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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Population structure and phylogeography of three closely related tree peonies

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(6)

Published: June 1, 2023

Abstract Paeonia decomposita , rotundiloba and rockii are three closely related species of Sect. Moutan is distributed in the montane area Eastern Hengduan Mountain region. Understanding population history these tree peony could contribute to unraveling evolutionary patterns undergrowth this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) two chloroplast markers ( matK ycf1 ) reconstruct phylogeographic pattern populations. In total, 228 individuals from 17 populations were analyzed study. Three clades (Clade I – Clade III) four maternal A D) reconstructed. Molecular dating suggested that young lineages diverged during late Pliocene early Pleistocene, younger than uplift Mountains but older last glacial maximum (LGM). Significant structures detected at both markers. Furthermore, peonies overall equilibrium climatic oscillations Pleistocene. The simulated palaeoranges LGM period mostly overlapped, which have led cross‐breeding events. propose an scenario mountain orogenesis around triggered parapatric isolation between peonies. Subsequent fluctuations drove migration range recontact along valleys. This detailed provides new insights into mountain‐valley systems.

Language: Английский

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RAD-sequencing improves the genetic characterization of a threatened tree peony (Paeonia ludlowii) endemic to China: Implications for conservation

Plant Diversity, Journal Year: 2022, Volume and Issue: 45(5), P. 513 - 522

Published: July 20, 2022

Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one world's most famous tree peonies. However, only several wild populations remain in Yarlung Zangbo Valley (Nyingchi Shannan regions, Xizang) China due increasing anthropogenic impact on natural habitats. We used genome-wide single nucleotide polymorphisms elucidate spatial pattern variation, population structure demographic history P. from fragmented region comprising entire range this species, aiming provide a basis for conserving resources Unlike uniformity among revealed previous studies, we found low but varied levels intra-population diversity, which lower diversity was detected compared those Nyingzhi region. These patterns may be likely associated different sizes caused by micro-environment differences these two regions. Additionally, differentiation (Fst = 0.0037) were at species level. This line evidence, combined result significant between closest lack isolation distance, suggested that shared ancestry now remnant rather than contemporary connectivity resulted subtle structure. Demographic inference probably experienced temporal sharp decline during period Last Glacial Maximum, subsequent bottleneck event resulting prehistoric human activities Qinghai-Tibet Plateau. All events, together current habitat fragment excavation might contribute status ludlowii. Our study improved characterization peony (P. ludlowii) China, inferences should considered when making situ ex actions evolutionary hotspot

Language: Английский

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Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Journal of Systematics and Evolution, Journal Year: 2022, Volume and Issue: 60(6), P. 1241 - 1262

Published: Feb. 12, 2022

Abstract Restriction site‐associated DNA sequencing (RAD‐seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD‐seq data are subject to allele dropout (ADO) due polymorphisms at enzyme cutting sites. We developed a new pipeline, Allele Dropout Remedy in our study the gymnosperm genus, Torreya , mitigate ADO outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR supplement Rad‐seq combination with plastome and mitochondrial gene sequences, morphology, fossil records, we reconstructed phylogenetic biogeographic histories genus tested hypotheses on anomalies biodiversity eastern Asian‐North American floristic disjunction. Our results showed that pipeline recovered many outgroup, improved yielded more robust phylogeny . Using fossilized birth–death model divergence–extinction–cladogenesis method, resolved detailed history suggested Jurassic origin spanning Laurasia differential speciation extinction among continents accounting modern diversity, which is biased toward Asia (EA). The also supported vicariance widespread ancestor EA North America (NA) mid‐Eocene, cross Beringian exchange early Paleogene before vicariant isolation, contrast “out NA” pattern common gymnosperms EA” hypothesis proposed genus. Furthermore, observed discordance between nuclear plastid phylogenies jackii suggesting lineage sorting genomes species or genome capture T.

Language: Английский

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Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 172, P. 107485 - 107485

Published: April 19, 2022

Language: Английский

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