Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 8, 2022

Subfamily Rubioideae is the largest of main lineages in coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes other major clades within this group plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from organellar genomes nuclear ribosomal DNA, we here use a large number low-copy genes obtained via target capture approach to infer phylogenetic Rubioideae. We included 101 representing all but two (the monogeneric Foonchewieae Aitchinsonieae) currently recognized tribes, one non-monogeneric tribe were represented by more than genus. Using 353 targeted universal Angiosperms353 probe set investigated impact type, analytical approach, potential paralogs on reconstruction. inferred robust hypothesis vast majority (or all) nodes being highly supported across analyses datasets few incongruences between topologies. The results similar those novel also identified. found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS levels support gene tree congruence. full (353 genes) potentially paralogous removed (186 increased incongruence slightly. pattern conflict at short internal branches often consistent high incomplete lineage sorting (ILS) due rapid speciation group. concatenation- coalescence-based trees agreed, observed discordance approaches may be best explained their differences accounting for ILS. greatly improved our confidence understanding phylogeny, highlighted previously uncertain possibility explore sources underlying discordance.

Language: Английский

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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 27, 2024

Resolving the phylogeny of rapidly radiating lineages presents a challenge when building Tree Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that diversified at Pliocene-Pleistocene boundary.

Language: Английский

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Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Published: May 27, 2024

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking step-change in the generation of data phylogenetic inference. While this advancement facilitated resolution many relationships, conflict continues to be reported, often attributed genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common evolution. The proliferation methods designed analyse target presence these can overwhelming researchers, especially students. In review, we guide researchers through bioinformatic workflow, with particular focus on robust inference conflict. Through highlight key considerations reducing artefactual conflict, synthesise strategies managing paralogs, explain causes measurement summarise current investigating biological underlying draw from examples Australian flora, review is broadly relevant any researcher working data. We conclude inherent inevitable but when properly managed, provide unprecedented insight into extraordinary complex histories plants.

Language: Английский

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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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Phylogenetic relationships and the repeated loss of traits associated with sicklebill pollination in Centropogon subgenus Centropogon (Campanulaceae)

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: March 10, 2025

Centropogon subgenus comprises 55 species found primarily in midelevation Andean forests featuring some of the most curved flowers among angiosperms. Floral curvature is linked to coevolution with sicklebill hummingbird, which pollinates species. Despite charismatic flowers, there limited knowledge about phylogenetic relationships and floral evolution. We conducted first densely sampled phylogenomic analysis clade using methods that account for incomplete lineage sorting on a sequence capture dataset generated lineage-specific probe set. Using comparative methods, we test correlated evolution two traits central pollination. improve understanding by more than doubling past taxon sampling. confirm monophyly sections, non-monophyly remaining sections. The characterized high gene tree discordance. Three widespread display contrasting dynamics, C. cornutus forming granulosus solanifolius non-monophyletic, biogeographically clustered lineages. Correlated inflorescence structure has led multiple putative losses adds growing body literature plant clades This phylogeny serves as foundational framework further macroevolutionary investigations into environmental biogeographic factors shaping pollination-related traits.

Language: Английский

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