scholarly journals Hierarchical Modelling of Haplotype Effects on a Phylogeny

2021 ◽  
Vol 11 ◽  
Author(s):  
Maria Lie Selle ◽  
Ingelin Steinsland ◽  
Finn Lindgren ◽  
Vladimir Brajkovic ◽  
Vlatka Cubric-Curik ◽  
...  
Keyword(s):  
Hierarchical Model ◽  
Phylogenetic Relationships ◽  
Haplotype Network ◽  
Mitochondrial Haplotype ◽  
Extensive Literature ◽  
Specific Effects ◽  
Comparable Performance ◽  
Phenotype Model ◽  
Flow Of Information ◽  
Specific Haplotype

We introduce a hierarchical model to estimate haplotype effects based on phylogenetic relationships between haplotypes and their association with observed phenotypes. In a population there are many, but not all possible, distinct haplotypes and few observations per haplotype. Further, haplotype frequencies tend to vary substantially. Such data structure challenge estimation of haplotype effects. However, haplotypes often differ only due to few mutations, and leveraging similarities can improve the estimation of effects. We build on extensive literature and develop an autoregressive model of order one that models haplotype effects by leveraging phylogenetic relationships described with a directed acyclic graph. The phylogenetic relationships can be either in a form of a tree or a network, and we refer to the model as the haplotype network model. The model can be included as a component in a phenotype model to estimate associations between haplotypes and phenotypes. Our key contribution is that we obtain a sparse model, and by using hierarchical autoregression, the flow of information between similar haplotypes is estimated from the data. A simulation study shows that the hierarchical model can improve estimates of haplotype effects compared to an independent haplotype model, especially with few observations for a specific haplotype. We also compared it to a mutation model and observed comparable performance, though the haplotype model has the potential to capture background specific effects. We demonstrate the model with a study of mitochondrial haplotype effects on milk yield in cattle. We provide R code to fit the model with the INLA package.

scholarly journals Hierarchical modeling of haplotype effects based on a phylogeny

2020 ◽  
Author(s):  
Maria Lie Selle ◽  
Ingelin Steinsland ◽  
Finn Lindgren ◽  
Vladimir Brajkovic ◽  
Vlatka Cubric-Curik ◽  
...  
Keyword(s):  
Network Model ◽  
Hierarchical Model ◽  
Phylogenetic Relationships ◽  
Hierarchical Modeling ◽  
Low Frequency ◽  
Haplotype Network ◽  
Extensive Literature ◽  
Mitochondrial Haplotypes ◽  
Comparable Performance ◽  
Phenotype Model

AbstractThis paper introduces a hierarchical model to estimate haplotype effects based on phylogenetic relationships between haplotypes and their association with observed phenotypes. In a population there are usually many, but not all possible, distinct haplotypes and few observations per haplotype. Further, haplotype frequencies tend to vary substantially - few haplotypes have high frequency and many haplotypes have low frequency. Such data structure challenge estimation of haplotype effects. However, haplotypes often differ only due to few mutations and leveraging these similarities can improve the estimation of haplotype effects. There is extensive literature on this topic. Here we build on these observations and develop an autoregressive model of order one that hierarchically models haplotype effects by leveraging phylogenetic relationships between the haplotypes described with a directed acyclic graph. The phylogenetic relationships can be either in a form of a tree or a network and we therefore refer to the model as the haplotype network model. The haplotype network model can be included as a component in a phenotype model to estimate associations between haplotypes and phenotypes. The key contribution of this work is that by leveraging the haplotype network structure we obtain a sparse model and by using hierarchical autoregression the flow of information between similar haplotypes is estimated from the data. We show with a simulation study that the hierarchical model can improve estimates of haplotype effects compared to an independent haplotype model, especially when there are few observations for a specific haplotype. We also compared it to a mutation model and observed comparable performance, though the haplotype model has the potential to capture background specific effects. We demonstrate the model with a case study of modeling the effect of mitochondrial haplotypes on milk yield in cattle.

scholarly journals Is there a host-associated molecular and morphological differentiation between sympatrically occurring individuals of the invasive leaf miner Cameraria ohridella?

2019 ◽  
Vol 13 (6) ◽  
pp. 853-864
Author(s):  
Iwona Melosik ◽  
Urszula Walczak ◽  
Julia Staszak ◽  
Katarzyna Winnicka ◽  
Edward Baraniak
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Effect ◽  
Population Expansion ◽  
Morphological Differentiation ◽  
Haplotype Network ◽  
Leaf Miner ◽  
Mitochondrial Haplotype ◽  
Horse Chestnut ◽  
Nonrandom Mating

Abstract The leaf-miner moth Cameraria ohridella, a pest in Central Europe, causes severe damage to trees. Host-associated differentiation (HAD) for this species has been suggested previously based on the occurrence of a specific mitochondrial haplotype. We assessed genetic diversity and population structure for sympatrically occurring individuals collected in association with two host species, Ohio buckeye (Aesculus glabra) and horse chestnut (Ae. hippocastanum), using six microsatellite loci (SSR) and mtDNA sequences that encode parts of cytochrome oxidase I and II. To infer population structure and assign individuals to clusters, we employed Bayesian clustering. We further characterized the relationships between genetic distance and geographical distance (IBD) in analyzed samples. Although our results derived from the SSR loci analyses demonstrating that there was no population substructuring caused by the hosts, we found evidence of differences in wing size, which might be attributed to the quality of food resources available to larvae. The population structure with K = 2 cannot be interpreted as the result of IBD; rather, it reflects a population differentiation due to demographic or genetic processes (e.g., an origin of invaders). Although genetic diversity was relatively high (He> 0.5), the population had a deficiency of heterozygotes (FIS > 0), which was most likely due to nonrandom mating and, possibly, a Wahlund effect. A star-like haplotype network and negative Tajima’s D support the genetic effect of bottleneck followed by population expansion. Based on presumably neutral markers, we conclude that C. ohridella appeared to be a good model for studying evolution toward a generalist invasive species, rather than HAD.

Interference suppression in bilingualism: Stimulus-Stimulus vs. Stimulus-Response conflict

2021 ◽  
pp. 1-13
Author(s):  
Lihua Xia ◽  
Thomas H. Bak ◽  
Antonella Sorace ◽  
Mariana Vega-Mendoza
Keyword(s):  
Cognitive Control ◽  
Language Proficiency ◽  
Interference Suppression ◽  
Response Conflict ◽  
Stimulus Response ◽  
Specific Effects ◽  
Visual Orienting ◽  
Adult Participants ◽  
Comparable Performance

Abstract Studies examining the potential effects of bilingualism on interference suppression show inconsistent results. Our study approaches this topic by distinguishing two potential subcomponents within interference suppression (i.e., Stimulus-Stimulus and Stimulus-Response conflict). We investigated the two subcomponents through their operationalisation in different tasks and examined the role of language proficiency in modulating it. A sample of 111 young adult participants performed four non-linguistic cognitive tasks measuring both visual and auditory domains of cognitive control. Bilinguals outperformed monolinguals in tasks involving Stimulus-Stimulus conflict, but showed comparable performance in tasks involving Stimulus-Response conflict. Specific effects of language proficiency on cognitive control were observed: group differences in auditory inhibition and visual orienting were only observed between high-proficient bilinguals and monolinguals. Taken together, types of conflicts involved in interference tasks and language proficiency could differentially affect performance in monolinguals and bilinguals.

scholarly journals Phylogenetic Relationships among Populations of the Vineyard Snail Cernuella virgata (Da Costa, 1778)

ISRN Zoology ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Jasna Puizina ◽  
Sanja Puljas ◽  
Željana Fredotović ◽  
Ivica Šamanić ◽  
Grgur Pleslić
Keyword(s):  
Genetic Variability ◽  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Western Europe ◽  
Population Analysis ◽  
Shell Growth ◽  
Shell Height ◽  
Haplotype Network ◽  
Coi Gene ◽  
Island Population

Cernuella virgata (Da Costa, 1778) (Mollusca: Hygromiidae), commonly known as the “vineyard snail,” is endemic species in Mediterranean and Western Europe including the British Isles, but in the Eastern USA and Australia it represents an introduced invasive species. The present work examines the genetic variability and phylogenetic relationships among the four populations of this land snail sampled along the east Adriatic region of Croatia using mitochondrial markers (partial 16S rDNA and COI gene) in addition to traditional methods of shell’s shape analysis. All the three molecular-phylogenetic approaches (median joining haplotype network analysis and Bayesian analysis, as well as maximum likelihood analysis) revealed two-three major subnetworks for both 16S rDNA and COI, with a clear distinction between south Adriatic haplotypes (Pisak) and north Adriatic haplotypes (Krk and Cres). The population from Karlobag was comprised of both north and south haplotypes, thus representing a putative contact zone between these two groups. The morphometric analysis showed that individuals from Cres island population were statistically significantly wider and higher than individuals from Pisak population. Analysis of the SW/SH ratio and the relationship between shell width and shell height showed no differences in shell growth between the two examined populations, indicating equal shell growth and shape, which gives the possibility that differences in size of individuals between those two populations could be influenced by biotic (physiological) or abiotic (environmental) factors. This study represents the first analysis of genetic variability and relatedness among native populations of C. virgata.

Taxonomic and systematic implications of the revision of the phylogenetic relations in the genus Ectinogonia Spinola 1837 (Coleoptera: Buprestidae) of Central Chile

Zootaxa ◽  
2019 ◽  
Vol 4603 (1) ◽  
pp. 159
Author(s):  
SIMÓN ANGUITA-SALINAS ◽  
RODRIGO M. BARAHONA-SEGOVIA ◽  
ELIE POULIN ◽  
ÁLVARO ZÚÑIGA-REINOSO
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Variability ◽  
Haplotype Network ◽  
Species Level ◽  
The Other ◽  
Nominal Species ◽  
Central Chile ◽  
Phylogenetic Relations ◽  
Taxonomic History ◽  
Traditional Taxonomy

Ectinogonia Spinola 1837 is composed of 22 species to date, but its taxonomic history has been complex and is still unresolved. The species of the Santiagan Province of Central Chile are particularly complex because they show important morphological variability and overlapping traits, making species identification and delimitation difficult. The main goal of the present study is to show the phylogenetic relationships among species of Ectinogonia of the Santiagan province and discuss the taxonomic and systematic implications of our findings. Phylogeny reconstructions as well as a haplotype network disclosed four groups, partially inconsistent with the traditional taxonomy. Actually, the two Ectinogonia speciosa subspecies (E. speciosa speciosa (Germain 1856) and E. speciosa oscuripennis Cobos 1954) belong to two distinct clades, which are not reciprocally monophyletic, meaning that Ectinogonia speciosa is polyphyletic. On the other hand, the two other clades each contain, two nominal species (E. buquetii (Spinola 1837) and E. vidali Moore & Guerrero 2017, and E. isamarae Moore 1994 and E. speciosa oscuripennis Cobos 1954) without reciprocal haplotype sorting. These results suggest that: (1) E. speciosa oscuripennis should be raised to species level and (2) the following new synonymies are proposed: E. isamarae Moore 1994 is synonymised with E. oscuripennis Cobos 1954 and E. vidali Moore & Guerrero 2017 is synonymised with E. buquetii (Spinola 1837).

Interactions Between Mitochondrial Haplotype and Dietary Macronutrient Ratios Confer Sex-Specific Effects on Longevity in Drosophila melanogaster

2019 ◽  
Vol 74 (10) ◽  
pp. 1573-1581 ◽  
Author(s):  
Venkatesh Nagarajan-Radha ◽  
James Rapkin ◽  
John Hunt ◽  
Damian K Dowling
Keyword(s):  
Drosophila Melanogaster ◽  
Genotypic Variation ◽  
Dietary Quality ◽  
Mitochondrial Haplotype ◽  
Diverse Range ◽  
Specific Effects ◽  
Dietary Nutrients ◽  
Mitochondrial Genotype ◽  
Genetic Strains ◽  
Isocaloric Diets

Abstract Recent studies have demonstrated that modifications to the ratio of dietary macronutrients affect longevity in a diverse range of species. However, the degree to which levels of natural genotypic variation shape these dietary effects on longevity remains unclear. The mitochondria have long been linked to the aging process. The mitochondria possess their own genome, and previous studies have shown that mitochondrial genetic variation affects longevity in insects. Furthermore, the mitochondria are the sites in which dietary nutrients are oxidized to produce adenosine triphosphate, suggesting a capacity for dietary quality to mediate the link between mitochondrial genotype and longevity. Here, we measured longevity of male and female fruit flies, across a panel of genetic strains of Drosophila melanogaster, which vary only in their mitochondrial haplotype, when fed one of the two isocaloric diets that differed in their protein-to-carbohydrate ratio. The mitochondrial haplotype affected the longevity of flies, but the pattern of these effects differed across the two diets in males, but not in females. We discuss the implications of these results in relation to an evolutionary theory linking maternal inheritance of mitochondria to the accumulation of male-harming mitochondrial mutations, and to the theory exploring the evolution of phenotypic plasticity to novel environments.

scholarly journals A Novel Classification of Supply Chain Risks: A Review

2019 ◽  
Vol 9 (3) ◽  
pp. 4301-4305 ◽  
Author(s):  
M. S. Shahbaz ◽  
S. Sohu ◽  
F. Z. Khaskhelly ◽  
A. Bano ◽  
M. A. Soomro
Keyword(s):  
Supply Chain ◽  
Extensive Literature ◽  
Supply Chain Risk Management ◽  
Supply Chain Risk ◽  
Supply Chain System ◽  
Side Process ◽  
Risk Sources ◽  
Supply Chain Risks ◽  
Flow Of Information

Every organization is a complex supply chain system. If any fragment of this supply chain is disturbed, it will directly affect the entire structure. Numerous studies have been conducted to categorize the supply chain risk sources, but very few available cover all types of risks. This study did an extensive literature review and content analysis on the subject. A supply chain is the flow of information, material, and money starting from suppliers and ending to end-users. To cover all types of risks, risk sources must be based on three perspectives: (i) internal to the firm, (ii) external to the firm but internal to the supply chain, and (iii) external to the supply chain. Risks can be categorized into seven types under these three perspectives. Regarding internal risks, three types of risks come from the supply side, process side, and demand side, while these members of the supply chain are connected with the supply affected by logistic side risks, finance side risks, and collaboration side risks. The external environment also affects the supply chain so the seventh type of risks comes from environmental side risks. This study extends the literature of supply chain risk management by identifying new risk sources. This study will help the managers to understand what kind of risks can affect their supply chain. Future study can be conducted to empirically verify these risks sources.

Our understanding of neural codes rests on Shannon's foundations

2019 ◽  
Vol 42 ◽  
Author(s):  
Charles R. Gallistel
Keyword(s):  
Brain Structure ◽  
Neural Tissue ◽  
Neural Codes ◽  
Flow Of Information

Abstract Shannon's theory lays the foundation for understanding the flow of information from world into brain: There must be a set of possible messages. Brain structure determines what they are. Many messages convey quantitative facts (distances, directions, durations, etc.). It is impossible to consider how neural tissue processes these numbers without first considering how it encodes them.

Abstraction: An alternative neurocognitive account of recognition, prediction, and decision making

2020 ◽  
Vol 43 ◽  
Author(s):  
Valerie F. Reyna ◽  
David A. Broniatowski
Keyword(s):  
Decision Making ◽  
Software Engineering ◽  
Systems Engineering ◽  
Evidence Based ◽  
Extensive Literature ◽  
Trace Theory ◽  
Fuzzy Trace Theory ◽  
Abstract Representations ◽  
Technical Systems

Abstract Gilead et al. offer a thoughtful and much-needed treatment of abstraction. However, it fails to build on an extensive literature on abstraction, representational diversity, neurocognition, and psychopathology that provides important constraints and alternative evidence-based conceptions. We draw on conceptions in software engineering, socio-technical systems engineering, and a neurocognitive theory with abstract representations of gist at its core, fuzzy-trace theory.

Architecture of Radiolitid Rudist (Mollusca) Shell-Wall Structures and its Phylogenetic Implications

1975 ◽  
Vol 33 ◽  
pp. 686-687
Author(s):  
David H. Sturm ◽  
Bob F. Perkins
Keyword(s):  
Phylogenetic Relationships ◽  
Outer Wall ◽  
Shell Microstructure ◽  
Shell Wall ◽  
Wall Structures ◽  
Phylogenetic Implications ◽  
Cellular Wall ◽  
Superfamily Analysis ◽  
Central Texas

Each of the seven families of rudists (Mollusca, Bivalvia, Hippuritacea) is characterized by distinctive shell-wall architectures which reflect phylogenetic relationships within the superfamily. Analysis of the complex, calcareous, cellular wall of the attached valve of the radiolite rudist Eoradiolites davidsoni (Hill) from the Comanche Cretaceous of Central Texas indicates that its wall architecture is an elaboration of the simpler monopleurid rudist wall and supports possible radiolite-monopleurid relationships.Several well-preserved specimens of E. davidsoni were sectioned, polished, etched, and carbon and gold coated for SEM examination. Maximum shell microstructure detail was displayed by etching with a 0.7% HC1 solution from 80 to 100 seconds.The shell of E. davidsoni comprises a large, thick-walled, conical, attached valve (AV) and a small, very thin, operculate, free valve (FV) (Fig. 1a). The AV shell is two-layered with a thin inner wall, in which original structures are usually obliterated by recrystallization, and a thick, cellular, outer wall.

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