Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies (Paeonia delavayi and Paeonia ludlowii)

Zhao, Yu-Juan; Yin, Gen-Shen; Pan, Yuezhi; Tian, Bo; Gong, Xun

doi:10.3389/fgene.2020.595334

Cited by 13 publications

(12 citation statements)

References 76 publications

(111 reference statements)

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“…Moreover, the uplift of HDM also likely influenced the diversification of this genus. The HDM experienced extensive uplift caused by the collision between the Indian plate and Eurasia, occurring after the Miocene and reaching its peak elevation before the Late Pliocene [ 85 , 86 ]. This geological event triggered a series of topographical and climatic changes.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Song,

Liu,

Zhao

et al. 2024

BMC Plant Biol

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Background The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. Results In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma). Conclusion The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

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Section: Discussionmentioning

confidence: 99%

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Song,

Liu,

Zhao

et al. 2024

BMC Plant Biol

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“…potaninii ), indicating that the P. delavayi plastome is paraphyletic. However, prior assessment of the nuclear genome indicated that P. delavayi is monophyletic [ 7 , 9 ]. These conflicting phylogenetic signals may be explained by plastid capture [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

“…Over the past two decades, numerous studies were conducted on the molecular phylogenetics of P. delavayi [ 5 – 7 ]. Some research supports the monophyletic nature of P. delavayi [ 6 , 9 ], but other studies have contradicted this claim, suggesting that P. delavayi may be paraphyletic [ 5 , 10 ]. Each study may have limitations related to the molecular tool used (for instance, findings based on single or limited molecular fragments might not be representative of the entire genome) or sampling technique (e.g., from a single population, thus not representing the whole species), so the phylogenetics of P. delavayi remains inconclusive.…”

Section: Introductionmentioning

confidence: 99%

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

Chen

Silva³

et al. 2023

BMC Plant Biol

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Backgroud Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution. Methods In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia. Results Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group. Conclusions Overall, this study’s research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.

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“…In general, all the Osphya species occurred in the Northern Hemisphere, within the latitude zone ranging from 20° N to 35° N, corresponding to the temperate and subtropical regions. The overall distribution pattern of Osphya was discontinuous and uneven ( Figure 2 ), which may have been caused by the joint effects of the geological history and environmental adaptions [ 87 ].…”

Section: Discussionmentioning

confidence: 99%

Climate Change Impacts on the Potential Distribution Pattern of Osphya (Coleoptera: Melandryidae), an Old but Small Beetle Group Distributed in the Northern Hemisphere

Tong

Liu

Wang

et al. 2023

Insects

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Exploring the development of species distribution patterns under climate change is the basis of biogeography and macroecology. However, under the background of global climate change, few studies focus on how the distribution pattern and the range of insects have or will change in response to long-term climate change. An old but small, Northern-Hemisphere-distributed beetle group Osphya is an ideal subject to conduct the study in this aspect. Here, based on a comprehensive geographic dataset, we analyzed the global distribution pattern of Osphya using ArcGIS techniques, which declared a discontinuous and uneven distribution pattern across the USA, Europe, and Asia. Furthermore, we predicted the suitable habitats of Osphya under different climate scenarios via the MaxEnt model. The results showed that the high suitability areas were always concentrated in the European Mediterranean and the western coast of USA, while a low suitability exhibited in Asia. Moreover, by integrating the analyses of biogeography and habitat suitability, we inferred that the Osphya species conservatively prefer a warm, stable, and rainy climate, and they tend to expand towards higher latitude in response to the climate warming from the past to future. These results are helpful in exploring the species diversity and protection of Osphya.

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Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies (Paeonia delavayi and Paeonia ludlowii)

Cited by 13 publications

References 76 publications

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

Climate Change Impacts on the Potential Distribution Pattern of Osphya (Coleoptera: Melandryidae), an Old but Small Beetle Group Distributed in the Northern Hemisphere

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