Phylogenomics shed light on the complex evolutionary history of a gymnosperm genus showing East Asian–Tethyan disjunction

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

Published: Jan. 3, 2025

Abstract When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species Asia three Mediterranean region. Here we used target‐capture sequencing obtained 1991 single‐copy nuclear genes, plus complete plastomes, to infer evolutionary history . Our phylogenomic reconstruction resolved four well supported clades , but revealed significant phylogenetic conflicts, inter‐lineage gene flow, incomplete lineage sorting tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between ancestors Himalayan–Hengduan Mountains subtropical clades, whereas orogenic climatic changes may have facilitated flow within clade. Molecular dating suggested that recent common ancestor appeared around middle Eocene period then became continuously distributed across Eurasia. when diverged, been driven Eocene/Oligocene declines global temperature, reinforced ecogeographic barrier created uplift Qinghai–Tibet Plateau. Niche shifts clade, signatures selection genes for drought salt tolerance, probably indicate adaptation local conditions. Overall, our study in‐depth analyses are powerful tools deciphering complex origin organisms, especially gymnosperms.

Language: Английский

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Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Feb. 7, 2020

The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya Rhaphiolepis have been supported to form a clade, the monophyly at genus level has never well tested their phylogenetic positions Maleae still remain uncertain. This study aims reconstruct robust phylogeny ER framework with broad taxon sampling clarify relationship between Rhaphiolepis. employed sequences whole plastome (WP) entire nuclear ribosomal DNA (nrDNA) repeats assembled from genome skimming approach included 83 samples representing 76 32 genera Rosaceae, especially Maleae. Maximum Likelihood (ML) Bayesian Analysis (BI) based on three datasets, i.e., WP, coding (CDS), nrDNA, strongly paraphyly Eriobotrya, within which was nested. Our plastid tree sister Heteromeles, nrDNA tree, however, did not resolve placement Strong incongruence trees is most likely explained by hybridization events, may played an important role evolutionary history clade. Molecular, morphological, geographic evidence all supports merge Rhaphiolepis, nomenclatural priority. We herein transferred 36 taxa also proposed new name, loquata B.B.Liu & J.Wen, for economically loquat, as specific epithet "japonica" pre-occupied

Language: Английский

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The case for the continued use of the genus name Mimulus for all monkeyflowers

Taxon, Journal Year: 2019, Volume and Issue: 68(4), P. 617 - 623

Published: Aug. 1, 2019

Language: Английский

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Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

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

Published: March 20, 2020

With its large proportion of endemic taxa, complex geological past, and location at the confluence highly diverse Malesian Australian floristic regions, Papuasia - region comprising Bismarck Archipelago, New Guinea, Solomon Islands represents an ideal natural experiment in plant biogeography. However, scattered knowledge flora limited representation herbaria have hindered our understanding drivers diversity. Focusing on woody angiosperm genus Schefflera (Araliaceae), we ask whether morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, where (within or elsewhere) they diversified. To address questions, use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with angiosperm-wide bait kit targeting 353 single-copy nuclear loci) genome shotgun (which allows retrieval regions high-copy number, e.g., organellar DNA) historical herbarium collections. reconstruct evolutionary history molecular phylogenies with Bayesian inference, maximum likelihood, pseudo-coalescent approaches, co-estimate divergence times ancestral areas framework. We find strong support for most morphological groupings, as currently circumscribed, show efficacy Angiosperms-353 probe resolving both deep shallow phylogenetic relationships. infer sequence colonization to explain present-day distribution Papuasia: from Sunda Shelf, arrived Woodlark plate (present-day eastern Guinea) late Oligocene (when Guinea was submerged) and, subsequently (throughout Miocene), it migrated westwards (to Maoke Bird's Head Plates thereon) further diversified, agreement previous reconstructions.

Language: Английский

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Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1201 - 1216

Published: June 27, 2021

Premise Both universal and family‐specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, equally as capable resolving intergeneric custom kits. Furthermore, strength combining from both to mitigate bias provide a more robust result resolve evolutionary relationships. Methods We sampled 23 Ochnaceae genera two kits, Angiosperms353 kit kit. maximum likelihood inference concatenated matrix loci multispecies‐coalescence approaches infer family. explored informativeness impact missing on resolution tree support. Results For set, concatenation approach provided results congruent those Ochnaceae‐specific set. Filtering was most impactful relaxed threshold being optimum scenario. The set resolved consistent topologies using methods, no major improvements were obtained after filtering. Merging resulted well‐supported tree. Conclusions improved upon played an important role reconstruction. backbone well family specific All analyses indicated Sauvagesia L. Campylospermum Tiegh. currently circumscribed polyphyletic require revised delimitation.

Language: Английский

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