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This report presents the first natural hybrid of Bulbophyllum in Taiwan. Bulbophyllum ×omerumbellatum T.P. Lin shows some features similar to those of either purported parental species, viz., B. umbellatum and B. omerandrum, but most features are intermediate. A full description, photographs, line drawings, occurrence, ecology, and comparison of morphological characters among Bulbophyllum ×omerumbellatum and its parental species are presented. [ABSTRACT FROM AUTHOR]

This report presents 1 new orchid from Taiwan, viz., Goodyera maculata T.P. Lin. New insights revealed a progenitor and progeny relationship between Cheirostylis chinensis and Che. takeoi. I also present trimorphic flowers of Calanthe lyroglossum and dimorphic Gastrodia flexistyla. [ABSTRACT FROM AUTHOR]

This report presents 3 new orchids from Taiwan, i.e., Oreorchis wumanae T.P. Lin, Cymbidium x oblancifolium Z.J. Liu & S.C. Chen, and Cheirostylis tortilacinia var. wutaiensis T.P. Lin. A color variant of the flower of Oberonia formosana is also presented. [ABSTRACT FROM AUTHOR]

This report presents three new orchids of Taiwan, i.e., Habenaria alishanensis T.P. Lin & D.M. Huang, Neottia cinsbuensis T.P. Lin & D.M. Huang, and Nephelaphyllum tenuiflorum Blume. [ABSTRACT FROM AUTHOR]

This report presents three new orchids of Taiwan, i.e., Aphyllorchis montana Reichb. f. forma pingtungensis T.P. Lin, Cheirostylis pusilla Lindl. var. simplex T.P. Lin, and Cheirostylis nantouensis T.P. Lin. [ABSTRACT FROM AUTHOR]

This is a comprehensive name list of native orchids of Taiwan identified since the publication of Flora of Taiwan Vol. 5, second edition (2000). The 330 species, subspecies, varieties and natural hybrids of native orchids reported in that publication increases to 455 in the current list. Type information and selected references, diagnostic notices for each species are reported herein for reference. [ABSTRACT FROM AUTHOR]

This report presents three new orchids in Taiwan, i.e., Epipactis fascicularis T.P. Lin, Neottia piluchiensis T.P. Lin,and Platanthera nantousylvatica T.P. Lin. [ABSTRACT FROM AUTHOR]

In this report three new orchids to Taiwan, i.e., Cephalantheropsis longipes, Habenaria tsaiana and Nervilia linearilabia are presented. Cephalantheropsis dolichopoda (Fukuy.) Lin is a new combination from Calanthe dolichopoda Fukuy. Liparis sp. is an unknown species also included for reference. [ABSTRACT FROM AUTHOR]

In this report six new orchids to Taiwan, i.e., Bulbophyllum confragosum, Bulbophyllum hirundinis var. puniceum, Bulbophyllum albociliatum var. shanlinshiense, Nervilia ratis, Oberonia linguae and Goodyera velutina var. albo-nervosa are presented. [ABSTRACT FROM AUTHOR]

The genus Chamaecyparis (Cupressaceae) is comprised of six taxa native to East Asia and North America. Two independent lineages from eastern North America to East Asia and from western North America to East Asia have been identified from phylogenetic analyses based on variation in plastid DNA (ptDNA). However, the trees inferred from a nuclear ribosomal internal transcribed spacer (nrITS), the NEEDLY intron 2, and combined data from genetic and morphological characters of other studies are incongruent with the tree inferred from ptDNA. In this study, we sequenced the plastid matK gene as well as other sequences acquired from GenBank including the matK, rbcL, and nrITS sequences to reconstruct the phylogenetic trees of Chamaecyparis. The phylogenetic topology inferred from matK was congruent with the previous inference obtained using other ptDNA markers while the rbcL and ITS trees were congruent with previously inferred trees using the combined data and ITS sequences, respectively. Relatively less- (rbcL) and more-informative sites (ITS) may lead to different lineage sorting and incongruent phylogenetic topologies, which were evidenced by rejection of evolutionary homogeneity between ptDNA and ITS sequences in the partition homogeneity test. The phylogenetic tree reconstructed using matK and other ptDNA strongly supports the geographically disjunct distribution of Chamaecyparis in North America and East Asia. A dispersal-vicariance analysis, and geologic and fossil evidence indicated that at least two independent dispersal events occurred from North America to East Asia, which support the previous biogeographic inference by ptDNA. The use of biparental inherited markers for biogeographic inferences should be done with caution. [ABSTRACT FROM AUTHOR]

Background and Aims: Positive selection in the α-crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation. [ABSTRACT FROM PUBLISHER]

Abstract Phylogeographical and mismatch analysis of chloroplast DNA (cpDNA) variation were used to infer the temporal dynamics of distributional and demographic history of Taiwan fir (Cunninghamia konishii ). We examined 64 and 52 trees from 17 populations of C. konishii and 14 provenances of C. lanceolata , respectively, by sequencing three intergenic spacers and one intron using cpDNA universal primers. Of the aligned 1888 base pairs (bp) sequence, 30 varied among 28 haplotypes, which consisted of three transitions, 14 transversions and 13 indels. One ancestral haplotype was found in 86 individuals across the surveyed range of both species, C. konishii and C. lanceolata , which was distributed in all populations and provenances. The 28 haplotypes also included 15 C. konishii specific and 12 C. lanceolata -specific haplotypes. Ancestral haplotype was found fixed in five populations of C. konishii and five provenances of C. lanceolata . Other haplotypes occurred mainly as singletons. The levels of population differentiation studied are relatively low in both Cunninghamia species. The nucleotide diversity (θ ) of chloroplast DNA sequences within C. konishii was slightly higher than that of C. lanceolata . Excess in singletons as well as star-like phylogeny of haplotypes suggested no clearcut migration patterns of C. konishii after glacial maximum. One probable demographic history of C. konishii is the postglacial population growth of C. konishii after a glacial bottleneck event. This inference is supported by the combined results of fossil pollen record, low nucleotide diversity, significant Tajima's d -value, phylogeographical analysis and unimodal mismatch distribution. Similarities and discrepancies between our results and those of Lu et al. (2001) are discussed. [ABSTRACT FROM AUTHOR]

Inferring the evolutionary history of a group of closely related species can be challenging. Genetic diversity, structure, and multilocus phylogeny were studied to shed light on the evolutionary processes that shapes diversity in three closely related Lecanorchis species (L. cerina, L. suginoana, and L. thalassica). In this study, we surveyed nucleotide and genetic variation, respectively, using nuclear internal transcribed spacer 1 (nrITS1) and amplified fragment length polymorphism (AFLP) in individuals of Lecanorchis species. Both nrITS1 parsimonious and AFLP neighbor-joining trees showed paraphyly indicated that lineage sorting for these species may be incomplete. ITS1 haplotype sharing was found within L. cerina, within L. suginoana, and between L. suginoana and L. thalassica. Higher AFLP diversity was observed in L. cerina than that in L. suginoana and in L. thalassica, indicating larger population size in L. cerina. Two contrasting patterns of AFLP genetic differentiation between geographic neighbors relative to geographic distant populations were observed. Two major AFLP genetic components were found in individuals of Lecanorchis species examined. Individuals of L. cerina and of L. thalassica were classified into either component with high probabilities. Most individuals of L. suginoana were classified into one of these components, but two individuals showed apparent admixture of these components. The evidence of paraphyly, haplotype sharing, higher L. cerina diversity, sharing and admixture of genetic components, and the contrasting patterns of genetic differentiation suggest that both incomplete lineage sorting and secondary gene flow could have occurred in these closely related species, though at different temporal scale. [ABSTRACT FROM AUTHOR]

Background and Aims Evolutionary and ecological roles of the chloroplast small heat shock protein (CPsHSP) have been emphasized based on variations in protein contents; however, DNA sequence variations related to the evolutionary and ecological roles of this gene have not been investigated. In the present study, a basal angiosperm, Machilus, together with the eudicot Rhododendron were used to illustrate the evolutionary dynamics of gene divergence in CPsHSPs. Methods Degenerate primers were used to amplify CPsHSP-related sequences from 16 Rhododendron and eight Machilus species that occur in Taiwan. Manual DNA sequence alignment was carried out according to the deduced amino acid sequence alignment performed by CLUSTAL X. A neighbour-joining tree was generated in MEGA using conceptual translated amino acid sequences from consensus sequences of cloned CPsHSP genes from eight Machilus and 16 Rhododendron species as well as amino acid sequences of CPsHSPs from five monocots and seven other eudicots acquired from GenBank. CPsHSP amino acid sequences of Funaria hygrometrica were used as the outgroups. The aligned DNA and amino acid sequences were used to estimate several parameters of sequence divergence using the MEGA program. Separate Bayesian inference of DNA sequences of Rhododendron and Machilus species was analysed and the resulting gene trees were used for detection of putative positively selected amino acid sites by the Codeml program implemented in the PAML package. Mean hydrophobicity profile analysis was performed with representative amino acid sequences for both Rhododendron and Machilus species by the Bioedit program. The computer program SplitTester was used to examine whether CPsHSPs of Rhododendron lineages and duplicate copies of the Machilus CPsHSPs have evolved functional divergence based on the hydrophobicity distance matrix. Key Results Only one copy of the CPsHSP was found in Rhododendron. However, a higher evolutionary rate of amino acid substitutions in the Hymenanthes lineage of Rhododendron was inferred. Two positively selected amino acid sites may have resulted in higher hydrophobicity in the region of the α-crystallin domain (ACD) of the CPsHSP. By contrast, the basal angiosperm, Machilus, possessed duplicate copies of the CPsHSP, which also differed in their evolutionary rates of amino acid substitutions. However, no apparent relationship of ecological relevance toward the positively selected amino acid sites was found in Machilus. Conclusions Divergent evolution was found for both Rhododendron lineages and the paralogues of CPsHSP in Machilus that were directed to the shift in hydrophobicity in the ACD and/or methionine-rich region, which might have played important roles in molecular chaperone activity. [ABSTRACT FROM AUTHOR]

This report presents one new orchid of Taiwan, viz., Bulbophyllum cryptomeriicola T.P. Lin and S.K. Yu. Bulbophyllum cryptomeriicola is a member of the section Ephippium with a sub-umbellate inflorescence, ciliate upper sepal and petals, glabrous lateral sepals which are much longer than the median one, and a stelidium without a tooth. [ABSTRACT FROM AUTHOR]

The membrane protein AtTLP18.3 of Arabidopsis (Arabidopsis thaliana) contains a domain of unknown function, DUF477; it forms a polysome with photosynthetic apparatuses in the thylakoid lumen. To explore the molecular function of AtTLP18.3, we resolved its crystal structures with residues 83 to 260, the DUF477 only, and performed a series of biochemical analyses to discover its function. The gene expression of AtTLP18.3 followed a circadian rhythm. X-ray crystallography revealed the folding of AtTLP18.3 as a three-layer sandwich with three a-helices in the upper layer, four E-sheets in the middle layer, and two α-helices in the lower layer, which resembles a Rossmann fold. Structural comparison suggested that AtTLP18.3 might be a phosphatase. The enzymatic activity of AtTLP18.3 was further confirmed by phosphatase assay with various substrates (e.g. p-nitrophenyl phosphate, 6,8-difluoro-4-methylumbelliferyl phosphate, O-phospho-L-serine, and several synthetic phosphopeptides). Furthermore, we obtained the structure of AtTLP18.3 in complex with O-phospho-L-serine to identify the bindingsite of AtTLP18.3. Our structural and biochemical studies revealed that AtTLP18.3 has the molecular function of a novel acid phosphatase in the thylakoid lumen. DUF477 is accordingly renamed the thylakoid acid phosphatase domain. [ABSTRACT FROM AUTHOR]

Immature seeds can acquire the traits of desiccation tolerance and germination after precocious maturation. This process is associated with the accumulation of non-reducing sugars and late embryogenesis abundant (LEA) proteins. LEA proteins were first identified from late developmental seeds and were proposed to be associated with desiccation tolerance. In the present study, we examined whether purified LEA fusion proteins from soybean seeds can maintain the integrity of artificial liposomes under desiccation. We also studied the relationship between the protective effects of LEA protein-sucrose glasses and desiccated membrane. GmPM6 (LEA II) but not GmPM16 (LEA IV) provided significant protection to dehydrated liposomes. However, neither GmPM6- nor GmPM16-sucrose glasses could protect these liposomes. We discuss the functions of cellular glass in mature orthodox seeds. [ABSTRACT FROM AUTHOR]

Aim The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer programtcs. Nested clade analysis was conducted with the computer programceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programsarlequin andhapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the softwarecontrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [ABSTRACT FROM AUTHOR]

In this study, we examined spatial patterns of chloroplast DNA (cpDNA) variation in a total of 30 populations ofCastanopsis carlesiiHayata (Fagaceae), a subtropical and temperate tree species, including 201 individuals sampled throughout Taiwan. By sequencing two cpDNA fragments using universal primers (thetrnL intron and thetrnV-trnM intergenic spacer), we found a total of 1663 bp and 21 polymorphic sites. These gave rise to a total of 28 cpDNA haplotypes. The level of differentiation among the populations studied was relatively high (GST = 0.723). Two ancestral haplotypes are widely distributed. The Central Mountain Ridge (CMR) of Taiwan represents an insurmountable barrier to the east–west gene flow ofC. carlesii. Among the populations studied, three separated populations, at Lienhuachih, Fushan and Lichia, have high nucleotide diversity. Estimates ofNST– GST for populations on both sides of the CMR indicate that no phylogeographical structure exists. According to the genealogical tree, number of rare haplotype and population genetic divergence, this study suggests that two potential refugia existed during the last glaciation: the first refugium was located in a region to the north of Hsuehshan Range (HR) and west of the CMR; the second refugium was located in south, especially southeastern Taiwan. In fact, the second refugium happens to be the same as that reported forQuercus glauca. A‘star-like’ genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test and mismatch distribution also suggest demographic expansion recovering from a bottleneck. [ABSTRACT FROM AUTHOR]

This report presents one new hybrid orchid of Taiwan, i.e., Gastrochilus xhsuehshanensis which resulted from hybridization between G. formosanus and G. rantabunensis. Also, the existence of both Cyrtosia javanica and Cypripedium macranthos in Taiwan is questionable, and these were excluded from the Taiwanese orchid flora. [ABSTRACT FROM AUTHOR]

This report presents two new orchids of Taiwan, i.e., Cheirostylis octodactyla f. cymbiformes and Gastrodia rubinea. Lecanorchis bihuensis is revised and emended with new information [ABSTRACT FROM AUTHOR]

This report presents two new mycoheterotrophic orchids of Taiwan, i.e., Cyrtosia septentrionalis (Rchb.f.) Garay and Gastrodia kaohsiungensis T.P. Lin. The genus Cyrtosia in Taiwan is also reviewed. The pollinia of Galeola lindleyia and G. falconeri share the same morphology as two species of Cyrtosia found in Taiwan. The pollinia may provide new evidence to merge Galeola with Cyrtosia. [ABSTRACT FROM AUTHOR]

This report presents three new orchids of Taiwan, i.e., Epipogium meridianus T.P. Lin, Liparis monoceros T.P. Lin, and Nervilia septemtrionarius T.P. Lin. Epipogium meridianus could be a hybrid between E. roseum and E. kentingensis. [ABSTRACT FROM AUTHOR]

ETHYLENE RESPONSE FACTOR1 (ERF1) is an upstream component in both jasmonate (JA) and ethylene (ET) signaling and is involved in pathogen resistance. Accumulating evidence suggests that ERF1 might be related to the salt stress response through ethylene signaling. However, the specific role of ERF1 in abiotic stress and the molecular mechanism underlying the signaling cross talk still need to be elucidated. Here, we report that ERF1 was highly induced by high salinity and drought stress in Arabidopsis (Arabidopsis thaliana). The salt stress induction required both JA and ET signaling but was inhibited by abscisic acid. ERFl-overexpressing lines (35S:ERF1) were more tolerant to drought and salt stress. They also displayed constitutively smaller stomatal aperture and less transpirational water loss. Surprisingly, 35S:ERF1 also showed enhanced heat tolerance and up-regulation of heat tolerance genes compared with the wild type. Several suites of genes activated by JA, drought, salt, and heat were found in microarray analysis of 35S:ERF1. Chromatin immunoprecipitation assays found that ERF1 up-regulates specific suites of genes in response to different abiotic stresses by stress-specific binding to GCC or DRE/CRT. In response to biotic stress, ERF1 bound to GCC boxes but not DRE elements; conversely, under abiotic stress, we observed specific binding of ERF1 to DRE elements. Furthermore, ERF1 bound preferentially to only one among several GCC box or DRE/CRT elements in the promoter region of its target genes. ERF1 plays a positive role in salt, drought, and heat stress tolerance by stress-specific gene regulation, which integrates JA, ET, and abscisic acid signals. [ABSTRACT FROM AUTHOR]

Selaginella tamariscina, one of the most primitive vascular plants, can remain alive in a desiccated state and resurrect when water becomes available. To evaluate the nature of desiccation tolerance in this plant, we compared the composition of soluble sugars and saturation ratios of phospholipids (PLs) between hydrated and desiccated tissues of S. tamariscina using gas chromatography. In this study, differences in gene expression and ABA contents were also analyzed during dehydration. The results revealed that trehalose (at >130 mg g−1 DW) was the major soluble sugar, and low saturated fatty acid content in PLs (0.31) was maintained in both hydrated and desiccated tissues. In addition, the ABA content of S. tamariscina increased 3-fold, and genes involved in ABA signaling and cellular protection were up-regulated while photosystem-related genes were down-regulated during dehydration. The biochemical and molecular findings suggest that both constitutive and inducible protective molecules contribute to desiccation tolerance of S. tamariscina. [ABSTRACT FROM AUTHOR]

Although glutathione S-transferases (GSTs) are thought to play major roles in oxidative stress metabolism, little is known about the regulatory functions of GSTs. We have reported that Arabidopsis {Arabidopsis thaliana) GLUTATHIONE S-TRANSFERASE U17 (AtGSTUU; Atlgl0370) participates in light signaling and might modulate various aspects of development by affecting glutathione (GSH) pools via a coordinated regulation with phytochrome A. Here, we provide further evidence to support a negative role of AtGSTU17 in drought and salt stress tolerance. When AtGSTUU was mutated, plants were more tolerant to drought and salt stresses compared with wild-type plants. In addition, atgstuU accumulated higher levels of GSH and abscisic acid (ABA) and exhibited hyposensitivity to ABA during seed germination, smaller stomatal apertures, a lower transpiration rate, better development of primary and lateral root systems, and longer vegetative growth. To explore how atgstul7 accumulated higher ABA content, we grew wild-type plants in the solution containing GSH and found that they accumulated ABA to a higher extent than plants grown in the absence of GSH, and they also exhibited the atgstul7 phenotypes. Wild-type plants treated with GSH also demonstrated more tolerance to drought and salt stresses. Furthermore, the effect of GSH on root patterning and drought tolerance was confirmed by growing the atgstul7 in solution containing L-buthionine-(S,R)-sulfoximine, a specific inhibitor of GSH biosynthesis. In conclusion, the atgstuU phenotype can be explained by the combined effect of GSH and ABA. We propose a role of AtGSTU17 in adaptive responses to drought and salt stresses by functioning as a negative component of stress-mediated signal transduction pathways. [ABSTRACT FROM AUTHOR]

Transcriptional activities of plants play important roles in responses to environmental stresses. ETHYLENE RES1 ONSE FACTOR53 (AtERF53) is a drought-induced transcription factor that belongs to the AP2/ERF superfamily and has a highly conserved AP2 domain. It can regulate drought-responsive gene expression by binding to the GCC box and/or the dehydration-responsive element in the promoter of downstream genes. Overexpression of AtERF53 driven by the cauliflower mosaic virus 35S promoter resulted in an unstable drought-tolerant phenotype in T2 transgenic Arabidopsis (Aral idopsis thaliana) plants. Using a yeast two-hybrid screen, we identified a RING domain ubiquitin E3 ligase, RGLG2, which interacts with AtERF53 in the nucleus. The copine domain of RGLG2 exhibited the strongest interacting activity. We also demonstrated that RGLG2 could move from the plasma membrane to the nucleus under stress treatment. Using an in vitro ubiquitination assay, RGLG2 and its closest sequelog, RGLG1, were shown to have E3 ligase activity and mediated AtERF53 ubiquitination for proteasome degradation. The rglg1rglg2 double mutant but not the rglg1 or rglg1 single mutant exhibited a drought-tolerant phenotype when compared with wild-type plants. AtERF53-green fluorescent proteins expressed in the rglg1rglg2 double mutants were stable. The 35S:AtERF53-green fluorescent protein / rglg1rglg2 showed enhanced AtERF53-regulated gene expression and had greater tolerance to drought stress than the rglg1rglg1 double mutant. In conclusion, RGLG2 negatively regulates the drought stress response by mediating AtERF53 transcriptional activity in Arabidopsis. [ABSTRACT FROM AUTHOR]

Background: Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species. Results: Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples. Conclusions: Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples. [ABSTRACT FROM AUTHOR]

Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, A VR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. saliva), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high πnon/πsyn ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen-host shift from Italian millet to rice. [ABSTRACT FROM AUTHOR]

Based on fossil pollen, the distribution range of Taiwan fir [Abies kawakamii (Hay.) Ito] (Pinaceae) is smaller than it was 50 000 years ago. To characterize the present refuge populations of A. kawakamii, which survive only in subalpine forests in Taiwan, we surveyed nuclear genes and chloroplast intergenic spacers to assess the genetic diversity of Taiwan fir. Populations maintain high genetic diversity and contain similar numbers of haplotypes for the GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) fragment. Haplotypes for GapC are generally widespread, and population-specific haplotypes accounted for 2.5% of the total. Differentiation among populations is very low (GST = 0.01). Only three haplotypes were detected for the cpDNA marker, and every population had one or two haplotypes. In a neutrality test, the variation in nucleotides did not deviate from that expected with neutral evolution for either marker. A retreat route to higher elevations was not evident from either the GapC or cpDNA markers. Hsuehshan was the site of the most divergent population in Taiwan. We concluded that uniform genetic diversity, low differentiation, low numbers of population-specific haplotypes, and neutral evolution characterize contemporary refuge populations of Taiwan fir. [ABSTRACT FROM AUTHOR]

In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (HE = 0.741) and low population differentiation (FST = 0.042) but shows isolation by distance. The most divergent populations, according to the average FST for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversifies that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers. [ABSTRACT FROM AUTHOR]

Aims To unravel isolation and differentiation of the genetic structure of the Euphrasia transmorrisonensis complex, a showy herb, among alpine regions of mountain peaks in subtropical Taiwan and to infer its evolutionary history. Location Alpine ecosystems of high-montane regions of Taiwan. Methods Phylogenetic analyses of the trnL intron and the trnL– trnF intergenic spacer of chloroplast (cp) DNA, and the intertranscribed spacer (ITS) of nuclear ribosomal (nr) DNA between 18S and 26S were carried out on 18 populations of the E. transmorrisonensis complex in Taiwan. Results In total, 10 haplotypes for cpDNA and 14 haplotypes for nrDNA were detected. Three population groups located in the northern, north-eastern, and south-central regions of the Central Mountain Range (CMR) were revealed according to the frequencies of haplotypes and haplotype lineages of nrDNA. Balancing selection might have played a role in the evolution of Euphrasia in Taiwan. Main conclusions By integrating the spatial-genetic patterns of cpDNA and nrDNA, two possible evolutionary histories of Euphrasia in Taiwan were inferred. The favourable hypotheses for interpreting the data suggest at least three origins of the E. transmorrisonensis complex in Taiwan, corresponding to each nuclear lineage in the northern (II), northern/north-eastern (I), and central/southern regions (III) with subsequent hybridization between lineages I and II and lineages II and III. These lineage boundaries are strengthened by the finding that haplotypes of C derived from cpDNA were found in the geographical region of lineage II of nrDNA, while haplotypes of A derived from cpDNA were found in the region of lineage III of nrDNA . Thus, the origin of chloroplasts exclusive to lineages II and III supports their long-term isolation from one another. [ABSTRACT FROM AUTHOR]

This paper described current phylogeographical patterns of chloroplastic DNA variation of Trochodendron aralioides, a temperate tree species, and inferred its possible refugium in Taiwan. This information was compared with the known phylogeographical pattern of subtropical tree species. A total of 24 populations were sampled including 20 from Taiwan, two each from the Ryukyus and Japan. A haplotype network was constructed by computer program TCS, various parameters of genetic diversity were calculated and neutrality was tested by computer program DnaSP. To examine the similarity of genetic structure among populations, a maximum parsimony tree was reconstructed by computer program PAUP*. The results of isozyme of T. aralioides from a previous publication were incorporated into this study to infer the phylogeographical history. Nine haplotypes according to six substitutions, two indels and one inversion of the two cpDNA intergenic spacer fragments ( petG- trnP and petA- psbJ) of T. aralioides were recognized. Genetic structure of the population of Japan is totally different from those of Taiwan and the Ryukyus. In Taiwan, the genetic structure was differentiated among populations revealed by Gst = 0.700 and Nst = 0.542, and the population genetics was clearly spatially structured. Two population groups were recognized. The first group was distributed islandwide and extended to the Ryukyus. The second group contained five of the seven known haplotypes, and was restricted to the area between latitude 24°46′ and 24°06′ N. In Taiwan, north-central area between latitude 24°46′ and 24°06′ N is potentially a refugium during the last glaciations. This finding is contradicted to subtropical species as Cyclobalanopsis glauca. [ABSTRACT FROM AUTHOR]

The objective of this research was to use random amplified polymorphic DNA (RAPD) and isozyme analysis to investigate genetic variation in narrowly distributed populations of Amentotaxus formosana Li. A total of 20 loci from 10 enzyme systems were analysed in 50 individual trees from each of the two natural populations. No isozyme variation was observed in the Tsatsayalai population. Phosphoglucose isomerase (Pgi-1) was the only polymorphic enzyme in the Tawu population, giving 5 per cent polymorphic loci with 0.008 expected heterozygosity. No genetic distance was found between these two populations using isozymes. Amentotaxus formosana demonstrated a high proportion of monomorphic RAPD fragments, about 79 per cent, for 20 arbitrary oligonucleotide primers. High similarity (0.994) was found between the Tawu and Tsatsayalai populations. RAPD markers provided further confirmation of the low levels of genetic variation in A. formosana detected by isozyme analysis. The value of isozyme analysis was emphasized by the finding of the rare allele, Pgi-1a, which was present only in the Tawu population. Based on the analysis of 110 individuals, representing 16 per cent of a native population, it was found that the younger tree category had a higher frequency of Pgi-1a (0.125) than the older tree category (0.053), resulting in an expected heterozygosity of 0.250 and 0.105, respectively. It was inferred that the appearance of the Pgi-1a allele could be the result of a mutation in the Tawu population and that selection is acting directly upon trees carrying this allele. [ABSTRACT FROM AUTHOR]