Plastid DNA Sequences Research Articles

Spatial Distribution of Genetic, Ploidy, and Morphological Variation of the Edaphic Steno-Endemic Alyssum moellendorfianum (Brassicaceae) from the Western Balkans.

Polyploidy is a powerful mechanism driving genetic, physiological, and phenotypic changes among cytotypes of the same species across both large and small geographic scales. These changes can significantly shape population structure and increase the evolutionary and adaptation potential of cytotypes. Alyssum moellendorfianum, an edaphic steno-endemic species with a narrow distribution in the Balkan Peninsula, serves as an intriguing case study. We conducted a comprehensive analysis of genetic diversity and population structure across the species' range, employing an array of genetic techniques (nuclear microsatellites, amplified fragment length polymorphisms, and plastid DNA sequences), flow cytometry (FCM), morphometry, and pollen analysis. The study reveals two genetic lineages: spatially distributed diploid and tetraploid cytotypes. Clear divergence between diploids and tetraploids was shown by AFLP, while plastid DNA sequences confirmed private haplotypes in each of the studied populations. Higher genetic diversity and allelic richness following the north-south pattern were documented in tetraploids compared to diploids, as indicated by nuclear microsatellites. Morphometric analysis via principal component analysis (PCA) and canonical discriminant analysis (CDA) did not reveal any divergence between diploid and tetraploid cytotypes. Nonetheless, a distinction in pollen size was clearly observed. The results suggest an autopolyploid origin of tetraploids from diploid ancestors. Despite the population fragmentation in a very small geographic range, these populations harbour high genetic diversity, which would allow them to remain stable if natural processes remain undisturbed.

Phylogenetics and reticulation among koelerioid clades, part I: Contraction of Trisetum, expansion of Acrospelion, Graphephorum, and Tzveleviochloa; Graciliotrisetum gen. nov. and resurrection of Aegialina (Poaceae, Pooideae, Poeae, Aveninae)

AbstractKoelerioid grasses (subtribe Aveninae, tribe Poeae; Pooideae) resolve into two major clades, here called Koelerioid Clades A and B. Phylogenetic relationships among koelerioid grasses are investigated using plastid DNA sequences of rpl32‐trnL, rps16‐trnK, rps16 intron, and ITS regions, focusing on Trisetum, Acrospelion, and some annual species (Rostraria p.p. and Trisetaria p.p.) closely related to Trisetum flavescens in Koelerioid Clade A. Phylogenetic analyses of several selected data sets performed for 80 taxa and using maximum likelihood and Bayesian methods, revealed mostly congruent topologies in the nuclear and plastid trees, but also reticulation affecting several lineages. Trisetum is restricted to one species, T. flavescens, which is a sister to the clade formed by Trisetum gracile and Trisetaria aurea. The latter two species are classified here in the genus Graciliotrisetum gen. nov. The sister clade includes three species of Rostraria and Trisetaria lapalmae, all of which are classified here in a resurrected genus, Aegialina, which includes four species. Acrospelion is enlarged to include 13 species after the addition of other species formerly classified in Trisetum sect. Trisetum and T. sect. Acrospelion. We also transfer Trisetum ambiguum, Trisetum longiglume, and Koeleria mendocinensis to Graphephorum; and Helictotrichon delavayi to Tzveleviochloa, expanding these genera to eight and six species, respectively. We evaluate cases of reticulate evolution between Koelerioid Clades A and B and within Koelerioid Clade A, which probably gave rise to Graphephorum, Rostraria cristata, and Rostraria obtusiflora. Finally, we comment on polyploidy and biogeographic patterns in koelerioid grasses. We propose the following 26 new combinations: Acrospelion alpestre, Acrospelion altaicum, Acrospelion argenteum, Acrospelion bertolonii, Acrospelion buschianum, Acrospelion buschianum subsp. transcaucasicum, Acrospelion fuscum, Acrospelion laconicum, Acrospelion macrotrichum, Acrospelion rigidum, Acrospelion rigidum subsp. teberdense, Acrospelion tamonanteae, Acrospelion velutinum, Aegialina lapalmae, Aegialina pubescens, Aegialina pumila, Aegialina pumila subsp. fuscescens, Aegialina salzmannii, Aegialina salzmannii subsp. cossoniana, Graciliotrisetum aureum, Graciliotrisetum gracile, Graphephorum ambiguum, Graphephorum longiglume, Graphephorum mendocinense, Graphephorum orthochaetum, and Tzveleviochloa delavayi. Lectotypes are designated for the names Aegialitis tenuis, Aira melicoides, Avena aspera var. parviflora, Avena delavayi, Koeleria grisebachii var. mendocinensis, Koeleria pubescens subsp. cossoniana, Koeleria pumila, Koeleria salzmannii, Phalaris pubescens, Trisetum aureum, Trisetum cernuum, Trisetum fuscescens, Trisetum longiglume, and Trisetum wolfii; and we designate one neotype for Alopecurus litoreus.

Hemipiliazhuxiensis (Orchideae, Orchidaceae), a new species from Hubei Province, China.

Hemipiliazhuxiensis (Orchidaceae), is a new species discovered in the Shibali Long Canyon National Nature Reserve, Zhuxi County, Hubei Province, China. It is morphologically similar to Hemipiliahenryi and Hemipiliacrassicalcarata, but differs in having an oblong, simple labellum with a slightly involute margin, an upcurved apex, and a spur shorter than the ovary. Molecular phylogenetic analyses, using nuclear (nrITS) and plastid (combined matK, psaB, psbA-trnH, rbcL and trnL-F) DNA sequences, confirm that H.zhuxiensis is closely related to Hemipiliahenryi and Hemipiliacrassicalcarata, supporting its recognition as a new species in the H.sectionHemipilia as defined by Tang et al. (2015).

Evidence for a Miocene pulse of diversification of the tropical American clade of the Brazil nut family (Lecythidaceae)

ABSTRACT The tropical American species of the Brazil nut family, Lecythidaceae, are abundant in the tree flora, with some economically important species. Yet, the phylogenetic relationships and pace of diversification within this family are understudied. Here, we used shotgun sequencing data for 86 of the 228 currently accepted species in the exclusively tropical American subfamily Lecythidoideae in a phylogenomic context. For each sampled species, we built the full plastid DNA sequence, and also extracted nuclear DNA for 571 regions using the new bioinformatics pipeline REFMAKER, which we used to produce a time-calibrated phylogenetic hypothesis. Our analysis shows that phylogenetic inference from plastid and nuclear DNA alignments resulted in different topologies. The nuclear DNA topology strongly suggests that genus Lecythis should be split into at least four genera. Samples of the genus Eschweilera formed a monophyletic group, with the exception of one sampled species (Eschweilera amazoniciformis S.A.Mori). The Bertholletia clade, which contains the majority of the Lecythidoideae species, and all Lecythis and Eschweilera species, started diversifying around 27.5 Ma, with an accelerated rate of diversification starting in the middle Miocene (c. 12 Ma). The clade sister to Bertholletia (including Corythophora, Eschweilera, and Corrugata, Chartacea and Poiteaui clades) includes at least 124 species and it has diversified less than 10 Ma. This time frame of diversification coincides with major changes in tropical American landscapes and climate associated with the Andean uplift.

Disentangling conflicting molecular phylogenetic signals in nuclear and plastid DNA of the western Eurasian-Mediterranean grass genus Cynosurus and its relatives (Poaceae subtribes Cynosurinae and Parapholiinae)

The western Eurasian-Mediterranean grass genus Cynosurus, comprising about 11 species, is morphologically well delimited by the regular occurrence of conspicuous sterile spikelets distal to the fertile ones on the outer, abaxial side of the inflorescences. However, our molecular phylogenetic study using nuclear ribosomal DNA (ITS, ETS) and plastid DNA sequences (trnL–F, matK) has shown that the genus is not monophyletic in its current delimitation, but consists of three distinct lineages. These lineages were found to be closely related to a group of 6–7 genera taxonomically assigned to the subtribe Parapholiinae. These Parapholiinae genera were consistently monophyletic in our analyses, but the suggested relationships to the three lineages of Cynosurus varied depending on the particular DNA region examined. This was the case for both plastid and nuclear DNA, with cytonuclear discordance and ‘chloroplast capture’ indicating earlier hybridization. Interestingly, hybridization also proved to be the most likely explanation even with regard to the 18S–26S cistrons of the nuclear ribosomal DNA, where an exceptional evolutionary divergence between ITS and ETS was found. The results highlight and illustrate the important role of hybridization in the evolution of grasses. In terms of taxonomy, our findings argue against maintaining a polyphyletic genus Cynosurus s.l. but instead argue for dividing it into three monophyletic genera: Cynosurus s.s., Falona, which is reestablished here, and Ciliochloa, which is described as a new genus. In addition, it is proposed that the two subtribes Cynosurinae and Parapholiinae be combined into a single subtribe Cynosurinae, which is also monophyletic. The possible genetic background of the formation of sterile spikelets and the occasional occurrence of inflorescences with consistently fertile spikelets are discussed. New combinations are Ciliochloa effusa, C. effusa var. obliquata, C. effusa var. fertilis, C. elegans, C. gracilis, C. turcomanica and Falona colorata.

Insular environment-dependent introgression from an arid-grassland orchid to a wetland orchid on an oceanic island.

Adaptive introgression plays a vital role in allowing recipient species to adapt and colonize new environments. However, our understanding of such environment-dependent introgressions is primarily limited to specific plant taxa in particular settings. In Japan, two related orchid species, the autonomously self-pollinating Pogonia minor and the outcrossing Pogonia japonica, typically inhabit dry grasslands and wetlands, respectively. Intriguingly, an island ecotype of P. japonica exists in arid, wind-swept, open sites on volcanic mountain slopes on Kozu Island, in the oceanic Izu Islands. To investigate potential introgression and its implications between P. japonica and P. minor on Kozu Island, we applied a comprehensive approach that included examining morphological traits, genome-wide SNP data, and plastid DNA sequences. We also examined the breeding systems of these species on Kozu Island through artificial pollination experiments to determine if introgression from P. minor has endowed the P. japonica ecotype with selfing capabilities. Extensive sampling on Kozu Island revealed that all P. japonica specimens exhibit signs of introgression from P. minor, suggesting the absence of pure P. japonica populations on the island. Furthermore, the chloroplast haplotypes of the insular P. japonica ecotype consistently match those of P. minor, indicating a predominantly asymmetrical initial hybridization with P. minor acting mainly as the maternal parent in the formation of F1 hybrids. Despite the advantages of self-fertilization in isolated environments, the insular P. japonica does not exhibit autogamy. Consequently, the scarcity of moist habitats, rather than selection pressure for selfing, likely contributes to the observed widespread introgression. Our study strongly suggests that the arid-environment-adapted P. minor has introgressed into the insular ecotype of P. japonica, enabling its successful colonization of arid volcanic mountain slopes of the oceanic island.

Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa

BackgroundUnlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on (i) any potential biases in their distribution in relation to specific nuclear genomic features, (ii) their contribution to the emergence of new genes and gene regions, and (iii) their impact on the expression of target nuclear genes.ResultsIn agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their overall transcription levels and broadness were only lower when involved exonic regions; the occurrence of plastid DNA generally did not result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among specific superfamilies of retrotransposons and several classes of RNA genes, including those participating in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and a specific class of regulatory RNAs. A significant fraction of NUPT RNA genes was found to be functionally expressed, thus potentially contributing to the nuclear pool.ConclusionsOur results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of (i) genome complexity and (ii) the nuclear pool of RNA genes.

 Mazusjiangshiense (Mazaceae), a new species from China: evidence from morphological and molecular analyses.

Utilising both morphological and molecular analyses, this study unveils Mazusjiangshiensesp. nov., a novel addition to the Mazaceae family, discovered in Shaowu County, Fujian Province, China. The comprehensive description and illustrations provided here are a result of a meticulous exploration of its morphological features. While bearing a resemblance to M.gracilis, this new-found species is distinguished by three distinct characteristics: its stems are delicately soft, its leaves possess a membranous quality and the ovary is notably villous at the apex. Integration of molecular evidence, derived from the nuclear ribosomal DNA (nrITS) and three plastid DNA sequences (rps16, rbcL and trnL-trnF), unequivocally supports the classification of M.jiangshiense as a distinct species. Notably, the molecular analysis positions it as a sister species to M.spicatus, underscoring the phylogenetic relationships within the genus Mazus. Our research not only introduces M.jiangshiense as a novel taxonomic entity, but also provides a nuanced understanding of its morphological differences and molecular affinities, enriching our comprehension of the diversity and evolutionary relationships of Mazaceae.

Molecular phylogeny and taxonomy of Phlomoides (Lamiaceae subfamily Lamioideae) in China: Insights from molecular and morphological data

Phlomoides, with 150–170 species, is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae (Lamiaceae). With about 60 species, China is one of three major biodiversity centers of Phlomoides. Although some Phlomoides species from China have been included in previous molecular phylogenetic studies, a robust and broad phylogeny of this lineage has yet to be completed. Moreover, given the myriad new additions to the genus, the existing infrageneric classification needs to be evaluated and revised. Here, we combine molecular and morphological data to investigate relationships within Phlomoides, with a focus on Chinese species. We observed that plastid DNA sequences can resolve relationships within Phlomoides better than nuclear ribosomal internal and external transcribed spacer regions (nrITS and nrETS). Molecular phylogenetic analyses confirm the monophyly of Phlomoides, but most previously defined infrageneric groups are not monophyletic. In addition, morphological analysis demonstrates the significant taxonomic value of eight characters to the genus. Based on our molecular phylogenetic analyses and morphological data, we establish a novel section Notochaete within Phlomoides, and propose three new combinations as well as three new synonyms. This study presents the first molecular phylogenetic analyses of Phlomoides in which taxa representative of the entire genus are included, and highlights the phylogenetic and taxonomic value of several morphological characters from species of Phlomoides from China. Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future.

Molecular phylogeny reveals that Lagochilus lorestanicus (Lamiaceae, Leonureae) belongs to Acanthoprasium (Lamiaceae, Marrubieae)

ABSTRACT The taxonomic classification of the recently described Lagochilus lorestanicus within the genus Lagochilus is traditionally based on its morphological characters. We present here a phylogenetic hypothesis for the genus Lagochilus (Lamiaceae, tribe Leonureae) based on plastid (trnL-trnF and matK) and nuclear (ITS) DNA sequence data, using maximum parsimony, maximum likelihood and Bayesian approaches. Our analysis indicates that while representative species from the Iranian flora are assembled in a sub-clade nested in the clade Spinosi, L. lorestanicus is retrieved in the Acanthoprasium clade in the tribe Marrubieae. The taxonomic placement of Lagochilus lorestanicus in Acanthoprasium is also corroborated by re-examination of morphological characters. Consequently, the species is transferred to the genus Acanthoprasium, which was previously restricted to Italy and France (i.e. A. frutescens) and Cyprus (i.e. A. integrifolium). The intra-specific morphological variations as well as the conservation status of Lagochilus lorestanicus are discussed.

Middle Pleistocene climate change influenced northward divergence and cold adaptation in an Asian lady’s slipper orchid, Cypripedium macranthos Sw. (Orchidaceae)

Abstract The Pleistocene was characterized by climate fluctuations with rapid transitions between glacial and interglacial periods. East Asia’s land bridge dynamics and monsoon system during the Middle Pleistocene transition (MPT) further constrained species distributions and dispersals, which promoted local adaptation and species diversification, making East Asia an excellent location to study species biogeography. Cypripedium macranthos Sw., a terrestrial orchid, diverged in the Pleistocene and became widespread in Russia, China, Korea, and Japan. Many populations are now at risk due to illegal harvesting or habitat loss. With comprehensive sampling including 171 individuals among 22 populations across the entire distribution range, together with plastid DNA sequencing, we have explored the origin and impact of palaeoclimate on its spatial genetic structure and historical biogeography. Regression-based analyses commonly used in landscape genetics were also applied to investigate the effects of precipitation, temperature, and wind on gene flow. The results revealed northeastern China as the probable cradle of C. macranthos, with northeastward divergence and range expansion during the MPT, aided by monsoon shifts and wind-driven seed dispersal. Isolation by environment was detected with winter temperature as a driver for north–south divergence controlling for an effect of isolation by distance, revealing cold adaptation of the northern populations or temperature-driven genetic differentiation. We also emphasize the founder speciation of an unique variety on Rebun Island of Japan. The widespread but genetically and ecologically divergent C. macranthos populations highlight the need for more conservation attention on northern populations under global warming.

Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome of Moringa oleifera reveals unanticipated complexity in NUPTs´ formation

BackgroundBeyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA.ResultsHere, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms.ConclusionsOur results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.

Genista anglica s.l. (Fabaceae): genetic similarities between Iberian and Italian populations

Genista anglica L. (Fabaceae) is a Western European plant, widespread from Northern Morocco to Southern Sweden, with two geographically isolated populations in Calabria (Italy). Based on morphological characters, some authors considered the southern Italian populations as two different species: Genista silana and Genista brutia. Recent phylogeographical studies reveal that the G. silana and G. brutia populations share genetic similarities with some populations of the widespread G. anglica from Northwestern of Iberian Peninsula, despite a distance of approximately 2000 km. Previously, other authors suggested anthropogenic introduction of these plants in the South of Italy, but this hypothesis has not been thoroughly investigated. To unravel the uncertain origin of the isolated Italian populations, we conducted a more detailed study about the genetic relationships between southern Italian populations and Northwestern of Iberian Peninsula populations of G. anglica s.l., using plastid DNA sequences. Our results show identical and similar haplotypes in some of the populations of the Northwestern of Iberian Peninsula and the Italian populations, which supports the hypothesis of a recent anthropogenic introduction.

Phylogenetic relationships and biogeography in Hedysarum (Hedysareae, Fabaceae) with a focus on Central Asian taxa

AbstractCentral Asia, especially the Tian‐Shan and Pamir‐Alay, is a biodiversity hotspot for Hedysarum (Fabaceae) with a high number of endemic species. However, to date, studies of the genus Hedysarum based on molecular data have included only a few species distributed in this region. To fill this gap, we analysed 110 Hedysarum species, 36 of which were from the Tian‐Shan and Pamir‐Alay Mountains of Central Asia. We performed phylogenetic analyses, divergence time estimates, and biogeographic analyses using both the internal transcribed spacers of nuclear ribosomal DNA (nrDNA ITS) and three plastid DNA (cpDNA) sequences (trnL‐trnF, matK, psbA‐trnH). Our phylogenetic analysis grouped the species of Hedysarum into three sections: H. sect. Hedysarum, sect. Multicaulia, and sect. Stracheya, which are largely consistent with previous phylogenetic classifications. Accordingly, most of the Central Asian species we studied (28 spp.) were placed in H. subsect. Crinifera within H. sect. Multicaulia. Our divergence time and biogeographic analyses indicate that Hedysarum likely originated in West Asia and/or East Asia during the Early Miocene or Middle Miocene and subsequently dispersed to adjacent areas of Eurasia, as well as North America via the Bering Land Bridge. The likely area of origin for H. sect. Multicaulia is West Asia, while East Asia appears to be the center of origin for H. sect. Hedysarum and sect. Stracheya. In addition, we suggest that the rapid radiation of the species of H. subsect. Crinifera occurred in the Tian‐Shan and Pamir‐Alay Mountains, as well as the Turkish‐Iranian Plateau, and that geological and climatic changes were the main causes of speciation in Hedysarum.

Molecular Phylogeny and Genetic Diversity of Carpathian Members of the Genus Muscari Inferred from Plastid DNA Sequences

Molecular Phylogeny and Genetic Diversity of Carpathian Members of the Genus Muscari Inferred from Plastid DNA Sequences

Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

This study illustrates and describes Cymbidium × fugongense, a natural hybrid of Cymbidium wenshanense and Cymbidium eburneum or Cymbidium maguanense, from Yunnan Province, China. Morphologically, it has white-pink sepals and petals; petals are mottled and contain purple-red patches at their centres. The midlobe of lip is purple-red, with occasionally purple-red mottling on the base and apex of side lobes. The column is purple-red and mottled ventrally. Molecular analysis of plastid DNA (matK and rbcL) sequence data confirmed the natural hybrid as related to C. wenshanense, whereas the nuclear (ITS) DNA clearly supported a relationship of this material to species of C. subgenus Cyperorchis.

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos.

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

A phylogenetic analysis of the Korean endemic species <i>Paraphlomis koreana</i> (Lamiaceae) inferred from nuclear and plastid DNA sequences

<i>Paraphlomis koreana</i> (Lamiaceae) was newly named and added to Korean flora in 2014. <i>Paraphlomis</i> belongs to the tribe Paraphlomideae, along with <i>Ajugoides</i> and <i>Matsumurella</i>. However, a recent study has suggested that <i>P. koreana</i> is morphologically similar to <i>Matsumurella chinensis</i>, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of <i>P. koreana</i> within the tribe and compare its genetic relationship with <i>M. chinensis</i>. We sequenced an additional complete plastid genome for an individual of <i>P. koreana</i> and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of <i>P. koreana</i>. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (<i>rpl16</i> intron, <i>rpl32</i>-trnL, <i>rps16</i> intron, and <i>trnL-F</i>) covering 13 <i>Paraphlomis</i> species and <i>M. chinensis</i> were conducted. Phylogenetic analyses concordantly supported that <i>P. koreana</i> forms a monophyletic group with <i>M. chinensis</i>. Moreover, our study revealed that <i>P. koreana</i> includes nrDNA sequences of <i>M. chinensis</i> as minor intraindividual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of <i>P. koreana</i> within <i>Paraphlomis</i> should be reconsidered.

The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic

Rapid diversification of a group is often associated with exploiting an ecological opportunity and/or the evolution of a key innovation. However, how the interplay of such abiotic and biotic factors correlates with organismal diversification has been rarely documented in empirical studies, especially for organisms inhabiting drylands. Fumarioideae is the largest subfamily in Papaveraceae and is mainly distributed in temperate regions of the Northern Hemisphere. Here, we used one nuclear (ITS) and six plastid (rbcL, atpB, matK, rps16, trnL-F, and trnG) DNA sequences to investigate the spatio-temporal patterns of diversification and potential related factors of this subfamily. We first present the most comprehensive phylogenetic analysis of Fumarioideae to date. The results of our integrated molecular dating and biogeographic analyses indicate that the most recent common ancestor of Fumarioideae started to diversify in Asia during the Upper Cretaceous, and then dispersed multiple times out of Asia in the Cenozoic. In particular, we discover two independent dispersal events from Eurasia to East Africa in the late Miocene, suggesting that the Arabian Peninsula might be an important exchange corridor between Eurasia and East Africa in the late Miocene. Within the Fumarioideae, increased speciation rates were detected in two groups, Corydalis and Fumariinae. Corydalis first experienced a burst of diversification in its crown group at ∼ 42 Ma, and further accelerated diversification from the mid-Miocene onwards. During these two periods, Corydalis had evolved diverse life history types, which could have facilitated the colonization of diverse habitats originating from extensive orogenesis in the Northern Hemisphere as well as Asian interior desertification. Fumariinae underwent a burst of diversification at ∼ 15 Ma, which temporally coincides with the increasing aridification in central Eurasia, but is markedly posterior to the shifts in habitat (from moist to arid) and in life history (from perennial to annual) and to range expansion from Asia to Europe, suggesting that Fumariinae species may have been pre-adapted to invade European arid habitats by the acquisition of annual life history. Our study provides an empirical case that documents the importance of pre-adaptation on organismal diversification in drylands and highlights the significant roles of the synergy of abiotic and biotic factors in promoting plant diversification.

Spergularia hanoverensis (Caryophyllaceae): Validation and Recircumscription of a Misinterpreted Species from South Africa.

The name "Spergularia hanoverensis Simon" has been misapplied to an endemic taxon confined to inland semidesert ecosystems in central-western South Africa. It is commonly accepted as a small annual species occurring in saline habitats in a wide elevation range, but its identity still remains obscure. In the context of taxonomic and phylogenetic research on the African species of Spergularia, we found that the name was never validly published. After revision of herbarium material housed in South African herbaria, a voucher collected from Hanover was found at PRE bearing some labels handwritten by E. Simon that suggest it might be an intended type for the name. Additional herbarium material and wild populations from the Karoo region were identified that matched the samples in that voucher, and taxonomic research was conducted to clarify their identity. Among other characters, those Karoo plants show a woody dense compact habit, woody perennial at base; stems prostrate to ascendent; leaves entirely glabrous, somewhat glaucous; large white-hyaline conspicuous stipules; inflorescence glanduliferous, many-flowered subdichasial cyme, with minute bracts; flowers small, with white petals approximately equalling sepals in length, stamens 7-8, and styles free from base; capsule small, with seeds dimorphic, unwinged to broadly winged, with testa always densely tuberculate. Molecular analyses of plastid (trnL-trnF region) and nuclear ribosomal (5.8S-ITS2 region) DNA sequence data support morphological differentiation of the Karoo plants, for which the name S. hanoverensis is here effectively published. A full morphological description and data on ecology, habitat, distribution, and taxonomic and phylogenetic relationships of S. hanoverensis are compared to other members of the "South African group", namely S. glandulosa, S. namaquensis, and S. quartzicola, from which the new species considerably differs. The adaptative significance of dimorphic seeds of S. hanoverensis is briefly commented on in the context of the species habitat preference. An identification key is presented for the South African related taxa.