Distance-Based Phylogenetic Methods

Xia, Xuhua

doi:10.1007/978-3-319-90684-3_15

Cited by 5 publications

(1 citation statement)

References 849 publications

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“…Modern sequencing technology can quickly generate many viral genomic sequences from which a viral tree can be constructed. If the viral tree can be properly rooted, then the parameters µ and T A can be estimated given a tree of viral strains with sample collection times used for calibrating a molecular clock [ 6 , 7 , 8 , 9 , 10 , 11 ]. The most recent common ancestor of SARS-CoV-2 was dated in two recent studies to October–November 2019 [ 12 ] and mid-August [ 5 ], respectively.…”

Section: Introductionmentioning

confidence: 99%

Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time

Xia

2023

Viruses

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Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains. Large trees with SARS-CoV-2 genomes beyond the first few months are needed to increase the likelihood of finding SARS-CoV-2 lineages that might have originated at the same time as (or even before) those early Wuhan strains. I extended a previously published rapid rooting method to model evolutionary rate as a linear function instead of a constant. This substantially improves the dating of the common ancestor of sampled SARS-CoV-2 genomes. Based on two large trees with 83,688 and 970,777 high-quality and full-length SARS-CoV-2 genomes that contain complete sample collection dates, the common ancestor was dated to 12 June 2019 and 7 July 2019 with the two trees, respectively. The two data sets would give dramatically different or even absurd estimates if the rate was treated as a constant. The large trees were also crucial for overcoming the high rate-heterogeneity among different viral lineages. The improved method was implemented in the software TRAD.

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Section: Introductionmentioning

confidence: 99%

Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time

Xia

2023

Viruses

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A Gene-Inspired Malware Detection Approach

Chen¹,

Shan²,

Liang³

et al. 2019

J. Phys.: Conf. Ser.

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Genetic data collection, pedigrees, and phylogenies

Simmonds¹,

Niskanen²,

Jensen³

et al. 2021

Demographic Methods Across the Tree of Life

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This chapter presents the role of genetic data in demographic studies. It focuses on two particular challenges faced in demographic analyses that can be solved using genetic data: estimating relatedness between individuals in a population and identifying drivers of cross-taxon variation in life history. The challenge of estimating relatedness is addressed with genetic pedigrees, and phylogenies allow comparisons of drivers of life history across taxa. These two different methods have several unifying features and histories. A past reliance on observational data in both cases limited taxonomic breadth of demographic analyses and reduced accuracy. With recent advances in genetic data collection and processing, in addition to improved computational methods, we are now in a position to use genetic data to expand demographic analyses across the Tree of Life. This chapter gives an overview of the whole process of constructing genetic pedigrees and reconstructing genetic phylogenies: beginning with the state-of-the-art, walking through the data collection steps required to obtain and process genetic material, and finishing with discussion and comparison of the diverse array of methods to construct genetic pedigrees and phylogenetic trees.

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Distance-Based Phylogenetic Methods

Cited by 5 publications

References 849 publications

Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time

Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time

A Gene-Inspired Malware Detection Approach

Genetic data collection, pedigrees, and phylogenies

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