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Article ; Online: The ongoing evolution of UShER during the SARS-CoV-2 pandemic.

Hinrichs, Angie / Ye, Cheng / Turakhia, Yatish / Corbett-Detig, Russell

2023 Volume 56, Issue 1, Page(s) 4–7

MeSH term(s)	Humans ; SARS-CoV-2 ; Pandemics ; COVID-19/epidemiology ; Longitudinal Studies ; Evolution, Molecular
Language	English
Publishing date	2023-12-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-023-01622-5
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Article ; Online: Tracking and curating putative SARS-CoV-2 recombinants with RIVET.

Smith, Kyle / Ye, Cheng / Turakhia, Yatish

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 9

Abstract: Motivation: Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that ... ...

Abstract	Motivation: Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation. Results: We present RIVET-a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants and organize the relevant information in a web interface that would help greatly accelerate the process of identifying and tracking recombinants. Availability and implementation: RIVET-based web interface displaying the most updated analysis of potential SARS-CoV-2 recombinants is available at https://rivet.ucsd.edu/. RIVET's frontend and backend code is freely available under the MIT license at https://github.com/TurakhiaLab/rivet and the documentation for RIVET is available at https://turakhialab.github.io/rivet/. The inputs necessary for running RIVET's backend workflow for SARS-CoV-2 are available through a public database maintained and updated daily by UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/).
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; Databases, Factual ; Documentation ; Software
Language	English
Publishing date	2023-08-31
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad538
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Article: Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages.

Chen, Heidi I / Turakhia, Yatish / Bejerano, Gill / Kingsley, David M

bioRxiv : the preprint server for biology

2023

Abstract: Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced ... ...

Abstract	Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that
Language	English
Publishing date	2023-01-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.30.526059
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Article ; Online: Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.

Chen, Heidi I / Turakhia, Yatish / Bejerano, Gill / Kingsley, David M

Molecular biology and evolution

2023 Volume 40, Issue 9

Abstract: Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years ... ...

Abstract	Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
MeSH term(s)	Animals ; Fishes/genetics ; Genomics ; Genotype ; Smegmamorpha/genetics ; Animal Fins
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msad188
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Article ; Online: Tracking and curating putative SARS-CoV-2 recombinants with RIVET

Smith, Kyle / Ye, Cheng / Turakhia, Yatish

bioRxiv

Abstract: Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being ... ...

Abstract	Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation. We present RIVET - a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants, and organizes the relevant information in a web interface that would help greatly accelerate the process identifying and tracking recombinants.
Keywords	covid19
Language	English
Publishing date	2023-02-19
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.02.17.529036
Database	COVID19

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Article: Maximum likelihood pandemic-scale phylogenetics.

De Maio, Nicola / Kalaghatgi, Prabhav / Turakhia, Yatish / Corbett-Detig, Russell / Minh, Bui Quang / Goldman, Nick

bioRxiv : the preprint server for biology

2022

Abstract: Phylogenetics plays a crucial role in the interpretation of genomic ... ...

Abstract	Phylogenetics plays a crucial role in the interpretation of genomic data
Language	English
Publishing date	2022-07-18
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.03.22.485312
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Article ; Online: Maximum likelihood pandemic-scale phylogenetics.

De Maio, Nicola / Kalaghatgi, Prabhav / Turakhia, Yatish / Corbett-Detig, Russell / Minh, Bui Quang / Goldman, Nick

Nature genetics

2023 Volume 55, Issue 5, Page(s) 746–752

Abstract: Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses of SARS-CoV-2 genomes have shed light on the virus's ... ...

Abstract	Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses of SARS-CoV-2 genomes have shed light on the virus's origins, spread, and the emergence and reproductive success of new variants. However, most phylogenetic approaches, including maximum likelihood and Bayesian methods, cannot scale to the size of the datasets from the current pandemic. We present 'MAximum Parsimonious Likelihood Estimation' (MAPLE), an approach for likelihood-based phylogenetic analysis of epidemiological genomic datasets at unprecedented scales. MAPLE infers SARS-CoV-2 phylogenies more accurately than existing maximum likelihood approaches while running up to thousands of times faster, and requiring at least 100 times less memory on large datasets. This extends the reach of genomic epidemiology, allowing the continued use of accurate phylogenetic, phylogeographic and phylodynamic analyses on datasets of millions of genomes.
MeSH term(s)	Humans ; Phylogeny ; COVID-19/epidemiology ; COVID-19/genetics ; SARS-CoV-2/genetics ; Likelihood Functions ; Pandemics ; Bayes Theorem
Language	English
Publishing date	2023-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-023-01368-0
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Article ; Online: Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.

Schull, James K / Turakhia, Yatish / Hemker, James A / Dally, William J / Bejerano, Gill

Genome biology and evolution

2022 Volume 14, Issue 3

Abstract: We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a ... ...

Abstract	We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared with morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.
MeSH term(s)	Animals ; Genome ; Genomics ; INDEL Mutation ; Mammals ; Nucleotides ; Phylogeny
Chemical Substances	Nucleotides
Language	English
Publishing date	2022-03-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evac013
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Article: Identifying SARS-CoV-2 regional introductions and transmission clusters in real time.

McBroome, Jakob / Martin, Jennifer / de Bernardi Schneider, Adriano / Turakhia, Yatish / Corbett-Detig, Russell

Virus evolution

2022 Volume 8, Issue 1, Page(s) veac048

Abstract: The unprecedented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too ... ...

Abstract	The unprecedented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too computationally expensive to apply to densely sampled, rapidly expanding datasets when results are needed immediately to inform public health action. For example, public health is often concerned with identifying clusters of closely related samples, but the sheer scale of the data prevents manual inspection and the current computational models are often too expensive in time and resources. Even when results are available, intuitive data exploration tools are of critical importance to effective public health interpretation and action. To help address this need, we present a phylogenetic heuristic that quickly and efficiently identifies newly introduced strains in a region, resulting in clusters of infected individuals, and their putative geographic origins. We show that this approach performs well on simulated data and yields results largely congruent with more sophisticated Bayesian phylogeographic modeling approaches. We also introduce Cluster-Tracker (https://clustertracker.gi.ucsc.edu/), a novel interactive web-based tool to facilitate effective and intuitive SARS-CoV-2 geographic data exploration and visualization across the USA. Cluster-Tracker is updated daily and automatically identifies and highlights groups of closely related SARS-CoV-2 infections resulting from the transmission of the virus between two geographic areas by travelers, streamlining public health tracking of local viral diversity and emerging infection clusters. The site is open-source and designed to be easily configured to analyze any chosen region, making it a useful resource globally. The combination of these open-source tools will empower detailed investigations of the geographic origins and spread of SARS-CoV-2 and other densely sampled pathogens.
Language	English
Publishing date	2022-06-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veac048
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Article ; Online: DecentTree: scalable Neighbour-Joining for the genomic era.

Wang, Weiwen / Barbetti, James / Wong, Thomas / Thornlow, Bryan / Corbett-Detig, Russ / Turakhia, Yatish / Lanfear, Robert / Minh, Bui Quang

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 9

Abstract: Motivation: Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of generating new ... ...

Abstract	Motivation: Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which Neighbour-Joining is a useful approach, new implementations of existing methods are warranted. Results: Here, we present DecentTree, which provides highly optimized and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g. it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g. RapidNJ) when generating a tree of 64 000 SARS-CoV-2 genomes. Availability and implementation: DecentTree is open source and freely available at https://github.com/iqtree/decenttree. All code and data used in this analysis are available on Github (https://github.com/asdcid/Comparison-of-neighbour-joining-software).
MeSH term(s)	Humans ; Phylogeny ; COVID-19 ; SARS-CoV-2/genetics ; Genomics ; Gene Library
Language	English
Publishing date	2023-08-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad536
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