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

Identification of Different Varieties of Oil Peony Seeds Combining ICP-MS with Chemometrics and Assessment of Associated Health Risk

Peony seed is an excellent oil crop, and peony seed oil is rich in unsaturated fatty acids needed by the human body. In this study, inductively coupled plasma mass spectrometry (ICP-MS), fingerprint, and chemometrics, the correlation between the content of inorganic elements in oil peony seeds, their origins, and varieties were investigated. Meanwhile, estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and carcinogenic risks (CR) were combined to evaluate the comprehensive health risks of heavy metals in peony seed oil. The results showed that the difference in the content of inorganic elements could identify the varieties of oil peony seeds. Sr, K, Ca, V, Al, Fe, Cu, Ba, As, Ga, Co, and Rb were the characteristic inorganic elements that played a role in identification. In addition, The THQs and HIs (< 1) for non-carcinogenic elements indicated no risk. The CRs indicated that the carcinogenic harm was negligible. The study concluded that three varieties of peony seed oil would not pose any health hazard. It provided an effective comprehensive method for the identification of oil peony seeds and predicted the potential health risks of edible peony seed oil, providing a reference for the development and consumption of peony seed oil food.

The role of Pleistocene dispersal in shaping species richness of sky island wintergreens from the Himalaya-Hengduan Mountains

In addition to topography and climate, biogeographic dispersal has been considered to influence plant diversity in the Himalaya-Hengduan Mountains (HHM), yet, the mode and tempo of sky island dispersal and its influence on species richness has been little explored. Through phylogenetic analysis of Gaultheria ser. Trichophyllae, a sky island alpine clade within the HHM, we test the hypothesis that dispersal has affected current local species richness. We inferred the dynamics of biogeographic dispersal with correlation tests on direction, distance, occurrence time, and regional species richness. We found that G. ser. Trichophyllae originated at the end of the Miocene and mostly dispersed toward higher longitudes (eastward). In particular, shorter intra-regional eastward dispersals and longer inter-regional westward dispersals were most frequently observed. We detected a prevalence of eastward intra-region dispersals in both glacial periods and interglacials. These dispersals may have been facilitated by the reorganization of paleo-drainages and monsoon intensification through time. We suggest that the timing of dispersal corresponding to glacial periods and the prevalence of intra-region dispersal, rather than dispersal frequency, most influenced the pattern of species richness of G. ser. Trichophyllae. This study facilitates a more comprehensive understanding of biodiversity in the sky islands within the HHM.

A historical stepping-stone path for an island-colonizing cactus across a submerged "bridge" archipelago

Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the "bridge" hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.

Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer-scale population-level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco-morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67-0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming-cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts.

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

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.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

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

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

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

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.

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

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.