Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(5), P. e0302365 - e0302365

Published: May 20, 2024

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage off-target proportion reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly resulted comprehensive dataset robust inference phylogenetic relationships, where most intratribal intertribal are resolved with strong support. While results were mostly agreement studies data, novel plastid perspective also detected. For example, our analyses provide support for SCOUT clade its sister relationship remaining members subfamily, which differs from but agrees recent data. However, several instances highly supported discordance identified across phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain majority discordant introgression may be better explanation some cases. Our further plastomes are, few exceptions, conserved mainly conform structure, gene content, order present flowering plants.

Language: Английский

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Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(17)

Published: Aug. 15, 2024

Most tree species underwent cycles of contraction and expansion during the Quaternary. These led to an ancient complex genetic structure that has since been affected by extensive gene flow strong local adaptation. The extent which hybridization played a role in this multi-layered is important be investigated. To study effect on joint population two dominant Eurasian boreal forest, Picea abies P. obovata, we used targeted resequencing obtained around 480 K nuclear SNPs 87 chloroplast 542 individuals sampled across most their distribution ranges. Despite clear pattern Isolation-by-Distance, distinct clusters emerged, indicating presence barriers corridors migration. Two cryptic refugia located large hybrid zone between critical shaping current distributions. repeatedly hybridized Pleistocene direction introgression depended latitude. Our suggests helped both overcome main shifts ranges glacial highlights importance considering whole instead separate entities retrieve demographic histories.

Language: Английский

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Revisiting the phylogeny of Primulaceae s.l. using whole plastid genomes: Highlighting phylogenetic conflicts and their implications

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 20, 2025

Abstract The family Primulaceae s.l. is estimated to comprise approximately 60 genera and 2600 species worldwide. Although extensive research has been conducted on the its subfamily boundaries, there a lack of systematic studies utilizing complete plastid genome data, leading uncertainties in phylogenetic positions certain key taxa, such as Stimpsonia . In this study, genomic data were collected from 67 accessions representing four subfamilies 28 within family. Phylogenetic trees constructed using coalescent concatenated approaches elucidate evolutionary history By employing comprehensive dataset genomes all subfamilies, robust framework for was established. Contentious relationships identified at early stages divergence Primula among Cyclamen relatives, probably due rapid diversification. Our support idea that sister remainder Primuloideae, contrast with placement Myrsinoideae based nuclear data. A cytonuclear discordance position also detected Aegiceras corniculatum time estimates study align previous findings, indicating significant diversification events during Eocene Oligocene epochs. These timeframes coincide major geological climatic changes, which likely have influenced distribution Primulaceae. results underscore complex lay groundwork future aimed unraveling intricate dynamics

Language: Английский

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Morphology and molecules revealed a remarkable new genus of Lamiaceae, a surprising discovery in south‐eastern Europe

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

Published: Feb. 18, 2025

Abstract Petrolamium crnojevicii gen. & sp. nov., a new distinct and remarkable monotypic genus of Lamiaceae, was discovered in the Dinaric karst southern Montenegro. This taxon exhibits unique combination morphological traits, including eglandular, mostly glabrous reniform leaves with 5–7 lobes prominent hydatodes at their tips. Its small pedicellate flowers feature included anthers styles within corolla tube, straight, narrow, emarginate to bifurcate posterior lip, an anterior lip entire, broadly elliptic‐oblong lateral lobes. The trigonous mericarps have truncated apex bear fatty tissue. Notably, has chromosome number 2 n = 32. A molecular phylogenetic analysis, based on 79 plastid protein‐coding genes 5 chloroplast markers placed subfamily Lamioideae, where it forms lineage, sister other members tribe Lamieae. is also from ecological point view, as exclusively inhabits floristically depauperate calcareous rock crevices very restricted distribution range. makes P. critically endangered species according IUCN criteria emphasizes need for immediate conservation efforts. study highlights importance ongoing floristic exploration, demonstrating that even regions long considered botanically well‐known, important discoveries can still emerge, extensively investigated plant families like Lamiaceae.

Language: Английский

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Species delimitation in the Polygonatum odoratum complex (Asparagaceae) based on phylogenomic and morphometric data

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

Published: Feb. 28, 2025

Abstract Defining species and delineating boundaries among closely related is challenging particularly for complexes with a recent history of diversification. The Polygonatum odoratum complex, consisting seven taxa, presents compelling example showing unresolved taxonomic boundaries. Here, we aim to delimit in the complex using genomic morphometric data. Target enrichment was employed analyze 40 accessions representing taxa complex. We inferred tree coalescent maximum likelihood approaches nuclear plastid Additionally, examined 14 morphological characters from 851 herbarium specimens conducted analysis factor mixed phylogenomic analysis, based on 297 genes, strongly supports presence three monophyletic clades diversification (<4 million years). Coupled our examinations, findings demonstrate existence distinct species, revising previous classification taxa. By applying an integrated concept, study resolves updates taxonomy P.

Language: Английский

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