TY Chiang | National Cheng Kung University (original) (raw)
Papers by TY Chiang
Genome, 1999
The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal... more The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymerase I promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.Key words: concerted evolution, hybridization, length heterogeneity, Miscanthus sin...
Contributions to Zoology
The nocturnal distribution and resource use by Ryukyu flying foxes was studied along 28 transects... more The nocturnal distribution and resource use by Ryukyu flying foxes was studied along 28 transects, covering five types of habitats, on Iriomote Island, Japan, from early June to late September, 2005. Bats were mostly encountered solitarily (66.8%) or in pairs (16.8%), with a mean linear density of 2.5 ± 0.6 bats/km of transect/night. Across the island, however, bat densities were distributed non-randomly among transect-nights, not correlated with transect length, and showed a slightly clumped distribution (variance/mean = 3.3). Outskirt trails contributed higher values to the relative importance of bat abundance, but the highest mean abundances occurred mostly at village sites on the west coast, which on average devoted only a quarter of their land area to agriculture/husbandry compared to those on the east coast. This supports our prediction that higher bat abundances are found in areas with less anthropogenic interference and more forest. Among habitats, the mean total abundance a...
Zhonghua yi xue za zhi = Chinese medical journal; Free China ed, 1999
Spread of hepatitis D virus (HDV) from mother to infant is rare and nucleotide evidence to docume... more Spread of hepatitis D virus (HDV) from mother to infant is rare and nucleotide evidence to document such transmission is lacking. The aim of this study was to screen the children of HDV-infected parents and compare the HDV nucleotide sequence between children and parents by phylogenetic analysis. Fifty-seven children of 28 HDV-infected parents (23 fathers and 5 mothers, including two couples) were enrolled. HDV genomes from sera of HDV-infected parents and their children were cloned and sequenced. Comparison and phylogenetic analysis of HDV genomes were based on a region from nucleotide 911 to 1260. The homology to nucleotide sequence among different genotypes was estimated by phylogenetic analysis. One of the eight children whose mothers were anti-HDV positive was positive for anti-HDV. Mean heterogeneity among different HDV clones from a single subject ranged from 0.29% to 1.15%. HDV sequences from the mother and her child (referred from southern Taiwan) were nearly identical (99....
The Journal of general virology, 1998
The hepatitis D virus (HDV) genotypes in 46 HDV-infected patients and 12 prostitutes were screene... more The hepatitis D virus (HDV) genotypes in 46 HDV-infected patients and 12 prostitutes were screened with Xhol restriction fragment length polymorphism (RFLP) analysis of reverse transcription PCR products of viral genomes and verified by phylogenetic analysis. The amplificates of three (6.5%) patients and two (17%) prostitutes showed a novel RFLP pattern different from those of the three known genotypes. Complete HDV genomic sequence identities between isolates with a novel RFLP and the HDV genotypes I, II and III were 72.3, 77.2 and 63.0%, respectively. Importantly, divergence was mostly seen in various regions related to replication or packaging. The novel isolates formed a monophyletic group (P < 0.05) and were most closely related to genotype II.
Genetics and Molecular Research, 2014
Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesti... more Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesticated Formosan Sambar deer (Cervus unicolor swinhoei). All loci were polymorphic, with 10-19 alleles per locus. The average observed heterozygosity across loci and samples was 0.310, ranging from 0 to 0.750 at each locus. All loci but one, CU18, deviated from Hardy-Weinberg equilibrium due to excessive homozygosity in these domesticated broodstocks, reflecting inbreeding. These microsatellite loci will be useful, not only for assessment of population structure and genetic variability, but also for conservation of wild deer populations in Taiwan.
Plant Molecular Biology, 1998
Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, ... more Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, from genomic DNA of Begonia nantoensis Lai et Chung Trivial name: Promoter of rbcL gene from B. nantoensis Description: Promoter of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) with 761 bp from B. nantoensis lies downstream of the atpB gene. Nucleotide sequence of the promoter for rbcL in B. nantoensis shows 79.9%, 76.3%, 72.8% identity with Malus domestica (X69749), Euphorbia characius (X69735), and Camellia sinensis (X69732) respectively.
Plant Molecular Biology, 1998
Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, ... more Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, from genomic DNA of Glycine soja Sieb. & Zucc., a wild soybean (isolate 043) collected from South China. Trivial name: rDNA ITS region of wild soybean Description: ITS region of ribosomal DNA lies between 18S and 28S rRNA genes was cloned from wild soybean, Glycine soja, with 216 bp in ITS1, 169 bp in 5.8S rRNA gene and 211 bp in ITS2. Nucleotide sequence of ITS region in Glycine soja shows 98.8% and 88.2% identity with cultivated soybean, Glycine max L., and Glycine falcata Benth. respectively. Acknowledgements. This research was supported by a grant from Academia Sinica, Taiwan, ROC, to Y.I.C.H. Figure 1. Nucleotide sequence of ITS region of rDNA from Glycine soja.
Molecular Ecology, 2005
The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-... more The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trn T-trn F and trn S-trn G sequence variation within Juniperus przewalskii , a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G ST = 0.772, N ST = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N ST > G ST , P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.
Molecular Ecology, 2001
The phylogegraphic pattern of Cycas taitungensis , an endemic species with two remaining populati... more The phylogegraphic pattern of Cycas taitungensis , an endemic species with two remaining populations in Taiwan, was investigated based on genetic variability and phylogeny of the atp B-rbc L noncoding spacer of chloroplast DNA (cpDNA) and the ribosomal DNA (rDNA) internal transcribed spacer (ITS) of mitochondrial DNA (mtDNA). High levels of genetic variation at both organelle loci, due to frequent intramolecular recombination, and low levels of genetic differentiation were detected in the relict gymnosperm. The apportionment of genetic variation within and between populations agreed with a migrant-pool model, which describes a migratory pattern with colonists recruited from a random sample of earlier existing populations. Phylogenies obtained from cpDNA and mtDNA were discordant according to neighbour-joining analyses. In total four chlorotypes (clades I − IV) and five mitotypes (clades A − E) were identified based on minimum spanning networks of each locus. Significant linkage disequilibrium in mitotype − chlorotype associations excluded the possibility of the recurrent homoplasious mutations as the major force causing phylogenetic inconsistency. The most abundant chlorotype I was associated with all mitotypes and the most abundant mitotype C with all chlorotypes; no combinations of rare mitotypes with rare chlorotypes were found. According to nested clade analyses, such nonrandom associations may be ascribed to relative ages among alleles associated with the geological history through which cycads evolved. Nested in networks as interior nodes coupled with wide geographical distribution, the most dominant cytotypes of CI and EI may represent ancestral haplotypes of C. taitungensis with a possible long existence prior to the Pleistocene glacial maximum. In contrast, rare chlorotypes and mitotypes with restricted and patchy distribution may have relatively recent origins. Newly evolved genetic elements of mtDNA, with a low frequency, were likely to be associated with the dominant chlorotype, and vice versa, resulting in the nonrandom mitotype − chlorotype associations. Paraphyly of CI and EI cytotypes, leading to the low level of genetic differentiation between cycad populations, indicated a short period for isolation, which allowed low possibilities of the attainment of coalescence at polymorphic ancestral alleles.
Molecular Ecology, 2006
Species whose geographical distribution encompasses both mainland and island populations provide ... more Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis , a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.
Molecular Ecology, 2001
Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range... more Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range dispersal. To examine the extent of seedling dispersal across oceans, we investigated the phylogeny and genetic structure among East Asiatic populations of Kandelia candel based on organelle DNAs. In total, three, 28 and seven haplotypes of the chloroplast DNA (cpDNA) atp B-rbc L spacer, cpDNA trn L-trn F spacer, and mitochondrial DNA (mtDNA) internal transcribed spacer (ITS) were identified, respectively, from 202 individuals. Three data sets suggested consistent phylogenies recovering two differentiated lineages corresponding to geographical regions, i.e. northern South-China-Sea + East-China-Sea region and southern South-China-Sea region (Sarawak). Phylogenetically, the Sarawak population was closely related to the Ranong population of western Peninsula Malaysia instead of other South-China-Sea populations, indicating its possible origin from the Indian Ocean Rim. No geographical subdivision was detected within the northern geographical region. An analysis of molecular variance (AMOVA) revealed low levels of genetic differentiation between and within mainland and island populations (Φ CT = 0.015, Φ SC = 0.037), indicating conspicuous long-distance seedling dispersal across oceans. Significant linkage disequilibrium excluded the possibility of recurrent homoplasious mutations as the major force causing phylogenetic discrepancy between mtDNA and the trn L-trn F spacer within the northern region. Instead, relative ages of alleles contributed to nonrandom chlorotype-mitotype associations and tree inconsistency. Widespread distribution and random associations (χ 2 = 0.822, P = 0.189) of eight hypothetical ancestral cytotypes indicated the panmixis of populations of the northern geographical region as a whole. In contrast, rare and recently evolved alleles were restricted to marginal populations, revealing some preferential directional migration.
Molecular Ecology, 2005
Both demographic history and dispersal mechanisms influence the apportionment of genetic diversit... more Both demographic history and dispersal mechanisms influence the apportionment of genetic diversity among plant populations across geographical regions. In this study, phylogeography and population structure of wild banana, Musa balbisiana , one of the progenitors of cultivated bananas and plantains in China were investigated by an analysis of genetic diversity of simple sequence repeat (SSR) fingerprint markers and cpDNA PCR-RFLP. A chloroplast DNA (cpDNA) genealogy of 21 haplotypes identified two major clades, which correspond to two geographical regions separated by the Beijiang and Xijiang rivers, suggesting a history of vicariance. Significant genetic differentiation was detected among populations with cpDNA markers, a result consistent with limited seed dispersal in wild banana mediated by foraging of rodents. Nuclear SSR data also revealed significant geographical structuring in banana populations. In western China, however, there was no detected phylogeograpahical pattern, possibly due to frequent pollen flow via fruit bats. In contrast, populations east of the Beijiang River and the population of Hainan Island, where long-range soaring pollinators are absent, are genetically distinct. Colonization-extinction processes may have influenced the evolution of Musa populations, which have a metapopulation structure and are connected by migrating individuals. Effective gene flow via pollen, estimated from the nuclear SSR data, is 3.65 times greater than gene flow via seed, estimated from cpDNA data. Chloroplast and nuclear DNAs provide different insights into phylogeographical patterns of wild banana populations and, taken together, can inform conservation practices.
Molecular Ecology, 2000
Nucleotide sequences of 3&amp;#39; end of the cytochrome b gene, tRNA genes, D-loop contr... more Nucleotide sequences of 3&amp;#39; end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5&amp;#39; end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P &amp;lt; 0.001) and among regions (PhiCT = 0.368, P &amp;lt; 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.
Molecular Biology and Evolution, 1999
Recombination between RNA sequences plays a role in the fast evolution of a few viruses. There ha... more Recombination between RNA sequences plays a role in the fast evolution of a few viruses. There has been no report on hepatitis D virus (HDV) recombination. In this study, we analyzed genetic recombination of HDV and its possible impact on evolution and clinical course. The aligned HDV sequences allowed us to construct a phylogenetic tree which supported the notion of distinct lineages of HDV. The tree was also used in the analysis of recombination using partial likelihoods assessed through optimization. Nine segments of the HDV genome with significant levels of genetic recombination were detected. Five segments were in the hypervariable region, and four were in the delta-antigen-coding region. None could be found in the well-conserved autocleavage region that is essential for replication. Recombination occurred both between and within types. The results of this study indicated that the remarkable variation in HDV genomic sequences, particularly in the hypervariable region, among different genotypes may at least partly result from multiple episodes of genetic recombination during evolution. Genetic recombination may play a significant role in increasing genetic diversity. Importantly, a genetic recombination (nt 1082-1093) occurred in one of the immunogenic domains of hepatitis delta virus antigen recognized by human and woodchuck antibodies (amino acids 174-195). Genetic recombination also occurred at another segment between nt 1517 and 1535, which was close to one of the predicted T-cell epitopes (amino acids 26-41). In longitudinal analysis of HDV genomes at different time points during chronic infection, novel dominant HDV strains with amino acid changes at these epitopes usually emerged after severe hepatitis attacks. In the comparison of HDV clones during or shortly after flare-up of liver disease, K a /K s ratios of Ͼ1 were frequently found, suggesting Darwinian positive selection. Therefore, recombination in these two segments may play an important role for HDV in the evasion of immunity.
Journal of Viral Hepatitis, 2000
The impact of transfusion-transmitted virus (TTV) infection on acute fulminant and non-fulminant ... more The impact of transfusion-transmitted virus (TTV) infection on acute fulminant and non-fulminant hepatitis is unclear. In this study, serum samples from 164 patients with acute hepatitis of various aetiologies, from 34 asymptomatic hepatitis B virus carriers and from 202 healthy adults were tested for TTV DNA by the semiconserved nested polymerase chain reaction. TTV viraemia was prevalent in patients with acute hepatitis C, in patients with acute hepatitis D virus superinfection and in patients with non-A-E hepatitis (27-30%) but the incidence was not significantly different from that of healthy controls (31 of 202, 15.3%). There were no significant differences in gender, age, presence of hepatitis G virus, the occurrence of fulminant hepatitis, or in serum albumin, bilirubin or alanine aminotransferase levels (9/30 vs 35/134) between patients with or without TTV viraemia. Seven of the nine TTV-positive patients with fulminant hepatitis were co-infected with hepatitis C, D or E. TTV clones from 18 subjects, with or without fulminant hepatitis, were sequenced and analysed phylogenetically. Eleven (61. 1%) belonged to TTV group 1, six (33.3%) to TTV group 2 and one to TTV group 3. No particular strain of TTV was associated with fulminant hepatitis. In summary, in Taiwan, TTV is prevalent in the general population as well as in patients with liver diseases. TTV plays an insignificant role in acute fulminant and non-fulminant hepatitis. Its influence on outcome requires a longitudinal study.
Journal of Plant Research, 2002
We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis... more We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In contrast to the paraphyly of the nearly neutral cpDNA alleles, differentiated RAPDs may have experienced diversifying selection.
Journal of Medical Virology, 1998
The clinical impact of GB virus-C (GBV-C)/hepatitis G virus (HGV) infection on various causes of ... more The clinical impact of GB virus-C (GBV-C)/hepatitis G virus (HGV) infection on various causes of acute hepatitis and fulminant hepatitis is controversial. In this study, serum samples from 164 patients with acute hepatitis of various causes, 34 asymptomatic hepatitis B virus (HBV) carriers, and 34 healthy adults were tested for GBV-C/HGV RNA by reverse transcription-nested polymerase chain reaction using primers based on the 5'-untranslated region. Nucleotide sequences of GBV-C/HGV RNA from various groups were compared. The prevalence of GBV-C/HGV RNA was significantly higher in patients with acute hepatitis D virus (HDV) superinfection than in HBV carriers or healthy controls (10/37 vs. 2/34, P < 0.02; 10/37 vs. 1/34, P < 0.005). GBV-C/HGV RNA was detected in 11.1% of acute hepatitis A patients, 9.5% of acute hepatitis B patients, 15.8% of acute hepatitis C patients, 12.5% of acute hepatitis E patients, 11.8% of chronic hepatitis B patients with acute exacerbation, and 11.1% in patients with non-A to -E hepatitis; each was not significantly higher than that in HBV carriers or healthy adults. There were no significant differences in gender, age, serum albumin, bilirubin, and alanine aminotransferase levels nor in the occurrence of fulminant hepatitis (6/28 vs. 36/136) between patients with or without GBV-C/HGV RNA. All six patients with fulminant hepatitis who had GBV-C/HGV RNA were complicated by infection with hepatitis B, C, or D. The GBV-C/HGV clones from 21 patients with or without fulminant hepatitis belonged to group 3. No particular strain of GBV-C/HGV was associated with fulminant hepatitis.
Journal of Fish Biology, 2007
Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China id... more Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China identified two major clades corresponding to two allopatric taxa, Glyptothorax fokiensis fokiensis and Glyptothorax fokiensis hainanensis. Reciprocal monophyly and a molecular clock separation between these two taxa of 2Á3 million years indicate these taxa should be elevated to species. Mismatch distributions and Fu's F S statistic suggest that both G. fokiensis and G. hainanensis have experienced recent population expansions. Analysis of molecular variance indicates that most of the genetic variation resides among populations within both species, with F ST ¼ 0Á645 for G. fokiensis and 0Á801 for G. hainanensis, suggesting restricted gene flow among populations. Significant correlations between the geographic and the genetic distances provide support for the importance of geographic isolations between populations. Nested clade analysis also confirms low levels of genetic exchanges between the two major groups and between populations within each group. The phylogeographical pattern among populations of Glyptothorax in East Asia can be attributed to historical fragmentations, demographic expansions and occasional long-distance dispersals stimulated by tectonic activity and Ice Age climate changes.
Journal of Fish Biology, 2010
Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis... more Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis sinensis from 12 drainages in Taiwan were identified as two major clades, exhibiting a southern and a northern distribution, north of TzengWen and south of TzengWen (including TzengWen), respectively. The divergence time between these two phylogroups was estimated at 7.34-9.06 million years before present (B.P.), but these two phylogroups were formed c. 3.41-4.23 and 2.22-2.75 M B.P., respectively. Moreover, geological events have been recalculated that Taiwan Island emerged above sea level at an estimate of c. 4-5 M B.P., and quickly became its present shape at c. 2 M B.P. through mountain building. These results suggest that these two major clades of C. sinensis in Taiwan might originate from two different continental populations, since the island's initial isolation in the Pliocene. Within southern Taiwan, the initial colonization was hypothesized to be in KaoPing River, followed by its northward dispersal. The high divergence between KaoPing and TzengWen was influenced by glaciations and landforms. Within north Taiwan, the colonization was from the Miaoli Plateau through western Taiwan to north-eastern and northern Taiwan. This dispersal pattern is concordant with the previously proposed hypothesis. Apparently, both geological and phylogeographic evidence suggested that river capture of the upper Takia River by the LanYang River promoted range expansion in freshwater fishes and also indicated that the Central Range within Taiwan did not act as a barrier to the dispersal of C. sinensis.
Journal of Fish Biology, 2008
Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only... more Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity (h ¼ 0Á989) and low nucleotide diversity (p ¼ 0Á009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations (F ST ¼ 0Á66). Significant haplotype heterogeneity was also detected among populations within regions (F SC ¼ 0Á41, P < 0Á001) and among regions (F CT ¼ 0Á43, P < 0Á05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0Á11-0Á39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B þ C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.
Genome, 1999
The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal... more The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymerase I promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.Key words: concerted evolution, hybridization, length heterogeneity, Miscanthus sin...
Contributions to Zoology
The nocturnal distribution and resource use by Ryukyu flying foxes was studied along 28 transects... more The nocturnal distribution and resource use by Ryukyu flying foxes was studied along 28 transects, covering five types of habitats, on Iriomote Island, Japan, from early June to late September, 2005. Bats were mostly encountered solitarily (66.8%) or in pairs (16.8%), with a mean linear density of 2.5 ± 0.6 bats/km of transect/night. Across the island, however, bat densities were distributed non-randomly among transect-nights, not correlated with transect length, and showed a slightly clumped distribution (variance/mean = 3.3). Outskirt trails contributed higher values to the relative importance of bat abundance, but the highest mean abundances occurred mostly at village sites on the west coast, which on average devoted only a quarter of their land area to agriculture/husbandry compared to those on the east coast. This supports our prediction that higher bat abundances are found in areas with less anthropogenic interference and more forest. Among habitats, the mean total abundance a...
Zhonghua yi xue za zhi = Chinese medical journal; Free China ed, 1999
Spread of hepatitis D virus (HDV) from mother to infant is rare and nucleotide evidence to docume... more Spread of hepatitis D virus (HDV) from mother to infant is rare and nucleotide evidence to document such transmission is lacking. The aim of this study was to screen the children of HDV-infected parents and compare the HDV nucleotide sequence between children and parents by phylogenetic analysis. Fifty-seven children of 28 HDV-infected parents (23 fathers and 5 mothers, including two couples) were enrolled. HDV genomes from sera of HDV-infected parents and their children were cloned and sequenced. Comparison and phylogenetic analysis of HDV genomes were based on a region from nucleotide 911 to 1260. The homology to nucleotide sequence among different genotypes was estimated by phylogenetic analysis. One of the eight children whose mothers were anti-HDV positive was positive for anti-HDV. Mean heterogeneity among different HDV clones from a single subject ranged from 0.29% to 1.15%. HDV sequences from the mother and her child (referred from southern Taiwan) were nearly identical (99....
The Journal of general virology, 1998
The hepatitis D virus (HDV) genotypes in 46 HDV-infected patients and 12 prostitutes were screene... more The hepatitis D virus (HDV) genotypes in 46 HDV-infected patients and 12 prostitutes were screened with Xhol restriction fragment length polymorphism (RFLP) analysis of reverse transcription PCR products of viral genomes and verified by phylogenetic analysis. The amplificates of three (6.5%) patients and two (17%) prostitutes showed a novel RFLP pattern different from those of the three known genotypes. Complete HDV genomic sequence identities between isolates with a novel RFLP and the HDV genotypes I, II and III were 72.3, 77.2 and 63.0%, respectively. Importantly, divergence was mostly seen in various regions related to replication or packaging. The novel isolates formed a monophyletic group (P < 0.05) and were most closely related to genotype II.
Genetics and Molecular Research, 2014
Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesti... more Primers for eight microsatellites were developed; they successfully amplified DNA from 20 domesticated Formosan Sambar deer (Cervus unicolor swinhoei). All loci were polymorphic, with 10-19 alleles per locus. The average observed heterozygosity across loci and samples was 0.310, ranging from 0 to 0.750 at each locus. All loci but one, CU18, deviated from Hardy-Weinberg equilibrium due to excessive homozygosity in these domesticated broodstocks, reflecting inbreeding. These microsatellite loci will be useful, not only for assessment of population structure and genetic variability, but also for conservation of wild deer populations in Taiwan.
Plant Molecular Biology, 1998
Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, ... more Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, from genomic DNA of Begonia nantoensis Lai et Chung Trivial name: Promoter of rbcL gene from B. nantoensis Description: Promoter of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) with 761 bp from B. nantoensis lies downstream of the atpB gene. Nucleotide sequence of the promoter for rbcL in B. nantoensis shows 79.9%, 76.3%, 72.8% identity with Malus domestica (X69749), Euphorbia characius (X69735), and Camellia sinensis (X69732) respectively.
Plant Molecular Biology, 1998
Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, ... more Source of sequence: Sequence was determined from a PCR product, which was ligated to a T-vector, from genomic DNA of Glycine soja Sieb. & Zucc., a wild soybean (isolate 043) collected from South China. Trivial name: rDNA ITS region of wild soybean Description: ITS region of ribosomal DNA lies between 18S and 28S rRNA genes was cloned from wild soybean, Glycine soja, with 216 bp in ITS1, 169 bp in 5.8S rRNA gene and 211 bp in ITS2. Nucleotide sequence of ITS region in Glycine soja shows 98.8% and 88.2% identity with cultivated soybean, Glycine max L., and Glycine falcata Benth. respectively. Acknowledgements. This research was supported by a grant from Academia Sinica, Taiwan, ROC, to Y.I.C.H. Figure 1. Nucleotide sequence of ITS region of rDNA from Glycine soja.
Molecular Ecology, 2005
The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-... more The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trn T-trn F and trn S-trn G sequence variation within Juniperus przewalskii , a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G ST = 0.772, N ST = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N ST > G ST , P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.
Molecular Ecology, 2001
The phylogegraphic pattern of Cycas taitungensis , an endemic species with two remaining populati... more The phylogegraphic pattern of Cycas taitungensis , an endemic species with two remaining populations in Taiwan, was investigated based on genetic variability and phylogeny of the atp B-rbc L noncoding spacer of chloroplast DNA (cpDNA) and the ribosomal DNA (rDNA) internal transcribed spacer (ITS) of mitochondrial DNA (mtDNA). High levels of genetic variation at both organelle loci, due to frequent intramolecular recombination, and low levels of genetic differentiation were detected in the relict gymnosperm. The apportionment of genetic variation within and between populations agreed with a migrant-pool model, which describes a migratory pattern with colonists recruited from a random sample of earlier existing populations. Phylogenies obtained from cpDNA and mtDNA were discordant according to neighbour-joining analyses. In total four chlorotypes (clades I − IV) and five mitotypes (clades A − E) were identified based on minimum spanning networks of each locus. Significant linkage disequilibrium in mitotype − chlorotype associations excluded the possibility of the recurrent homoplasious mutations as the major force causing phylogenetic inconsistency. The most abundant chlorotype I was associated with all mitotypes and the most abundant mitotype C with all chlorotypes; no combinations of rare mitotypes with rare chlorotypes were found. According to nested clade analyses, such nonrandom associations may be ascribed to relative ages among alleles associated with the geological history through which cycads evolved. Nested in networks as interior nodes coupled with wide geographical distribution, the most dominant cytotypes of CI and EI may represent ancestral haplotypes of C. taitungensis with a possible long existence prior to the Pleistocene glacial maximum. In contrast, rare chlorotypes and mitotypes with restricted and patchy distribution may have relatively recent origins. Newly evolved genetic elements of mtDNA, with a low frequency, were likely to be associated with the dominant chlorotype, and vice versa, resulting in the nonrandom mitotype − chlorotype associations. Paraphyly of CI and EI cytotypes, leading to the low level of genetic differentiation between cycad populations, indicated a short period for isolation, which allowed low possibilities of the attainment of coalescence at polymorphic ancestral alleles.
Molecular Ecology, 2006
Species whose geographical distribution encompasses both mainland and island populations provide ... more Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis , a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.
Molecular Ecology, 2001
Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range... more Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range dispersal. To examine the extent of seedling dispersal across oceans, we investigated the phylogeny and genetic structure among East Asiatic populations of Kandelia candel based on organelle DNAs. In total, three, 28 and seven haplotypes of the chloroplast DNA (cpDNA) atp B-rbc L spacer, cpDNA trn L-trn F spacer, and mitochondrial DNA (mtDNA) internal transcribed spacer (ITS) were identified, respectively, from 202 individuals. Three data sets suggested consistent phylogenies recovering two differentiated lineages corresponding to geographical regions, i.e. northern South-China-Sea + East-China-Sea region and southern South-China-Sea region (Sarawak). Phylogenetically, the Sarawak population was closely related to the Ranong population of western Peninsula Malaysia instead of other South-China-Sea populations, indicating its possible origin from the Indian Ocean Rim. No geographical subdivision was detected within the northern geographical region. An analysis of molecular variance (AMOVA) revealed low levels of genetic differentiation between and within mainland and island populations (Φ CT = 0.015, Φ SC = 0.037), indicating conspicuous long-distance seedling dispersal across oceans. Significant linkage disequilibrium excluded the possibility of recurrent homoplasious mutations as the major force causing phylogenetic discrepancy between mtDNA and the trn L-trn F spacer within the northern region. Instead, relative ages of alleles contributed to nonrandom chlorotype-mitotype associations and tree inconsistency. Widespread distribution and random associations (χ 2 = 0.822, P = 0.189) of eight hypothetical ancestral cytotypes indicated the panmixis of populations of the northern geographical region as a whole. In contrast, rare and recently evolved alleles were restricted to marginal populations, revealing some preferential directional migration.
Molecular Ecology, 2005
Both demographic history and dispersal mechanisms influence the apportionment of genetic diversit... more Both demographic history and dispersal mechanisms influence the apportionment of genetic diversity among plant populations across geographical regions. In this study, phylogeography and population structure of wild banana, Musa balbisiana , one of the progenitors of cultivated bananas and plantains in China were investigated by an analysis of genetic diversity of simple sequence repeat (SSR) fingerprint markers and cpDNA PCR-RFLP. A chloroplast DNA (cpDNA) genealogy of 21 haplotypes identified two major clades, which correspond to two geographical regions separated by the Beijiang and Xijiang rivers, suggesting a history of vicariance. Significant genetic differentiation was detected among populations with cpDNA markers, a result consistent with limited seed dispersal in wild banana mediated by foraging of rodents. Nuclear SSR data also revealed significant geographical structuring in banana populations. In western China, however, there was no detected phylogeograpahical pattern, possibly due to frequent pollen flow via fruit bats. In contrast, populations east of the Beijiang River and the population of Hainan Island, where long-range soaring pollinators are absent, are genetically distinct. Colonization-extinction processes may have influenced the evolution of Musa populations, which have a metapopulation structure and are connected by migrating individuals. Effective gene flow via pollen, estimated from the nuclear SSR data, is 3.65 times greater than gene flow via seed, estimated from cpDNA data. Chloroplast and nuclear DNAs provide different insights into phylogeographical patterns of wild banana populations and, taken together, can inform conservation practices.
Molecular Ecology, 2000
Nucleotide sequences of 3&amp;#39; end of the cytochrome b gene, tRNA genes, D-loop contr... more Nucleotide sequences of 3&amp;#39; end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5&amp;#39; end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P &amp;lt; 0.001) and among regions (PhiCT = 0.368, P &amp;lt; 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.
Molecular Biology and Evolution, 1999
Recombination between RNA sequences plays a role in the fast evolution of a few viruses. There ha... more Recombination between RNA sequences plays a role in the fast evolution of a few viruses. There has been no report on hepatitis D virus (HDV) recombination. In this study, we analyzed genetic recombination of HDV and its possible impact on evolution and clinical course. The aligned HDV sequences allowed us to construct a phylogenetic tree which supported the notion of distinct lineages of HDV. The tree was also used in the analysis of recombination using partial likelihoods assessed through optimization. Nine segments of the HDV genome with significant levels of genetic recombination were detected. Five segments were in the hypervariable region, and four were in the delta-antigen-coding region. None could be found in the well-conserved autocleavage region that is essential for replication. Recombination occurred both between and within types. The results of this study indicated that the remarkable variation in HDV genomic sequences, particularly in the hypervariable region, among different genotypes may at least partly result from multiple episodes of genetic recombination during evolution. Genetic recombination may play a significant role in increasing genetic diversity. Importantly, a genetic recombination (nt 1082-1093) occurred in one of the immunogenic domains of hepatitis delta virus antigen recognized by human and woodchuck antibodies (amino acids 174-195). Genetic recombination also occurred at another segment between nt 1517 and 1535, which was close to one of the predicted T-cell epitopes (amino acids 26-41). In longitudinal analysis of HDV genomes at different time points during chronic infection, novel dominant HDV strains with amino acid changes at these epitopes usually emerged after severe hepatitis attacks. In the comparison of HDV clones during or shortly after flare-up of liver disease, K a /K s ratios of Ͼ1 were frequently found, suggesting Darwinian positive selection. Therefore, recombination in these two segments may play an important role for HDV in the evasion of immunity.
Journal of Viral Hepatitis, 2000
The impact of transfusion-transmitted virus (TTV) infection on acute fulminant and non-fulminant ... more The impact of transfusion-transmitted virus (TTV) infection on acute fulminant and non-fulminant hepatitis is unclear. In this study, serum samples from 164 patients with acute hepatitis of various aetiologies, from 34 asymptomatic hepatitis B virus carriers and from 202 healthy adults were tested for TTV DNA by the semiconserved nested polymerase chain reaction. TTV viraemia was prevalent in patients with acute hepatitis C, in patients with acute hepatitis D virus superinfection and in patients with non-A-E hepatitis (27-30%) but the incidence was not significantly different from that of healthy controls (31 of 202, 15.3%). There were no significant differences in gender, age, presence of hepatitis G virus, the occurrence of fulminant hepatitis, or in serum albumin, bilirubin or alanine aminotransferase levels (9/30 vs 35/134) between patients with or without TTV viraemia. Seven of the nine TTV-positive patients with fulminant hepatitis were co-infected with hepatitis C, D or E. TTV clones from 18 subjects, with or without fulminant hepatitis, were sequenced and analysed phylogenetically. Eleven (61. 1%) belonged to TTV group 1, six (33.3%) to TTV group 2 and one to TTV group 3. No particular strain of TTV was associated with fulminant hepatitis. In summary, in Taiwan, TTV is prevalent in the general population as well as in patients with liver diseases. TTV plays an insignificant role in acute fulminant and non-fulminant hepatitis. Its influence on outcome requires a longitudinal study.
Journal of Plant Research, 2002
We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis... more We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In contrast to the paraphyly of the nearly neutral cpDNA alleles, differentiated RAPDs may have experienced diversifying selection.
Journal of Medical Virology, 1998
The clinical impact of GB virus-C (GBV-C)/hepatitis G virus (HGV) infection on various causes of ... more The clinical impact of GB virus-C (GBV-C)/hepatitis G virus (HGV) infection on various causes of acute hepatitis and fulminant hepatitis is controversial. In this study, serum samples from 164 patients with acute hepatitis of various causes, 34 asymptomatic hepatitis B virus (HBV) carriers, and 34 healthy adults were tested for GBV-C/HGV RNA by reverse transcription-nested polymerase chain reaction using primers based on the 5'-untranslated region. Nucleotide sequences of GBV-C/HGV RNA from various groups were compared. The prevalence of GBV-C/HGV RNA was significantly higher in patients with acute hepatitis D virus (HDV) superinfection than in HBV carriers or healthy controls (10/37 vs. 2/34, P < 0.02; 10/37 vs. 1/34, P < 0.005). GBV-C/HGV RNA was detected in 11.1% of acute hepatitis A patients, 9.5% of acute hepatitis B patients, 15.8% of acute hepatitis C patients, 12.5% of acute hepatitis E patients, 11.8% of chronic hepatitis B patients with acute exacerbation, and 11.1% in patients with non-A to -E hepatitis; each was not significantly higher than that in HBV carriers or healthy adults. There were no significant differences in gender, age, serum albumin, bilirubin, and alanine aminotransferase levels nor in the occurrence of fulminant hepatitis (6/28 vs. 36/136) between patients with or without GBV-C/HGV RNA. All six patients with fulminant hepatitis who had GBV-C/HGV RNA were complicated by infection with hepatitis B, C, or D. The GBV-C/HGV clones from 21 patients with or without fulminant hepatitis belonged to group 3. No particular strain of GBV-C/HGV was associated with fulminant hepatitis.
Journal of Fish Biology, 2007
Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China id... more Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China identified two major clades corresponding to two allopatric taxa, Glyptothorax fokiensis fokiensis and Glyptothorax fokiensis hainanensis. Reciprocal monophyly and a molecular clock separation between these two taxa of 2Á3 million years indicate these taxa should be elevated to species. Mismatch distributions and Fu's F S statistic suggest that both G. fokiensis and G. hainanensis have experienced recent population expansions. Analysis of molecular variance indicates that most of the genetic variation resides among populations within both species, with F ST ¼ 0Á645 for G. fokiensis and 0Á801 for G. hainanensis, suggesting restricted gene flow among populations. Significant correlations between the geographic and the genetic distances provide support for the importance of geographic isolations between populations. Nested clade analysis also confirms low levels of genetic exchanges between the two major groups and between populations within each group. The phylogeographical pattern among populations of Glyptothorax in East Asia can be attributed to historical fragmentations, demographic expansions and occasional long-distance dispersals stimulated by tectonic activity and Ice Age climate changes.
Journal of Fish Biology, 2010
Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis... more Mitochondrial DNA cytochrome b sequences (1140 bp) in 61 specimens of Chinese spiny loach Cobitis sinensis from 12 drainages in Taiwan were identified as two major clades, exhibiting a southern and a northern distribution, north of TzengWen and south of TzengWen (including TzengWen), respectively. The divergence time between these two phylogroups was estimated at 7.34-9.06 million years before present (B.P.), but these two phylogroups were formed c. 3.41-4.23 and 2.22-2.75 M B.P., respectively. Moreover, geological events have been recalculated that Taiwan Island emerged above sea level at an estimate of c. 4-5 M B.P., and quickly became its present shape at c. 2 M B.P. through mountain building. These results suggest that these two major clades of C. sinensis in Taiwan might originate from two different continental populations, since the island's initial isolation in the Pliocene. Within southern Taiwan, the initial colonization was hypothesized to be in KaoPing River, followed by its northward dispersal. The high divergence between KaoPing and TzengWen was influenced by glaciations and landforms. Within north Taiwan, the colonization was from the Miaoli Plateau through western Taiwan to north-eastern and northern Taiwan. This dispersal pattern is concordant with the previously proposed hypothesis. Apparently, both geological and phylogeographic evidence suggested that river capture of the upper Takia River by the LanYang River promoted range expansion in freshwater fishes and also indicated that the Central Range within Taiwan did not act as a barrier to the dispersal of C. sinensis.
Journal of Fish Biology, 2008
Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only... more Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity (h ¼ 0Á989) and low nucleotide diversity (p ¼ 0Á009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations (F ST ¼ 0Á66). Significant haplotype heterogeneity was also detected among populations within regions (F SC ¼ 0Á41, P < 0Á001) and among regions (F CT ¼ 0Á43, P < 0Á05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0Á11-0Á39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B þ C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.