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Metopius soror Chiu, 1962 was originally described based on a single female. This study reports the host record of M. soror on Nyctemera albofasciata (Wileman, 1911) for the first time and female oviposition behavior on the larva of N. adversata (Schaller, 1788). We also provide the first description of the male of M. soror.

Pines evolve with fire and have diverged into fire-avoiders and fire-adapters. Pine needles are resistant to microbial decomposition, and their accumulation serves as a major fuel source for forest fires. Facilitated needle decomposition reduces forest fuel loads and probably interacts with the adaptive strategies of pines. However, there is little information available regarding differences in microbiomes associated with needle decomposition of the two types of pine. In this study, we monitored the microbial communities in three compartments associated with needle decomposition, namely, fresh needles, needle litter, and humus, along altitudinal gradients at three sites of the fire-tolerator Pinus taiwanensis and one site of the fire-avoider Pinus morrisonicola in Taiwan. The humus microbiome was dominated by an overwhelming proportion of bacteria. As a reservoir of decomposers, humus bacteria accounted for > 70% of the litter communities and showed marked differences in composition between the two Pinus species, as determined by non-metric multidimensional scaling. Such differences were associated with the abundance of bacterial genes encoding lignin-degrading enzymes, which were highest in the P. morrisonicola stand. Additionally, the humus accumulating under this fire-avoider was characterized by low ammonium concentrations and lower pH compared with that under the fire-tolerator, which is indicative of conditions conducive to litter decomposition. Conclusively, our findings suggested that P. morrisonicola grows in more favorable conditions for needle decomposition compared with the habitats where the P. taiwanensis lives.

Pyrola morrisonensis, an evergreen herb in the family Ericaceae, is endemic to Taiwan. We examined mycorrhizal development and the associated fungi in this species. Nine plants were collected in a naturally regenerated forest in central Taiwan. The plants were genetically identical in their internal transcribed spacer (ITS) region, and their sequences matched the known sequence for P. morrisonensis. Fine roots of each plant were colonized by mycorrhizal fungi that formed mycorrhizas either with or without fungal mantles. DNA sequences of the ITS region of these fungi suggested that they belonged to mycorrhizal taxa that are common tree symbionts. Among them, members of Thelephoraceae were the dominant taxon in the host plants. These results indicate that P. morrisonensis is intimately associated with mycorrhizal fungi that might also connect with neighboring trees.

Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.

This is the accepted manuscript of the paper "Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar", published as final paper in "Global Change Biology Bioenergy Volume 11, Issue 1, 08 February 2019, Pages 118–151 https://doi.org/10.1111/gcbb.12566”. Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namelyPanicum virgatum(switchgrass), species of the generaMiscanthus(miscanthus),Salix(willow) andPopulus(poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

Background and Aims Germplasm with diverse, agronomically relevant traits forms the foundation of a successful plant breeding programme. Since 1993, the United Nations has been advocating the implementation of the Convention on Biological Diversity (CBD) and the subsequent 2002 Bonn Guidelines as international best practice on germplasm collection and use. In 2006, a European team made an expedition to Asia to collect wild germplasm of Miscanthus, a C4 perennial rhizomatous grass, for breeding an environmentally adaptable, resilient and high-yielding bioenergy crop. We outline general aspects of germplasm collection, conservation, breeding and biomass production evaluation while following the CBD’s guidelines, respecting biodiversity and conservation needs, and the ethical use of genetic resources. Methods Effective protocols, quarantine, methods for collecting seed and rhizomes, and a genebank for conservation were established. Versatile informatics and database architecture were used to assist in selection, flowering synchronization, crossing, evaluation, phenotyping and data integration. Approaches were formulated to comply with the CBD guidelines. Key Results A total of 303 accessions of M. sinensis, M. sacchariflorus and M. floridulus were collected from 158 geographically and environmentally diverse locations. These species were shown to accumulate different amounts of aerial biomass due to combinations of stem count, height and thickness. Progeny from one interspecies cross accumulated more biomass in early trials and has shown double the yield performance in years 3–4 compared with the existing commercial cultivar M. × giganteus. An example of an F1 hybrid has already demonstrated the long-term potential of exploiting this collection for a breeding programme. Conclusions By conforming to the CBD principles, the authors’ international collaboration provides a practical example of implementing the CBD. The collection widened the genetic diversity of Miscanthus available to allow for breeding of novel hybrids that exhibit more diverse traits to increase yield and resilience for growth on marginal land and in climate-challenged environments.

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Field trials in Europe with Miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M. × giganteus (M × g) combine both high yield potentials and low inputs in a wide range of soils and climates. Miscanthus hybrids are expected to play a major role in the provision of perennial lignocellulosic biomass across much of Europe as part of a lower carbon economy. However, even with favourable policies in some European countries, uptake has been slow. M × g, as a sterile clone, can only be propagated vegetatively, which leads to high establishment costs and low multiplication rates. Consequently, a decade ago, a strategic decision to develop rapidly multiplied seeded hybrids was taken. To make progress on this goal, we have (1) harnessed the genetic diversity in Miscanthus by crossing and progeny testing thousands of parental combinations to select several candidate seed-based hybrids adapted to European environments, (2) established field scale seed production methods with annual multiplication factors >1500×, (3) developed the agronomy for establishing large stands from seed sown plug plants to reduce establishment times by a year compared to M × g, (4) trialled a range of harvest techniques to improve compositional quality and logistics on a large scale, (5) performed spatial analyses of yield potential and land availability to identify regional opportunities across Europe and doubled the area within the bio-climatic envelope, (6) considered on-farm economic, practical and environmental benefits that can be attractive to growers. The technical barriers to adoption have now been overcome sufficiently such that Miscanthus is ready to use as a low-carbon feedstock in the European bio-economy.

Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.

Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

Summary Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.

Ludwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of the Ludwigia sect. Isnardia, which is a polyploid complex (x = 8) of five species distributed in North America. The phylogeny of L. sect. Isnardia was reconstructed based on sequences of cpDNA atpB-rbcL intergenic spacer and nrITS (internal transcribed spacer). Most L. sect. Isnardia species are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted at L. sect. Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploid L. spathulata are nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. Allopolyploid L. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggesting L. palustris as the paternal genome donor. Ludwigia brevipes may have arisen via bi-directional hybridization between L. palustris and L. arcuata followed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species of L. sect. Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution in L. sect. Isnardia.

Solanum is a large and morphologically diverse genus comprising almost 75% of the species in the family Solanaceae. Twenty species were recorded in Taiwan. Solanum miyakojimense Yamazaki & Takushi was published in 1991 as an endemic species in Miyako Islands, Ryukyu. A careful examination of herbarium collections supplemented by field studies confirmed the occurrence of this species in Lanyu, Taiwan. In this report we provide the description, line drawings, and colored photographs taken from the natural habitat to aid in identification of this species.

Rubus, comprising about 700 species in the world, is a large genus of the family Rosaceae. Thirty-five species and four additional varieties were recorded in the 2nd edition of Flora of Taiwan. In the course of our botanical inventory, Rubus amphidasys Focke, heretofore unknown in Taiwan, was collected from northern part of the island. Rubus amphidasys is easily distinguished from other congenors by having a mixture of densely bristly hairs and glandular hairs on branches and calyx. In addition, small prickles are rarely found on its stems. In this report we provide a description, line drawings, and colored photographs taken from the wild to aid in identification.

Chloranthus, a genus of the Chloranthaceae, comprises about 18 species in the world. In addition to the previously recorded C. oldhami in Taiwan, C. henryi is a new addition to the flora. It is easy to distinguish C. oldhami from C. henryi by the shape of stamen apices, and the existence or absence of styles. In the present work, a key to distinguish the genus Chloranthus in Taiwan, a line drawing, photographs, and distribution of C. henryi are provided.

In recent years we have witnessed the naturalization of many alien species of Asteraceae in Taiwan. In this report we document the recent naturalization of the Neotropical Austroeupatorium inulifolium (Kunth) R. M. King & H. Rob. at 1,300-1,400 m altitudes in the Central Mountain Range of Taiwan. We provide a description, a line drawing, and photographs to aid in identification.

According to the most recent monograph of the genus Deparia, Deparia petersenii is a species in the section Athyriopsis, which is one of the four sections of the genus Deparia. Because few diploids have been reported in the section Athyriopsis, no studies attempting to deduce how polyploid Athyriopsis species have originated have been conducted. We report here on the genetic structure and relationships of diploid D. petersenii, which is a new cytotype we discovered in Taiwan. Although the diploid populations have extensive morphological variation, the results of isozyme analysis indicate that the diploid plants belong to a single biological species. We examined the genetic relationship between the diploids and the other cytotypes (tetraploid and hexaploid) by sequencing variable chloroplast DNA regions (rbcL and ndhF). Two major haplotypes found in the diploids were shared with some of the tetraploids. Therefore, we concluded that the tetraploid D. petersenii has evolved from the diploid at least twice. T...

Burmannia comprises ca. 63 species and is one of the largest genera of the Burmanniaceae. Three species were recorded in the 2nd edition of Flora of Taiwan. In the course of our botanical inventory, Burmannia cryptopetala Makino was found in the northern and northeastern Taiwan, representing a new record species on this island. Burmannia cryptopetala is easily distinguished from other congeners by having perianth-tube 3-winged, and inner perianth-lobes lacking or inconspicuous. In this report we provide description, line drawing, and colored photographs taken from the natural habitat to aid in identification.

Asystasia gangetica (L.) T. Anderson subsp. micrantha (Nees) Ensermu, an Acanthaceae species native in Africa, India and Sri Lanka, has been recently found naturalized in the southern Taiwan. The naturalization of A. gangetica subsp. micrantha adds a new element to the flora of this island. Asystasia is easily distinguished from other genera of the Acanthaceae by corolla being zygomorphic, 4 stamens, 4-seeded and distinctly stipitate capsule. A. gangetica subsp. micrantha is characterized by ovate to oval leaves, and white flowers. This paper provides description of the genus and species, line drawing, and photographs.

Persicaria capitata (Buchanan-Hamilton ex D. Don) H. Gross, a species of the Polygonaceae widespread in mainland China and neighboring countries, has recently naturalized at ca. 2,000 m altitude in central Taiwan. Morphologically, P. capitata resembles P. chinensis, both belonging to section Cephalophilon, but can be easily distinguished from P. chinensis by accrescent and fleshy perianth in fruit. This paper provides a description of the species, line drawings, and color photographs to aid in identification.

Semiaquilegia adoxoides (DC.) Makino, a native species of the Ranunculaceae distributed in mainland China, western Japan, and South Korea, has recently been found in central Taiwan, adding a new record for this genus and species to the flora of this island. Semiaquilegia can be easily distinguished from other genera of the Ranunculaceae by its actinomorphic flowers, distinct petals, and free carpels. This paper provides descriptions of the genus and species, line drawing, and color photos.

Laportea, comprising ca. 22 species, is a genus of the Urticaceae. Two species were previously recorded in the 2nd edition of Flora of Taiwan. In the course of our botanical inventory, one additional weedy species, namely Laportea aestuans (L.) Chew, was found in the central Taiwan. Morphologically, L. aestuans is closely related to L. interrupta (L.) Chew by sharing ovate leaves. Branched racemes of L. aestuans are distinct from the unbranched racemes of L. interrupta. Laportea aestuans is a species mainly distributed at low elevations in central Taiwan.

Molecular Ecology Resources Editorial Office : 6270 University Blvd, Vancouver,BCV6T1Z4, Canada; International audience; This article documents the addition of 139 microsatellite marker loci and 90 pairs of single-nucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross-tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele-specific primers for Engraulis encrasicolus.

Myosotis arvensis (L.) Hill (Boraginaceae), a species native in the Europe, was naturalized recently in the northeast Taiwan. The introduction of M. arvensis adds a new element for both the genus and the species to the floristic composition of this island. Myosotis closely resembles Trigonotis, but can be easily distinguished from the latter and other genera of the Boraginaceae by having smooth and biconvex nutlets. This paper provides description of the genus and the species, line drawing, and color photos.

Background Gastrodia flabilabella is a mycoheterotrophic orchid that obtains carbohydrates and nutrients from its symbiotic mycorrhizal fungi. The species is an endemic and vulnerable species enlisted in the “A Preliminary Red List of Taiwanese Vascular Plants” according to the IUCN Red List Categories and Criteria Version 3.1. G. flabilabella dwells the underground of broadleaf and coniferous forest with richness litter. Based on herbarium records, this species is distributed in central Taiwan. Twenty eight microsatellite loci were developed in G. flabilabella and were tested for cross-species amplification in additional taxa of G. confusoides, G. elata, and G. javanica. We estimated the genetic variation that is valuable for conservation management and the development of the molecular identification system for G. elata, a traditional Chinese medicine herb. Results Microsatellite primer sets were developed from G. flabilabella using the modified AFLP and magnetic bead enrichment method. In total, 257 microsatellite loci were obtained from a magnetic bead enrichment SSR library. Of the 28 microsatellite loci, 16 were polymorphic, in which the number of alleles ranged from 2 to 15, with the observed heterozygosity ranging from 0.02 to 1.00. In total, 15, 13, and 7 of the loci were found to be interspecifically amplifiable to G. confusoides, G. elata, and G. javanica, respectively. Conclusions Amplifiable and transferable microsatellite loci are potentially useful for future studies in investigating intraspecific genetic variation, reconstructing phylogeographic patterns among closely related species, and establishing the standard operating system of molecular identification in Gastrodia.

Background Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. Findings Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. Conclusions These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species.

Melothria pendula L. (tribe Melothrieae), a New World Cucurbitaceace species, has been found in central Taiwan, and represents a new record of this genus and species for this island. This paper describes the morphology of the species and provides a line drawing and a key to the genera within the tribe Melothrieae in Taiwan.

Rhaphidophora hongkongensis Schott (Araceae) is here reported for the first time from Taiwan. The genus is also first reported from Taiwan proper. Description, line drawing, photograph, and a key to the Taiwanese species of Rhaphidophora are provided.

We report a species, Cissus elongata Roxb. which was collected from center and northern Taiwan. Cissus elongata is easily distinguished by the presence of five leaflets compared to the simple leaf in the other species of Taiwan. The populations from Hsinchu represents the northern distribution limit of C. elongata, which was previously known with the distributional range from Mainland China, Vietnam, India, Bhutan and Sikkim.

Background Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central–marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population. Methodology/Principal Findings We examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central–marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations. Conclusions/Significance The marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.

PREMISE OF THE STUDY Fifteen microsatellite loci were developed in an endangered species, Amentotaxus formosana, and were tested in an additional three species, A. argotaenia, A. yunnanensis, and A. poilanei, to evaluate the population structure for conservation efforts and reconstruct the phylogeographic patterns of this ancient lineage. METHODS AND RESULTS Polymorphic primer sets were developed from A. formosana; the number of alleles ranged from two to 10, with an observed heterozygosity ranging from 0 to 0.60. All of the loci were found to be interspecifically amplifiable. CONCLUSIONS These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct genetic units within species and establishing the phylogeographic patterns and the process of speciation among closely related species.

Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.

 Premise of the study: Transferable polymorphic microsatellite loci for four skullcaps, Scutellaria indica , S. taiwanensis , S. austrotaiwanensis , and S. playfairii , were developed for future studies of the mating system and population structure of these species. Interspecifi c amplifi cation was also tested in various Scutellaria species.  Methods and Results: Twelve novel polymorphic microsatellite loci were isolated from four S. taiwanensis specimens, and seven are interspecifi cally transferable. Microsatellite loci developed from S. austrotaiwanensis in a previous study were also analyzed in the other three species, and 12 loci were found to be transferable. Allele numbers of the total 24 loci for S. indica , S. taiwanensis , S. playfairii , and S. austrotaiwanensis are two to four, two, two to fiand two to three, respectively, with an expected heterozygosity ranging from 0.114 – 0.661, 0.062 – 0.499, 0.280 – 0.730, and 0.268 – 0.662, respectively. The interspecies transferability of these 24 loci was further tested in another 10 Scutellaria species, including three species native to Taiwan. Seventeen loci were found to be interspecifi cally amplifi able, especially among the Taiwan native species.  Conclusions: These highly polymorphic and transferable loci will be useful for future studies of the mating system of closely related Scutellaria species.

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0–17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25–1.75): 15.77 (7.48–114.09): 74.79 (36.27–534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383–0.856 × 10− 8 for synonymous substitutions per site per year and 0.036–0.081 × 10− 9 for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.