Integrating Phylogenies with Chronology to Assemble the Tree of Life DOI
Jose Barba‐Montoya, Jack M. Craig, Sudhir Kumar

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey published literature shows that individual are frequently restricted specific taxonomic groups due expertise investigators and evolutionary considerations, resulting in any given present minuscule fraction phylogenies. We novel approach, called chronological supertree algorithm (Chrono-STA), can build from such data by using node ages scaled time. Chrono-STA builds organisms integrating timetrees. It fundamentally differs existing generate consensus gene trees missing taxa, as does not impute nodal distances, use guide tree backbone, or reduce quartets. Analyses simulated empirical datasets show combine taxonomically timetrees extremely overlap. For data, distances assemble phylogenetic quartets did perform well. conclude via temporal dimension enhances accuracy reconstructed supertrees also

Language: Английский

Phylogenomics Of Boraginaceae and Boraginales Using Lineage-Specific and Angiosperms353 Loci DOI
James I. Cohen

Systematic Botany, Journal Year: 2025, Volume and Issue: 49(4), P. 749 - 767

Published: Jan. 6, 2025

Abstract— During the past 20 yr, phylogenetics of Boraginaceae has taken shape using plastid DNA regions and nuclear ribosomal internal transcribed spacer (ITS), but these only reflect a limited understanding evolutionary history family. Using hybridization-enrichment sequencing, 531 from lineage-specific Angiosperms353 loci were sequenced aligned for 49 species across Boraginaceae. Additionally, incorporated with broader dataset same 115 accessions Boraginales relatives. Based on multiple phylogenetic approaches datasets, resolved phylogenies quite similar to our current understanding, yet taxa recognized in different positions. These included: 1) Echiochiloideae as sister Cynoglossoideae instead rest entire family, 2) Moritzinae nested within Boragininae, 3) Lasiocaryeae Trichodesmeae not sisters. positions recovered, via methods, hundreds suggest that incomplete lineage sorting, hybridization, shifts substitution rates may have occurred during early origin In analyses Boraginales, Namaceae was non-monophyletic, providing evidence Hydrophyllaceae again be appropriate, Lennoaceae Ehretiaceae. While both sets allowed well-resolved well-supported phylogeny reconstructed, recovered some more intriguing relationships part because appear less conserved than those Angiosperms353. The two provide an interesting complement patterns evolution family order.

Language: Английский

Citations

1
Integrating phylogenies with chronology to assemble the tree of life DOI Creative Commons
Jose Barba‐Montoya, Jack M. Craig, Sudhir Kumar

et al.

Frontiers in Bioinformatics, Journal Year: 2025, Volume and Issue: 5

Published: April 30, 2025

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey published literature shows that individual are frequently restricted specific taxonomic groups due investigators' expertise and evolutionary considerations, resulting in any given present minuscule fraction phylogenies. We novel approach, called chronological supertree algorithm (Chrono-STA), can build from such data by using node ages scaled time. Chrono-STA builds integrating timetrees. It fundamentally differs existing generate consensus gene trees missing taxa, as does not impute nodal distances, use guide tree backbone, or reduce quartets. Analyses simulated empirical datasets show combine taxonomically timetrees extremely overlap. For data, distances assemble phylogenetic quartets did perform well. conclude via temporal dimension enhances accuracy reconstructed supertrees also

Language: Английский

Citations

0
Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny DOI Creative Commons
Edward L. Braun, Carl H. Oliveros, Noor D. White

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 3, 2024

The evolutionary histories of different genomic regions typically differ from each other and the underlying species phylogeny. This makes tree estimation challenging. Here, we examine performance phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, living birds. We compared trees generated by maximum likelihood (ML) analysis concatenated data, gene summary methods, SVDquartets. also conduct first empirical test “new” method called METAL (Metric algorithm for Estimation Trees based on Aggregation Loci), which is distances calculated data. conducted this novel dataset comprising more than 4,000 ultraconserved element (UCE) loci almost all bird families two existing UCE intron datasets sampled avian orders. identified “reliable clades” very likely to be present in true used them assess performance. ML analyses data recovered reliable clades with less greater robustness missing methods. clades, but only performed well largest datasets. Gene (weighted ASTRAL weighted ASTRID) well; they required concatenation. SVDquartets exhibited worst tested. In addition methodological insights, study provides estimate 99% currently recognized families. Only one 181 examined was consistently resolved differently concatenation versus suggesting it may possible achieve consensus deep extant

Language: Английский

Citations

3
A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction DOI
Ethan Tolman, Christopher D. Beatty, Manpreet K. Kohli

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 200, P. 108185 - 108185

Published: Aug. 30, 2024

Language: Английский

Citations

3
Integrating Phylogenies with Chronology to Assemble the Tree of Life DOI
Jose Barba‐Montoya, Jack M. Craig, Sudhir Kumar

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey published literature shows that individual are frequently restricted specific taxonomic groups due expertise investigators and evolutionary considerations, resulting in any given present minuscule fraction phylogenies. We novel approach, called chronological supertree algorithm (Chrono-STA), can build from such data by using node ages scaled time. Chrono-STA builds organisms integrating timetrees. It fundamentally differs existing generate consensus gene trees missing taxa, as does not impute nodal distances, use guide tree backbone, or reduce quartets. Analyses simulated empirical datasets show combine taxonomically timetrees extremely overlap. For data, distances assemble phylogenetic quartets did perform well. conclude via temporal dimension enhances accuracy reconstructed supertrees also

Language: Английский

Citations

1