Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China.

Numerous temperate plants and animals on the Qinghai-Tibet Plateau (QTP) are hypothesized to have differentiated due to vicariant allopatric speciation associated with the geologic uplifts. However, this hypothesis has rarely been tested through a phylogeographic study of relative species in a broader geographic context, including the QTP, Tianshan Mountains, Mongolian Plateau, and surrounding regions. To understand the speciation and diversification process of plants across this wide area, phylogeographic analysis were examined from and two other closely relative species comprising and .

Natural selection and repeated patterns of molecular evolution following allopatric divergence.

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection.

Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae).

Phylogenetic analyses using diverse datasets can yield conflicting inference of evolutionary history. Phylogenetic conflicts observed in both animal and plant systems have often been explained by two competing (but not mutually exclusive) hypotheses, i.e.

Ginkgo biloba's footprint of dynamic Pleistocene history dates back only 390,000 years ago.

Background: At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. Yet the status of these regions as refuge areas with naturally existing populations has been proven not earlier than one decade ago. Herein we elaborated the hypothesis that during the Pleistocene cooling periods G.

The Complete Chloroplast Genome of Chinese Bayberry (, Myricaceae): Implications for Understanding the Evolution of Fagales.

(Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales.

Molecular phylogenetics and biogeography of the mint tribe Elsholtzieae (Nepetoideae, Lamiaceae), with an emphasis on its diversification in East Asia.

Elsholtzia and its allied genera such as Collinsonia and Perilla (tribe Elsholtzieae, Lamiaceae) are an ecologically and economically important plant group consisting of ~71 species, with most species distributed in East and Southeast Asia, and several species in North America. Their phylogeny and historical biogeography resulting in a distant intercontinental disjunction are poorly understood. Here we use two nuclear (ETS, ITS) and five chloroplast (rbcL, matK, trnL-F, ycf1, ycf1-rps15) fragments to reconstruct the phylogeny, biogeographic history, and patterns of diversification of Elsholtzieae.

Development of microsatellite loci in Mediterranean sarsaparilla (; Smilacaceae) using transcriptome data.

Premise Of The Study: Although several microsatellite markers of (Smilacaceae) have been reported in a previous study, due to universality issues in cross-population amplification, we have newly developed microsatellite markers for based on transcriptome data to further investigate gene flow and genetic structure of its circum-Mediterranean, East African, and South Asian populations.

Methods And Results: A total of 4854 simple sequence repeat (SSR) primer pairs were designed from 99,193 contigs acquired from public transcriptome data of . Forty-six microsatellite loci were selected for further genotyping in 12 populations.

Unique parallel radiations of high-mountainous species of the genus Sedum (Crassulaceae) on the continental island of Taiwan.

We explored the temporal and spatial diversification of the plant genus Sedum L. (Crassulaceae) in Taiwan based on molecular analysis of nrITS and cpDNA sequences from East Asian Sedum members. Our phylogenetic and ancestral area reconstruction analysis showed that Taiwanese Sedum comprised two lineages that independently migrated from Japan and Eastern China.

Comparative Genomics and Phylogenomics of East Asian Tulips (, Liliaceae).

The genus Honda (Liliaceae), when it is treated as separate from , comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete chloroplast (cp) genomes.

Incongruent range dynamics between co-occurring Asian temperate tree species facilitated by life history traits.

Postglacial expansion to former range limits varies substantially among species of temperate deciduous forests in eastern Asia. Isolation hypotheses (with or without gene flow) have been proposed to explain this variance, but they ignore detailed population dynamics spanning geological time and neglect the role of life history traits. Using population genetics to uncover these dynamics across their Asian range, we infer processes that formed the disjunct distributions of Ginkgo biloba and the co-occurring Cercidiphyllum japonicum (published data).

Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China.

Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present.

Development of microsatellite loci in Scrophularia incisa (Scrophulariaceae) and cross-amplification in congeneric species.

Premise Of The Study: To elucidate the population genetics and phylogeography of Scrophularia incisa, microsatellite primers were developed. We also applied these microsatellite markers to its closely related species S. dentata and S.

Development of the first chloroplast microsatellite loci in Ginkgo biloba (Ginkgoaceae).

Premise Of The Study: To investigate population genetics, phylogeography, and cultivar origin of Ginkgo biloba, chloroplast microsatellite primers were developed. •

Methods And Results: Twenty-one chloroplast microsatellite markers were identified referring to the two published chloroplast genomes of G. biloba.

The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae).

Background: Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants.

Understanding the formation of Mediterranean-African-Asian disjunctions: evidence for Miocene climate-driven vicariance and recent long-distance dispersal in the Tertiary relict Smilax aspera (Smilacaceae).

Tethyan plant disjunctions, including Mediterranean-African-Asian disjunctions, are thought to be vicariant, but their temporal origin and underlying causes remain largely unknown. To address this issue, we reconstructed the evolutionary history of Smilax aspera, a hypothesized component of the European Tertiary laurel forest flora. Thirty-eight populations and herbarium specimens representing 57 locations across the species range were sequenced at seven plastid regions and the nuclear ribosomal internal transcribed spacer region.

Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures.

Background And Aims: LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.

Isolation and characterization of polymorphic microsatellite markers from the Chinese medicinal herb Atractylodes macrocephala (Asteraceae).

Atractylodes macrocephala Koidz. (Asteraceae) is an economically important Chinese medicinal herb. In this study, 15 polymorphic microsatellite markers were developed from A.

Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales--influences of gene partitions and taxon sampling.

The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales.

Development of microsatellite markers for the dove tree, Davidia involucrata (Nyssaceae), a rare endemic from China.

Premise Of The Study: Microsatellite primers were developed for the endangered Davidia involucrata to assess the population genetics and infer its evolutionary history.

Methods And Results: Using both the modified magnetic bead hybridization method and the dual-suppression PCR method, we isolated and characterized 12 polymorphic microsatellite loci using 134 individuals from five populations in southwestern China. The number of alleles per locus ranged from six to 21 (mean = 10.

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.

A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.

Isolation and characterization of microsatellite markers for Dipteronia dyerana (Sapindaceae), an endangered endemic species in China.

Premise Of The Study: Microsatellite markers were developed for Dipteronia dyerana, an endangered endemic species in China, to study the population genetics of this species.

Methods And Results: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 12 microsatellite markers that were successfully amplified showed polymorphism when tested on 31 individuals from two populations in the counties of Wenshan and Mengzi. Overall, the number of alleles per locus ranged between seven and 25, with an average of 12.

Isolation of compound microsatellite markers for the common Mediterranean shrub Smilax aspera (Smilacaceae).

Premise Of The Study: Microsatellite markers were developed for the common Mediterranean shrub Smilax aspera to study the population genetics of this species.

Methods And Results: Using the compound microsatellite marker technique, a total of 14 pairs of primers were developed for S. aspera, of which 11 were polymorphic, and three were monomorphic.