Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Language: Английский

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Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(5), P. 1020 - 1043

Published: March 11, 2022

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes 75 complete plastomes were used to infer the phylogenetic relationships estimate historical biogeography apple genus Malus sensu lato, economically important lineage disjunctly distributed in Northern Hemisphere involved known suspected hybridization allopolyploidy events. The phylogeny recovered monophyly s.l. (including Docynia); however, was be biphyletic plastid phylogeny. An ancient chloroplast capture event Eocene western North America best explains cytonuclear discordance. Our conflict analysis ILS, hybridization, could explain widespread gene tree One deep (Malus doumeri) one recent coronaria) detected Furthermore, our biogeographic integrating living fossil a East Asian-western American origin Eocene, followed by several extinction dispersal events Hemisphere. We also propose general workflow for assessing phylogenomic discordance using genome skimming sets.

Language: Английский

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Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

PhytoKeys, Journal Year: 2022, Volume and Issue: 205, P. 3 - 58

Published: Aug. 22, 2022

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically economically important group trees, shrubs lianas a pantropical distribution. Despite major advances last few decades towards aligning clades across Caesalpinioideae, generic delimitation remains state considerable flux, especially mimosoid clade. We test monophyly via phylogenomic analysis 997 nuclear genes sequenced targeted enrichment (Hybseq) for 420 147 currently recognised subfamily. show that 22 are non-monophyletic or nested other non-monophyly concentrated clade where 25% 90 found to be non-monophyletic. suggest two main reasons this pervasive non-monophyly: (i) extensive morphological homoplasy we document here handful traits and, particularly, repeated evolution distinctive fruit types were historically emphasised delimiting (ii) artefact lack taxonomic syntheses sampling previous phylogenies consequent failure identify span Old World New conversely amphi-Atlantic non-monophyletic, both which critical large Finally, discuss taxon era how assessing patterns gene tree conflict can provide additional insights into delimitation. This new framework provides foundations series papers reclassifying presented

Language: Английский

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Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: April 25, 2022

Abstract Background Deep-branching phylogenetic relationships are often difficult to resolve because signals obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- shallow-scale across all branches tree life. The olive family (Oleaceae) is composed 25 genera classified into five tribes with tribe Oleeae consisting four subtribes. Previous analyses showed that ILS and/or hybridization led incongruence family. It was essential distinguish signal conflicts, explore mechanisms uncertainties concerning family, especially at deep-branching nodes. Results We used whole plastid genome nuclear single nucleotide polymorphism (SNP) data infer assess variation rates among main clades also 2608 1865 orthologous genes Oleaceae subtribes Oleeae, respectively. Concatenated coalescence trees based on genome, SNPs multiple suggest events introgression during diversification Oleaceae. Additionally, there extreme heterogeneity substitution tribes. Furthermore, our results supported rather than ILS, factor discordance have originated via polyploidy, its most likely parentages ancestral Jasmineae or sister group, which a “ghost lineage,” Forsythieae. However, mainly responsible Oleeae. Conclusions This study showcases using sequence datasets (plastid genomes, thousands genes) diverse phylogenomic methods partition, heterogeneous models, quantifying branch lengths (QuIBL) analysis, species network analysis can facilitate untangling complex processes introgression, paleopolyploidization, ILS.

Language: Английский

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Phylogenomics and evolution of the Acer section Lithocarpa

Scientia Horticulturae, Journal Year: 2025, Volume and Issue: 341, P. 113988 - 113988

Published: Jan. 29, 2025

Language: Английский

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Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 163, P. 107235 - 107235

Published: June 17, 2021

Language: Английский

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Climate‐influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(5), P. 1183 - 1203

Published: Feb. 11, 2023

The north temperate region was characterized by a warm climate and rich thermophilic flora before the Eocene, but early diversifications of biome under global change shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression an important driving force speciation in plant diversity. Here, we applied analyses from biogeography phylogenetic networks to account for both introgression incomplete lineage sorting based on genomic data New World Vitis, charismatic component North American with known suspected gene flow among species. Biogeographic inference fossil evidence suggest grapes were widely distributed America Europe during Paleocene followed widespread extinction survival relicts tropical World. During warming Miocene, Vitis ancestor migrated northward refugia subsequent diversification region. We found strong incongruence reticulate evolution nuclear genes within recent ancient lineages Vitis. Furthermore, organellar genomes showed conflicts inferred species tree genomes. Our phylogenomic provided assessment wide occurrence which potentially represents one most mechanisms even entire Northern Hemisphere. scenario report here may be common model flowering plants adapted cooling fluctuation Neogene.

Language: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

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Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 11, 2023

Abstract The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) Streptophyta (consisting charophytes land plants). Lineages sister to core Chlorophyta, informally refer as prasinophytes, form grade mainly planktonic algae. Recently, one these lineages, Prasinodermophyta, which is previously grouped with has been identified lineage both Streptophyta. Resolving deep relationships among plants crucial for understanding historical impact algal diversity on ecology geochemistry, but proven difficult given ancient timing diversification events. Through extensive taxon gene sampling, we conduct large-scale phylogenomic analyses resolve reveal Prasinodermophyta raising questions about necessity classifying distinct phylum. We unveil that incomplete sorting cause discordance regarding placement Prasinodermophyta. Molecular dating suggest crown-group date back Paleoproterozoic-Mesoproterozoic. Our study establishes plausible link between oxygen levels in Paleoproterozoic-Mesoproterozoic origin Viridiplantae.

Language: Английский

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