Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

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

Published: July 30, 2024

Abstract In contrast to the traditional Tree of Life (ToL) paradigm, Web (WoL) model provides a more nuanced and precise depiction organismal phylogeny, particularly considering prevalent incongruence observed among gene/species trees. The lack generalized pipeline for teasing apart potential evolutionary mechanisms—such as Incomplete Lineage Sorting (ILS), hybridization, introgression, polyploidization, Whole-Genome Duplication—poses significant challenges delineation WoL. pear genus Pyrus , characterized by extensive hybridization events, serves an excellent investigating This study introduces novel Step-by-Step Exclusion (SSE) approach deciphering complexities inherent in Our findings indicate: 1) ILS, rather than is identified primary driver behind origin from arid regions Himalayas-Central Asia; 2) two subgenera have independent trajectories, facilitated geographical barriers that arose via uplift Tibetan Plateau increased aridity Central 3) ILS diversification Oriental pears, while alone has driven reticulate evolution Occidental pears; 4) establishment Silk Road during Han Dynasty acted conduit genetic exchange between pears. SSE universally applicable framework mechanisms defining WoL paradigm.

Language: Английский

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A taxon-rich and genome-scale phylogeny of Opisthokonta

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(9), P. e3002794 - e3002794

Published: Sept. 16, 2024

Ancient divergences within Opisthokonta—a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives—remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods established geological timeline diversification. We also sensitivity by subsampling or taxa from full data matrix based on filtering criteria previously shown to improve inference. found approximately 85% internal branches were congruent across matrices approaches used. Notably, use was substantial contributor observed incongruence: analyses same set orthologs showed high congruence 97% 98%, whereas resulted somewhat lower (87% 91%). Examination Holozoa relationships suggests instability varying gene may stem weak phylogenetic signals. Our results provide comprehensive framework will be useful for illuminating ancient evolutionary episodes concerning origin diversification 2 eukaryotic emphasize importance investigating effects resolve divergences.

Language: Английский

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A thorny tale: The origin and diversification of Cirsium (Compositae)

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 204, P. 108285 - 108285

Published: Jan. 11, 2025

Language: Английский

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Current state and future prospects of Horizontal Gene Transfer detection

NAR Genomics and Bioinformatics, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 7, 2025

Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is driving force evolutionary changes prokaryotes. It widely recognized that it contributes the emergence antimicrobial resistance (AMR), which poses particularly serious threat public health. Many computational approaches have developed study and detect HGT. However, application AI this field not investigated. In work, we conducted review provide information on current trend existing for detecting HGT decipher use field. Here, show growing interest detection, characterized by surge number approaches, including AI-based recent years. We organize into hierarchical structure groups based their methods how each group evolved. make recommendations discuss challenges detection general adoption particular. Moreover, future directions detection.

Language: Английский

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Systematics and biogeography of the Holarctic dragonfly genus Somatochlora (Anisoptera: Corduliidae)

Systematic Entomology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

Abstract The striped emeralds ( Somatochlora Selys) are a Holarctic group of medium‐sized metallic green dragonflies that mainly inhabit bogs and seepages, alpine streams, lakes, channels lowland brooks. With 42 species they the most diverse genus within Corduliidae (Odonata: Anisoptera). Systematic, taxonomic biogeographic resolution remains unclear, with numerous hypotheses relatedness based on wing veins, male claspers (epiproct paraprocts) nymphs. Furthermore, borisi was recently described as new Corduliochlora ) 17 morphological characters, but its position respect to is unclear. We present phylogenetic reconstruction using Anchored Hybrid Enrichment (AHE) sequences 40/42 (including ). Our data recover monophyly , C. recovered sister remaining . also three highly supported clades one mixed support; this lack likely due incomplete lineage sorting, third‐codon saturation iterative analyses run variations our dataset hybridization. we constructed for all 20 characters from literature which were used evaluate groups molecular data; support validity distinct Finally, divergence time estimation analysis indicate originated in Western North Hemisphere during Miocene, dispersal events Eastern (11, 7 5 Ma, respectively) across Beringian Land Bridge.

Language: Английский

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