterranean Forests ◽  
Migration Routes ◽  
Long Distance ◽  
Genome Wide ◽  
Western Morocco ◽  
Carob Tree ◽  
The Mediterranean

Intense research efforts on phylogeography over the last two decades uncovered major biogeographical trends and renewed our understandings of plant domestication in the Mediterranean. We aim to investigate the evolutionary history and the origin of domestication of the carob tree that has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to identify carob evolutionary units (CEUs) based on genetic diversity structure and geography. We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). The 56 populations sampled across the Mediterranean basin, classified as natural, semi-natural or cultivated, were examined. Although, RADseq data are consistent with previous studies identifying a strong West-to-East genetic structure and considerable admixture in some geographic parts, we reconstructed a new phylogeographic scenario with two migration routes occurring from a single refugium likely located in South-Western Morocco. Our results do not favour the regionally bound or single origin of domestication. Indeed, our findings support a cultivation model of locally selected wild genotypes, albeit punctuated by long-distance westward dispersals of domesticated varieties by humans, concomitant with major cultural waves by Romans and Arabs in the regions of dispersal. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in South-Western Morocco, South Spain and Eastern Mediterranean. Our study underscores the relevance of natural and seminatural habitats of Mediterranean forests and their refugia in the conservation efforts of tree crops.

scholarly journals Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection

2021 ◽  
Vol 22 (22) ◽  
pp. 12317
Author(s):  
Heng Zhang ◽  
Xu Zhang ◽  
Jia Zhao ◽  
Li Sun ◽  
Haiyan Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Dasypyrum Villosum ◽  
Promoter Regions ◽  
Lipase Gene ◽  
Long Distance ◽  
Enzyme Superfamily ◽  
Genome Wide ◽  
A Genome ◽  
Long Distance Movement

GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.

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