Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(19)

Published: May 5, 2025

Hawaiian lobeliads exhibit extensive adaptive radiations and are considered the largest plant clade (143 species) endemic to any oceanic archipelago. Rapid insular prone reticulate evolution, yet detecting hybridization is often limited by inadequate sampling of taxa or independent loci. We analyzed 633 nuclear loci (including tetraploid duplications) whole plastomes for 89% extant species derive phylogenies lobeliads. Nuclear data provide strong support nine major clades in both likelihood ASTRAL analyses. All genera/sections monophyletic except Clermontia Cyanea . plastome conflict on short, deep branches; tree resolves a fleshy-fruited Clermontia/Cyanea-Brighamia/Delissea , sister Polynesian Sclerotheca with capsular-fruited clade. Incomplete lineage sorting rapid radiation starting 8.5–11.3 Ma sufficient explain uncertainty cytonuclear discordance along backbone. Sequence reticulation within especially identify 42 interisland dispersal events: accord strict progression rule, involving movement next younger island hotspot chain, consistent theory. Plastid overestimate such events 17%. have undergone parallel elevational distribution flower length all islands, multiple founders some differences. lobeliad diversification was driven an early intergeneric divergence habitat, followed ecological speciation Clermontia/Cyanea combined widespread single-island endemism, frequent dispersal, occasional hybridization.

Language: Английский

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Phylogeny and new sectional classification for the Cape Clade of the genus Indigofera (Fabaceae: Indigofereae)

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: May 9, 2025

Abstract The genus Indigofera in the Greater Cape Floristic Region (GCFR) comprises a diverse assortment of species. Almost 90% region's species belong to Clade, while remaining are scattered among other three globally distributed clades. As prelude species‐level revision, we aimed revise sectional classification making use molecular and morphological data. We present near‐complete sampled phylogenies representing ca. 95% within GCFR, using nuclear ITS region plastid regions. Ancestral state reconstructions identified several characters that, as unique suites traits, can help distinguish different sections/subsections, rather than single diagnostic traits. A total‐evidence phylogeny based on both morphology data strongly supports recognition eight sections Clade. sect. Brachypodae , Digitatae Juncifoliae Oligophyllae Productae maintained refined from previous classifications. cytisoides I. merxmuelleri nudicaulis circumscribed into new monospecific ( Cytisoidae Merxmuelleranae Nudicaules ), characters. most sections, each further divided four subsections.

Language: Английский

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Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: March 17, 2020

Despite the commercial importance of Concord grape, its origin has remained unresolved for over 150 years without a comprehensive phylogenetic analysis. In this study we aimed to reconstruct evolutionary history grape using sequence data from four nuclear markers (AT103, GAI1, PHYA, and SQD1), six plastid (matK, psbA-trnH, petN-trnC, ycf1, trnL-F, trnS-G), genome. We sampled extensively Vitis species native northeastern North America as well representative Europe Asia, including commercially important vinifera (wine grape), European with hermaphroditic flowers, wild progenitor, V. subsp. sylvestris. also sequenced genome one accession compared recently published set plastomes. Phylogenetic analyses maximum likelihood Bayesian inference support hybrid grape. The results clearly pinpoint wine vinifera, maternal donor fox labrusca, which is common in America, paternal donor. Moreover, infer that breeding must have involved backcrossing F1 parent labrusca. This explains higher morphological similarity labrusca than vinifera. provides concrete genetic evidence widespread cultivar is, therefore, promising similar future studies focused on resolving ambiguous origins major crops or create successful fruit crops.

Language: Английский

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RADseq resolves the phylogeny of Hawaiian Myrsine (Primulaceae) and provides evidence for hybridization

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 58(6), P. 823 - 840

Published: Aug. 5, 2020

Abstract The Hawaiian radiation of Myrsine (primrose family, Primulaceae) is the only one among ten most species‐rich plant lineages that has never been included in a phylogenetic analysis. Our study based on RADseq dataset nearly all species and Sanger sequencing worldwide sampling related genera. as whole might be paraphyletic with respect to monotypic Macaronesian genera Heberdenia Pleiomeris , whereas resolved monophyletic. proved insufficient resolve lineage, fully relationships high support. consists three main lineages, which contains majority mainly confined Kauaʻi, other two primarily consist few widespread species. Although reconstructions delivered supported tree topologies, Quartet Sampling HyDe analyses reveal incongruence throughout phylogeny provide first molecular evidence extensive hybridization lineage.

Language: Английский

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Assessing the fit of the multi-species network coalescent to multi-locus data

Bioinformatics, Journal Year: 2020, Volume and Issue: 37(5), P. 634 - 641

Published: Sept. 22, 2020

With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These include events like hybridization, gene flow or horizontal transfer explicitly. However, the most accurate network inference methods are computationally heavy. Methods that scale to larger do not calculate full likelihood, such traditional likelihood-based tools for model selection applicable decide how many past hybridization best fit data. We propose here goodness-of-fit test quantify between data observed multi-locus data, and patterns expected under multi-species coalescent on candidate network.We identified weaknesses in previously proposed TICR test, corrections. The performance our new was validated by simulations real-world networks. Our provides one first rigorous selection, select adequate complexity at hand. also work identifying poorly inferred areas network.Software is available as Julia package https://github.com/cecileane/QuartetNetworkGoodnessFit.jl.Supplementary Bioinformatics online.

Language: Английский

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Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1217 - 1233

Published: June 8, 2021

Premise Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger‐sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within larger triternatum complex could be resolved. Therefore, we attempt resolve these boundaries here. Methods The Angiosperms353 probe set was employed ambiguity species using 48 accessions assigned L. packardiae , or . In addition exon data, 54 nuclear introns were extracted and complete for all samples. Three approaches used estimate evolutionary relationships define boundaries: STACEY, a Bayesian coalescent‐based tree analysis that takes incomplete lineage sorting into account; ASTRAL‐III, another analysis; concatenated approach MrBayes. Climatic factors, characters, soil variables measured analyzed provide additional support recovered groups. Results STACEY three major clades seven subclades, of which geographically structured, some correspond previously named taxa. No other had full agreement between parameters. niche leaflet width length predictive ability clades. Conclusions results suggest groups in process incipient speciation has been barrier resolving this previously. These hypothesized through sequencing multiple loci analyzing processes.

Language: Английский

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Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 184, P. 107808 - 107808

Published: May 6, 2023

Language: Английский

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Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(6), P. 1183 - 1197

Published: Jan. 15, 2021

Abstract Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand evolutionary process organisms using species‐rich Himalaya–Hengduan taxa bamboos ( Fargesia Franchet Yushania Keng). We constructed trees sampling strategies reconstruction methods based on genome skimming double digest restriction‐site‐associated DNA sequencing data. assessed congruence topologies generated from datasets employed several approaches reveal causes incongruence, including detection hybridization introgression PhyloNetworks D ‐statistic test (ABBA‐BABA test). found that, plastome‐based phylogeny, can be clustered into three groups was nested within one them, which contradicts nuclear–double sequencing‐based phylogeny. Moreover, genetic variation chloroplast significantly correlated geographical distribution. The strong signal incomplete lineage sorting, hybridization, introgression, cytoplasmic gene flow among genera species suggests that reticulate main cause for incongruence between nuclear datasets. Our results add evidence genomes distinct histories suggest prevalent rapidly diversifying groups.

Language: Английский

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Phylogenetic and functional trait‐based community assembly within Pacific Cyrtandra (Gesneriaceae): Evidence for clustering at multiple spatial scales

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(5)

Published: May 1, 2023

Tropical rainforest communities are often characterized by a small number of species-rich genera that contribute disproportionately to the alpha diversity in these habitats. In Pacific Basin, there nearly 200 species

Language: Английский

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TINNiK: inference of the tree of blobs of a species network under the coalescent model

Algorithms for Molecular Biology, Journal Year: 2024, Volume and Issue: 19(1)

Published: Nov. 5, 2024

The tree of blobs a species network shows only the tree-like aspects relationships taxa on network, omitting information substructures where hybridization or other types lateral transfer genetic occur. By isolating such regions inference can serve as starting point for more detailed investigation, indicate limit what may be inferrable without additional assumptions. Building our theoretical work identifiability from gene quartet distributions under Network Multispecies Coalescent model, we develop an algorithm, TINNiK, statistically consistent inference. We provide examples its application to both simulated and empirical datasets, utilizing implementation in MSCquartets 2.0 R package.

Language: Английский

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