Chloroplast DNA Regions Research Articles

Dispersal as a result of asymmetrical hybridization between two closely related oak species in China

Hybridization has played an important role in plant evolution. Less attention has been paid, however, to its role in dispersal. In this study, historical divergence and hybridization were investigated in two closely related Chinese oaks, Quercus mongolica and Q. liaotungensis, to estimate the role that hybridization played in their dispersal. We genotyped 27 Q. mongolica and Q. liaotungensis populations throughout the distributional range of the two oak species, using 14 single-copy nuclear genes and four noncoding chloroplast DNA regions. Bayesian cluster and population tree analyses indicated that there were three groups over all oak populations, namely, Q. mongolica, northwest–northern China (NW-NC) Q. liaotungensis, and northeastern China (NEC) Q. liaotungensis. Approximate Bayesian computation simulation supported an asymmetrical hybridization origin of NEC Q. liaotungensis, after a previous divergence between NW-NC Q. liaotungensis and Q. mongolica. IMa3 analyses suggested that Q. liaotungensis and Q. mongolica diverged in the NW-NC and NEC regions, respectively, and that NEC Q. liaotungensis arose from Q. mongolica, not from NW-NC Q. liaotungensis, and was greatly introgressed by NW-NC Q. liaotungensis. Oak populations in NW-NC and NEC regions held different chloroplast DNA haplotypes, and Q. liaotungensis in NEC shared most haplotypes with Q. mongolica populations, but none with NW-NC Q. liaotungensis populations, suggesting the maternal origin of NEC Q. liaotungensis from Q. mongolica. This study found clear signals of isolation divergence of Q. liaotungensis in NW-NC and Q. mongolica in NEC, and the results suggest that asymmetrical hybridization and introgression from Q. liaotungensis to Q. mongolica, mostly likely via pollen flow, facilitated Q. liaotungensis dispersal to NEC.

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS, Acc1, and Pgk1) and one chloroplast region (trnL‐F)

AbstractRoegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St1St2Y.

Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for 'duty of care' when cultivating honeybush.

BackgroundThe current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea.MethodsWe applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network.ResultsPopulations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels.ConclusionsOur findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.

Reassessment of Bournea Oliver (Gesneriaceae) based on molecular and palynological evidence

The former genus Bournea is endemic to China, including two species, has been under consideration for incorporation into the expanded genus Oreocharis s.l. in Gesneriaceae. The phylogenetic tree inferred from two DNA sequences (trnL-F and ITS) showed that this genus is deeply nested into Oreocharis s.l. However, the new tree from seven ones (atpB-rbcL, ndhH-rps15-ycf1, rpl132, trnC-trnD, trnL-F, trnT-trnL of chloroplast DNA and ITS regions) revealed that Bournea is the sister group of other of Oreocharis s.l. Furthermore, Bournea is morphologically different from other Oreocharis based on existing data. We suggest keeping Bournea as an independent genus in Gesneriaceae.

Reassessment of Bournea Oliver (Gesneriaceae) based on molecular and palynological evidence

The former genus Bournea is endemic to China, including two species, has been under consideration for incorporation into the expanded genus Oreocharis s.l. in Gesneriaceae. The phylogenetic tree inferred from two DNA sequences (trnL-F and ITS) showed that this genus is deeply nested into Oreocharis s.l. However, the new tree from seven ones (atpB-rbcL, ndhH-rps15-ycf1, rpl132, trnC-trnD, trnL-F, trnT-trnL of chloroplast DNA and ITS regions) revealed that Bournea is the sister group of other of Oreocharis s.l. Furthermore, Bournea is morphologically different from other Oreocharis based on existing data. We suggest keeping Bournea as an independent genus in Gesneriaceae.

Interspecific Hybridization and Introgression Influence Biodiversity—Based on Genetic Diversity of Central European Viola epipsila-V. palustris Complex

The Viola epipsila-V. palustris complex is a highly taxonomically complicated group of species in its entire circumboreal range of distribution. Habitat loss, forest flooding, and hybridization could lead to the extinction of V. epipsila. A hybrid index and principal component analysis (PCA) were used to select qualitative and quantitative morphological features to distinguish parent species and hybrids, inter simple sequence repeat (ISSR) markers to determine the genetic diversity of the populations, flow cytometry to estimate the genome size (GS), and non-coding chloroplast DNA (cpDNA) regions to indicate the directions of crosses. All taxa are very morphologically variable, and their features can change within a season. The most stable feature is the distance of the bracts on the pedicel from the rhizome. The genetic diversity of all taxa populations is low and highly influenced by selfing and vegetative propagation. The population structure is differentiated: populations of V. epipsila or V. palustris, mixed populations with both parent species, F1 hybrids and populations with introgressive forms occur in different regions. The interspecific GS variation corresponds to the ploidy level (4x = 2.52 pg, 8x = 4.26 pg, 6x = 3.42 pg). Viola epipsila is the mother plant of the hybrids. Research has shown the risk of V. epipsila extinction in Central Europe and the importance of local populations in studying the role of hybridization in reducing/maintaining/increasing biodiversity.

Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea.

Due to substantial population decline, the Korean orchid P. scolopendrifolia is considered endangered and highly threatened. Like many endangered species, it is vulnerable to biological and anthropogenic threats that can lead to the loss of genetic diversity and, ultimately, extinction. Therefore, the assessment of genetic diversity and population genetic structure is imperative for conservation. In this study, we newly developed 15 polymorphic microsatellite markers. Analyses of genetic diversity and population genetic structure that included 182 samples from 11 populations were conducted using microsatellite markers and four noncoding regions of chloroplast DNA. Our study revealed a relatively low level of genetic diversity (Ho = 0.529, He = 0.356), albeit harboring with private alleles based on microsatellite genotyping data, and high haplotype diversities based on chloroplast DNA sequences data. The results of STRUCTURE and PCoA based on microsatellite genotyping data showed population differentiations. An AMOVA based on chloroplast DNA sequence data further corroborated these conclusions, indicating about 70% of variations found among populations. Low genetic diversity and divergence among the population might have been caused by factors, such as asexual reproduction, demographic events (bottleneck and population expansion), geographic isolation, and low gene flow. The development and implication of conservation strategies and management of P. scolopendrifolia are proposed based on these results.

Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia.

Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (Corymbia hamersleyana) and Western Gidgee (Acacia pruinocarpa), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana.

Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

AbstractEnvironmental DNA (eDNA) metabarcodes allow for the simultaneous detection of multiple taxa if the barcode regions meet several key requirements including conserved primer‐binding sites, interspecific variability that exceeds intraspecific variability, and relatively short amplicons. Currently, there are no established metabarcoding assays for aquatic vascular plants, which could limit biodiversity assessments and the early detection of alien species. We used a combination of novel and pre‐existing primers to generate eDNA metabarcodes from three gene regions that are commonly used for plant barcoding: two regions of chloroplast DNA (rbcL and matK) plus a segment of an internal transcribed spacer (ITS2). We optimized the assay on a mock community of 25 known species and then applied it to wild samples collected from two waterbodies in southern Ontario, Canada (Black River and Seymour Lake). Our novel rbcL primers, which amplify a fragment of ~220 bp, provided the most comprehensive description of the mock community, identifying all but one of the taxa to species or genus. In addition, after pooling data from five sites within each sampled waterbody, metabarcodes generated by this same primer pair identified more taxa than all other primer pairs; more specifically, 20 and 26 taxa were identified from Black River and Seymour Lake, respectively, to species or genus. Across the two sites, nine of the identified taxa are alien invasive aquatic plants. Five of these invasive species have no previous reports from our sites, and in some cases have no known established Ontario populations; our data therefore suggest an urgent need to increase surveillance for these aliens. Overall, our study showed that eDNA metabarcoding with a novel rbcL primer pair provides a cost‐effective method for simultaneously detecting multiple aquatic vascular plant taxa and is a valuable tool for the early detection of invasive species.

<p><strong>Molecular reappraisal of relationships between <em>Photinia</em>, <em>Stranvaesia</em> and <em>Heteromeles</em> (Rosaceae, Maleae)</strong></p>

Photinia, Stranvaesia and Heteromeles are considered to be related genera belonging to the tribe Maleae of Rosaceae. Stranvaesia comprises five species distributed in eastern Asia while Photinia consists of about 30 species found in eastern Asia and Mexico. Heteromeles is a monotypic genus distributed in northwestern Mexico and southwestern US. Distinctions between these three genera rely on morphological features of leaves, flowers, and fruits, but some character states that are supposed to be diagnostic of Stranvaesia also occur in species of Photinia. In order to clarify the taxonomic delimitations of the three genera, sequences from one nuclear gene (PepC) and three intergenic chloroplast DNA regions (trnS-trnG, psbA-trnH and trnL-trnH) were used to estimate the phylogeny of Photinia, Stranvaesia and Heteromeles. All Maximum parsimony, maximum likelihood, and Bayesian analyses supported the conclusion that the evergreen species Stranvaesia davidiana should be merged into Photinia, and another two deciduous species S. amphidoxa and S. tomentosa should be transferred to the genus Pourthiaea. Additionally, one Photinia species P. bodinieri should be transferred into Stranvaesia. Finally, it is suggested that Heteromeles arbutifolia should be merged into Photinia. Taxonomic treatments have been made to those species mentioned above, three new combinations have been proposed and six lectotypes have been designated here.

Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses.

Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.

Genetic diversity of Tulipa suaveolens (Liliaceae) and its evolutionary relationship with early cultivars of T. gesneriana

Polychromatic Tulipa suaveolens occurs over a vast territory ranging from the Crimea to eastern Kazakhstan. Its phylogenetic relationship to cultivated T. gesneriana is still under discussion. We used sequences from the psbE–petL region of chloroplast DNA and the complete internal transcribed spacer of nuclear ribosomal DNA to examine the genetic variability of T. suaveolens specimens from European Russia and the adjoining regions. Our data set also included 8 varieties of cultivated T. gesneriana. The research on biogeographic patterns of plastid haplotype and nuclear ribotype distribution provides evidence that their origin and dispersal over the Lower and Middle Volga Region are linked to the Khazar or Early Khvalynian transgression of the Caspian Sea and subsequent events. In the Crimea and the adjacent regions, the pattern of haplotypes’ distribution indicates that their origin and expansion may be linked to the Karangat transgression of the Black Sea and the subsequent New Euxinian regression. Based on our results, we propose that T. suaveolens is the likeliest wild ancestor of early T. gesneriana.

It is not a disaster: molecular and morphologically based phylogenetic analysis of Rondeletieae and the Rondeletia complex (Cinchonoideae, Rubiaceae)

The circumscription of Rondeletieae has changed considerably over time. Historically, 85 genera have been included, characterized by small trees, imbricate corolla aestivation and capsules. Molecular studies led to a narrower circumscription and stressed out that Rondeletieae is mainly an Antillean clade. As historically circumscribed, Rondeletieae is both polyphyletic (involving several tribes, including Condamineae, Sipaneeae, etc.) and paraphyletic with respect to Guettardeae. Uncertainties persist on the tribal circumscription, and its generic limits and relationships. We report results of phylogenetic analyses under parsimony, maximum likelihood and Bayesian analyses including 179 taxa, using concatenated datasets of three chloroplast DNA regions (petD, trnL–F and trnK–matK), their DNA microstructural characters as well as morphology. Our objectives are to: test the monophyly of Rondeletieae and evaluate phylogenetic relationships, evaluate potential characters for tribal and generic delimitation and propose a circumscription for Rondeletieae according to phylogenetic hypothesis using morphological characters. The tribes Guettardeae and Rondeletieae are strongly supported as sister: quincuncial aestivation and spathulate corolla lobes are proposed as a unique combination of characters supporting this relationship. We did not find synapomorphies for each tribe, but there is a set of character combinations that allows distinguishing both tribes that includes the corolla and pollen ornamentation as well as fruit and seed morphology. After evaluating other genera not included in the phylogenies, our proposal is that Rondeletieae contains approximately 120 species in 20 neotropical genera: Acrosynanthus, Acunaeanthus, Blepharidium, Donnellyanthus, Mazaea, Phyllomelia, Rachicallis, Roigella, Rondeletia, Rovaeanthus, Suberanthus, Tainus, plus one tentatively included and recently described (Jamaicanthus).

The phylogenetic significance of the stem morpho-anatomy in the Hylocereeae (Cactoideae, Cactaceae)

The Hylocereeae is a monophyletic group in which eight genera are recognized based on molecular data. However, relationships between the genera remain partially resolved. In this study, combined analyses of molecular and structural characters for Hylocereeae were carried out with the aims of finding structural synapomorphies that support the genera and to resolve relationships between them. We studied sixty-nine species of the eight genera of Hylocereeae, as well as six Echinocereeae species as outgroup using light microscopy and scanning electron microscopy. Thirty-six morpho-anatomical characters were incorporated into a matrix and analyzed in combination with sequences of four chloroplast DNA regions. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference yielded a robust phylogenetic hypothesis and showed morphological synapomorphies. Four of the genera (Acanthocereus, Aporocactus, Epiphyllum, and Kimnachia) have at least one structural synapomorphy. Disocactus and Pseudorhipsalis can be recognized by a combination of characters, while Selenicereus and Weberocereus cannot be recognized by any structural vegetative character. There are structural synapomorphies that allow recognizing relationships between genera. The cortical and vascular characters are as important as the epidermal traits, a condition that had not been reported for another group within Cactaceae.

Evaluation of Phylogenetic Relationships by Using psbA-trnH IGS Region of Chloroplast DNA in the Species of the Genus Quercus L.

Kloroplast genoma ait psbA-trnH IGS bölgesi, en fazla nükleotid dizi farklılığı içeren bölgelerden biri olmasından dolayı barkodlama amacı ile bitkilerde sıklıkla kullanılan bölgelerden biridir. Bu amaçla meşelerde var olan taksonomik problemlerin çözümüne katkı sağlamak ve türler arasındaki filogenetik ilişkileri değerlendirmek adına bu bölge bu çalışmada tercih edilmiştir. İlk olarak psbA-trnH IGS bölgesine ait sekans bilgisi analizler için NCBI’den sağlanılmıştır. Daha sonra bu sekanslar hizalandırılmış ve varyasyon gösteren bölgeler için bir bazın diğerine değişim oranları, transisyon/transversiyon oranları, baz frekansları gibi analizler MEGA X programı kullanılarak yapılmıştır. Son olarak, türlerin birbirleri ile olan filogenetik ilişkilerini değerlendirmek adına Neighbor-joining dendrogram hazırlanmış ve analiz edilmiştir. Bu bölgenin meşe türlerinin seksiyonel ayrımı için yeterli varyasyona sahip olmasına karşın, tür ayrımında ve tanımlamasında sekans varyasyonlarının yetersiz kaldığı görülmüştür. Çalışmanın sonucu olarak psbA-trnH IGS sekansının meşelerde barkodlama amacı ile tek başına yetersiz olduğu, bununla birlikte farklı barkodlama bölgeleri ile kullanımının fayda sağlayacağı önerilmektedir.

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska.

Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long‐distance postglacial migration from south of the ice sheets resulted in the modern‐day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long‐term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range‐wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long‐term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern‐day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.

Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences.

BackgroundSpecies in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information.MethodsWe sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry.ResultsWe found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades.ConclusionsTwo species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

AbstractSaxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.

The complete chloroplast genome of Chinese medicine (Psoralea corylifolia): Molecular structures, barcoding and phylogenetic analysis

Psoralea corylifolia is one kind of traditional Chinese medicine used in China widely. In this study, we sequence the complete chloroplast genome of P. corylifolia, which is 153,114 bp in size and includes a pair of inverted repeats regions of 25,557 bp interspersed by a small single copy of 17,885 bp and a large single copy of 84,115 bp region. Approximately 98 simple sequence repeats, 14 forward, 2 reverse, 2 complement, 32 palindromic and 49 tandem repeats are identified in the P. corylifolia chloroplast genome. The chloroplast genomes of P. corylifolia and three Glycine species are conserved in gene order and content, but show high diversity within intergenic spacers. P. corylifolia with three Glycine species in Papilionoideae fall into the same clade based on 75 conserved coding-protein genes phylogenomic analysis. Moreover, four chloroplast DNA regions (ycf1, matK, accD, ndhF) can serve as the barcodes. In general, our findings will dedicate to better comprehension of the genome aspect as well as evolutionary status of P. corylifolia.

Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China.

Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.