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Article ; Online: Evaluation of the Relative Performance of the Subflattenings Method for Phylogenetic Inference.

Stevenson, Joshua / Holland, Barbara / Charleston, Michael / Sumner, Jeremy

2023 Volume 85, Issue 3, Page(s) 19

Abstract: The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny-and by extension the complete tree-using pattern counts from a sequence alignment. The relatively small number of possible ... ...

Abstract	The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny-and by extension the complete tree-using pattern counts from a sequence alignment. The relatively small number of possible internal edges among a set of taxa (compared to the number of binary trees) makes these methods attractive; however, more could be done to evaluate their effectiveness for inferring phylogenetic trees. This is the case particularly for subflattenings, and the work we present here makes progress in this area. We introduce software for constructing and evaluating subflattenings for splits, utilising a number of methods to make computing subflattenings more tractable. We then present the results of simulations we have performed in order to compare the effectiveness of subflattenings to that of flattenings in terms of split score distributions, and susceptibility to possible biases. We find that subflattenings perform similarly to flattenings in terms of the distribution of split scores on the trees we examined, but may be less affected by bias arising from both split size/balance and long branch attraction. These insights are useful for developing effective algorithms to utilise these tools for the purpose of inferring phylogenetic trees.
MeSH term(s)	Phylogeny ; Mathematical Concepts ; Models, Biological ; Software ; Algorithms
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-023-01120-z
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Article ; Online: Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models.

Liu, Qin / Charleston, Michael A / Richards, Shane A / Holland, Barbara R

Systematic biology

2023 Volume 72, Issue 1, Page(s) 92–105

Abstract: In molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of ... ...

Abstract	In molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of sequence evolution is homogeneous across sites and lineages. The Akaike Information Criterion (AIC), an estimator of Kullback-Leibler divergence, and the Bayesian Information Criterion (BIC) are popular tools to select models in phylogenetics. Recent work suggests that AIC should not be used for comparing mixture and partition models. In this work, we clarify that this difficulty is not fully explained by AIC misestimating the Kullback-Leibler divergence. We also investigate the performance of the AIC and BIC at comparing amongst mixture models and amongst partition models. We find that under nonstandard conditions (i.e. when some edges have small expected number of changes), AIC underestimates the expected Kullback-Leibler divergence. Under such conditions, AIC preferred the complex mixture models and BIC preferred the simpler mixture models. The mixture models selected by AIC had a better performance in estimating the edge length, while the simpler models selected by BIC performed better in estimating the base frequencies and substitution rate parameters. In contrast, AIC and BIC both prefer simpler partition models over more complex partition models under nonstandard conditions, despite the fact that the more complex partition model was the generating model. We also investigated how mispartitioning (i.e., grouping sites that have not evolved under the same process) affects both the performance of partition models compared with mixture models and the model selection process. We found that as the level of mispartitioning increases, the bias of AIC in estimating the expected Kullback-Leibler divergence remains the same, and the branch lengths and evolutionary parameters estimated by partition models become less accurate. We recommend that researchers are cautious when using AIC and BIC to select among partition and mixture models; other alternatives, such as cross-validation and bootstrapping, should be explored, but may suffer similar limitations [AIC; BIC; mispartitioning; partitioning; partition model; mixture model].
MeSH term(s)	Phylogeny ; Bayes Theorem ; Genomics
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syac081
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Article ; Online: Unattained geometric configurations of secondary structure elements in protein structural space.

Sykes, Janan / Holland, Barbara / Charleston, Michael

Journal of structural biology

2022 Volume 214, Issue 3, Page(s) 107870

Abstract: Discovery of new folds in the Protein Data Bank (PDB) has all but ceased. This could be viewed as evidence that all existing protein folds have been documented. Sampling bias has, however, been presented as an alternative explanation. Furthermore, ... ...

Abstract	Discovery of new folds in the Protein Data Bank (PDB) has all but ceased. This could be viewed as evidence that all existing protein folds have been documented. Sampling bias has, however, been presented as an alternative explanation. Furthermore, although we may know of all protein folds that do exist, we may not have documented all protein folds that could exist. While addressing completeness in the context of entire protein structures is extremely difficult, they can be simplified in a number of ways. One such simplification is presented: considering protein structures as a series of α helices and β sheets and analysing the geometric relationships between these successive secondary structure elements (SSEs) through torsion angles, lengths and distances. We aimed to find out whether all substructures that could be formed by triplets of these successive SSEs were represented in the PDB. When SSEs were defined with the assignment program Promotif, a gap was identified in the represented torsion angles of helix-strand-strand substructures. This was not present when SSEs were defined with an alternative assignment program with a smaller minimum SSE length, DSSP. We also looked at representing proteins as one-dimensional sequences of SSE types and searched for underrepresented motifs. Completely absent motifs occurred more often than expected at random. If a gap in SSE substructure space exists that could be filled or if a physically possible SSE motif is absent, associated gaps in protein structure space are implied, meaning that the PDB as we know it may not be complete.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Databases, Protein ; Protein Structure, Secondary ; Proteins/chemistry ; Proteins/genetics
Chemical Substances	Proteins
Language	English
Publishing date	2022-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2022.107870
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Article ; Online: A review of visualisations of protein fold networks and their relationship with sequence and function.

Sykes, Janan / Holland, Barbara R / Charleston, Michael A

Biological reviews of the Cambridge Philosophical Society

2022 Volume 98, Issue 1, Page(s) 243–262

Abstract: Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these ... ...

Abstract	Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these relationships is by considering the space of protein folds and how one might move from fold to fold through similarity, or potential evolutionary relationships. The many individual characterisations of fold space presented in the literature can tell us a lot about how well the current Protein Data Bank represents protein fold space, how convergence and divergence may affect protein evolution, how proteins affect the whole of which they are part, and how proteins themselves function. A synthesis of these different approaches and viewpoints seems the most likely way to further our knowledge of protein structure evolution and thus, facilitate improved protein structure design and prediction.
MeSH term(s)	Proteins/genetics ; Proteins/chemistry ; Proteins/metabolism ; Amino Acid Sequence
Chemical Substances	Proteins
Language	English
Publishing date	2022-10-09
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1423558-4
ISSN	1469-185X ; 0006-3231 ; 1464-7931
ISSN (online)	1469-185X
ISSN	0006-3231 ; 1464-7931
DOI	10.1111/brv.12905
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Article ; Online: Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study.

Fountain-Jones, Nicholas M / Vanhaeften, Robert / Williamson, Jan / Maskell, Janelle / Chua, I-Ly J / Charleston, Michael / Cooley, Louise

The Lancet. Microbe

2024 Volume 5, Issue 5, Page(s) e452–e458

Abstract: Introduction: Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 ...

Abstract	Introduction: Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 outcomes, but the extended effects of these drugs on viral evolution in patients with chronic infections remain uncertain. This study investigates how molnupiravir affects SARS-CoV-2 evolution in immunocompromised patients with prolonged infections. Methods: The study included five immunocompromised patients treated with molnupiravir and four patients not treated with molnupiravir (two immunocompromised and two non-immunocompromised). We selected patients who had been infected by similar SARS-CoV-2 variants and with high-quality genomes across timepoints to allow comparison between groups. Throat and nasopharyngeal samples were collected in patients up to 44 days post treatment and were sequenced using tiled amplicon sequencing followed by variant calling. The UShER pipeline and University of California Santa Cruz genome viewer provided insights into the global context of variants. Treated and untreated patients were compared, and mutation profiles were visualised to understand the impact of molnupiravir on viral evolution. Findings: Patients treated with molnupiravir showed a large increase in low-to-mid-frequency variants in as little as 10 days after treatment, whereas no such change was observed in untreated patients. Some of these variants became fixed in the viral population, including non-synonymous mutations in the spike protein. The variants were distributed across the genome and included unique mutations not commonly found in global omicron genomes. Notably, G-to-A and C-to-T mutations dominated the mutational profile of treated patients, persisting up to 44 days post treatment. Interpretation: Molnupiravir treatment in immunocompromised patients led to the accumulation of a distinctive pattern of mutations beyond the recommended 5 days of treatment. Treated patients maintained persistent PCR positivity for the duration of monitoring, indicating clear potential for transmission and subsequent emergence of novel variants. Funding: Australian Research Council.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/drug effects ; SARS-CoV-2/immunology ; Retrospective Studies ; Antiviral Agents/therapeutic use ; Antiviral Agents/pharmacology ; Immunocompromised Host ; Hydroxylamines/therapeutic use ; Hydroxylamines/pharmacology ; COVID-19 Drug Treatment ; Male ; Cytidine/analogs & derivatives ; Cytidine/therapeutic use ; Cytidine/pharmacology ; Female ; Middle Aged ; Mutation ; Aged ; COVID-19/immunology ; COVID-19/virology ; Evolution, Molecular ; Adult ; Genome, Viral/genetics
Chemical Substances	Antiviral Agents ; molnupiravir (YA84KI1VEW) ; Hydroxylamines ; Cytidine (5CSZ8459RP)
Language	English
Publishing date	2024-03-22
Publishing country	England
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(23)00393-2
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Book ; Online: Evaluation of the relative performance of the subflattenings method for phylogenetic inference

Stevenson, Joshua / Holland, Barbara / Charleston, Michael / Sumner, Jeremy

2022

Abstract: The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small number of possible ...

Abstract	The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small number of possible internal edges among a set of taxa (compared to the number of binary trees) makes these methods attractive, however more could be done to evaluate their effectiveness for inferring phylogenetic trees. This is the case particularly for subflattenings, and our work makes progress in this area. We introduce software for constructing and evaluating subflattenings for splits, utilising a number of methods to make computing subflattenings more tractable. We then present the results of simulations we have performed in order to compare the effectiveness of subflattenings to that of flattenings in terms of split score distributions, and susceptibility to possible biases. We find that subflattenings perform similarly to flattenings in terms of the distribution of split scores on the trees we examined, but may be less affected by bias arising from both split size/balance and long branch attraction. These insights are useful for developing effective algorithms to utilise these tools for the purpose of inferring phylogenetic trees. Comment: 21 pages, 13 figures
Keywords	Quantitative Biology - Populations and Evolution ; 92B05
Subject code	511
Publishing date	2022-05-04
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Benchmarking Methods of Protein Structure Alignment.

Sykes, Janan / Holland, Barbara R / Charleston, Michael A

Journal of molecular evolution

2020 Volume 88, Issue 7, Page(s) 575–597

Abstract: The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong; this can be done ... ...

Abstract	The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong; this can be done through alignment and comparison of protein structures. Dozens of different methods for Protein Structure Alignment (PSA) have been proposed that use a wide range of techniques. The aim of this study is to determine the ability of PSA methods to identify pairs of protein domains known to share differing levels of structural similarity, and to assess their utility for clustering domains from several different folds into known groups. We present the results of a comprehensive investigation into eighteen PSA methods, to our knowledge the largest piece of independent research on this topic. Overall, SP-AlignNS (non-sequential) was found to be the best method for classification, and among the best performing methods for clustering. Methods (where possible) were split into the algorithm used to find the optimal alignment and the score used to assess similarity. This allowed us to largely separate the algorithm from the score it maximizes and thus, to assess their effectiveness independently of each other. Surprisingly, we found that some hybrids of mismatched scores and algorithms performed better than either of the native methods at classification and, in some cases, clustering as well. It is hoped that this investigation and the accompanying discussion will be useful for researchers selecting or designing methods to align protein structures.
MeSH term(s)	Algorithms ; Cluster Analysis ; Models, Molecular ; Protein Conformation ; Sequence Alignment/methods ; Sequence Analysis, Protein/methods ; Software
Language	English
Publishing date	2020-07-28
Publishing country	Germany
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120148-7
ISSN	1432-1432 ; 0022-2844
ISSN (online)	1432-1432
ISSN	0022-2844
DOI	10.1007/s00239-020-09960-2
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Article: Long‐Term Spatiotemporal Dynamics and Factors Associated with Trends in Bare‐Nosed Wombats

Carver, Scott / Charleston, Michael / Hocking, Gregory / Gales, Rosemary / Driessen, Michael M.

journal of wildlife management. 2021 Apr., v. 85, no. 3

2021

Abstract: Geographically widespread species present challenges for conservation assessment. We used long‐term spotlight surveys to assess spatiotemporal dynamics of bare‐nosed wombats (Vombatus ursinus), encompassing 34 years of surveys for the Tasmanian mainland ... ...

Abstract	Geographically widespread species present challenges for conservation assessment. We used long‐term spotlight surveys to assess spatiotemporal dynamics of bare‐nosed wombats (Vombatus ursinus), encompassing 34 years of surveys for the Tasmanian mainland sub‐species (V. u. tasmaniensis, 1985–2018) and 25 years for the Flinders Island sub‐species (V. u. ursinus, 1994–2018). Wombat populations increased on the Tasmanian mainland by 2.59 times and on Flinders Island by 3.51 times (x¯ = 1.05 and 1.1 times increase/yr, respectively). At smaller spatial scales on mainland Tasmania, increases in wombat counts generally occurred within meteorological regions and regional zones, except for the Central North (West Tamar) region where a decrease in wombats is linked to a sarcoptic mange disease epizootic. We used generalized additive models to assess relationships between variables and wombat counts. The most supported variables at the mainland Tasmania scale were (in order of importance) year, positive associations with time‐lagged minimum temperature, Tasmanian devil (Sarcophilus harrisii) counts, and moonlight, and a negative association with time‐lagged rainfall. Among meteorological regions, variables associated with wombat counts exhibited some heterogeneity, with temperature and rainfall the most frequently associated variables. Our long‐term, large‐scale, and ecologically diverse analysis of bare‐nosed wombats supports spotlight monitoring as a valuable, relatively simple, and affordable survey method in Tasmania and beyond. © 2021 The Wildlife Society.
Keywords	Sarcophilus harrisii ; Vombatus ursinus ; epizootic diseases ; geographical distribution ; rain ; scabies ; surveys ; temperature ; wildlife management ; Tasmania
Language	English
Dates of publication	2021-04
Size	p. 449-461.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	410712-3
ISSN	0022-541X
ISSN	0022-541X
DOI	10.1002/jwmg.22014
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Why some countries but not others? Urbanisation, GDP and endemic disease predict global SARS-CoV-2 excess mortality patterns

Fountain-Jones, Nicholas M. / Charleston, Michael / Flies, Emily / Carver, Scott / Yates, Luke

medRxiv

Abstract: The global impact of the SARS-CoV-2 pandemic has been uneven, with some regions experiencing significant excess mortality while others have been relatively unaffected. Yet factors which predict this variation remain enigmatic, particularly at large ... ...

Abstract	The global impact of the SARS-CoV-2 pandemic has been uneven, with some regions experiencing significant excess mortality while others have been relatively unaffected. Yet factors which predict this variation remain enigmatic, particularly at large spatial scales. We used spatially explicit Bayesian models that integrate socio-demographic and endemic disease data at the country level to provide robust global estimates of excess SARS-CoV-2 mortality (P scores) for the years 2020 and 2021. We find that gross domestic product (GDP), spatial patterns and urbanization are strong predictors of excess mortality, with countries characterized by low GDP but high urbanization experiencing the highest levels of excess mortality. Intriguingly, we also observed that the prevalence of malaria and human immunodeficiency virus (HIV) are associated with country-level SARS-CoV-2 excess mortality in Africa and the Western Pacific, whereby countries with low HIV prevalence but high malaria prevalence tend to have lower levels of excess mortality. While these associations are correlative in nature at the macro-scale, they emphasize that patterns of endemic disease and socio-demographic factors are needed to understand the global dynamics of SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2023-08-09
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.08.06.23293729
Database	COVID19

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Article ; Online: Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time.

McComish, Bennet J / Charleston, Michael A / Parks, Matthew / Baroni, Carlo / Salvatore, Maria Cristina / Li, Ruiqiang / Zhang, Guojie / Millar, Craig D / Holland, Barbara R / Lambert, David M

Genome biology and evolution

2024 Volume 16, Issue 3

Abstract: Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these ... ...

Abstract	Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.
MeSH term(s)	Humans ; Genome ; Genetics, Population ; Mutation ; Microsatellite Repeats ; Polymorphism, Genetic
Language	English
Publishing date	2024-02-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evae017
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