A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data

AbstractBats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

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A Hierarchy of Multinomial Models for Multidimensional Source Monitoring

Methodology ◽

10.1027/1614-1881.1.1.2 ◽

2005 ◽

Vol 1 (1) ◽

pp. 2-17 ◽

Cited By ~ 21

Author(s):

Thorsten Meiser

Keyword(s):

Cognitive Processes ◽

Source Monitoring ◽

Source Information ◽

Model Comparisons ◽

Storage And Retrieval ◽

Multinomial Processing Tree ◽

Multinomial Models ◽

Hierarchical Relationship ◽

Statistical Framework ◽

Tree Models

Abstract. Several models have been proposed for the measurement of cognitive processes in source monitoring. They are specified within the statistical framework of multinomial processing tree models and differ in their assumptions on the storage and retrieval of multidimensional source information. In the present article, a hierarchical relationship is demonstrated between multinomial models for crossed source information ( Meiser & Bröder, 2002 ), for partial source memory ( Dodson, Holland, & Shimamura, 1998 ) and for several sources ( Batchelder, Hu, & Riefer, 1994 ). The hierarchical relationship allows model comparisons and facilitates the specification of identifiability conditions. Conditions for global identifiability are discussed, and model comparisons are illustrated by reanalyses and by a new experiment on the storage and retrieval of multidimensional source information.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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