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ABSTRACT: • Premise of the study: Microsatellite primers were developed for the endemic tree Litsea hypophaea (Lauraceae) in Taiwan to investigate its genetic diversity and population genetic structure and to investigate species delimitation within Litsea. • Methods and Results: Fifteen new simple sequence repeat markers were developed from L. hypophaea with a magnetic bead enrichment method. Most loci were also amplified from three closely related species, L. coreana, L. lii, and L. acutivena. The number of alleles and observed and expected heterozygosities across loci varied with a range of 1-25, 0.000-1.000, and 0.000-0.956, respectively. • Conclusions: The application of these microsatellite markers of L. hypophaea provides a tool for understanding genetic diversity and population differentiation. In addition, interspecific amplification suggests that these markers will also be useful for species identification of related taxa within Litsea in Taiwan.
American Journal of Botany 05/2012; 99(6):e251-4. · 2.66 Impact Factor
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ABSTRACT: Miscanthus sinensis (Poaceae) is typical of many dominant grasses of East Asia. Due to its characteristics of fast growth and high biomass, Miscanthus, a C4 plant, has been long explored for the potential usage as biofuel. In this study, we described the development of nine
microsatellite loci from M.sinensis for genetic studies. These new markers were tested in 25 individuals of five populations in three varieties. The number of
alleles ranged from 3 to 8. The expected (H
E) and observed (H
O) heterozygosities were 0.37–0.78 and 0.05–0.52, respectively. All microsatellite loci are significantly deviated from Hardy–Weinberg
expectations likely due to the population structure within samples. Linkage disequilibrium between four loci pairs were observed
from the total 36 pairwise comparisons of loci. Cross-species transferability revealed that all loci can be applied to its
closely related species, M.floridulus.
Conservation Genetics 05/2012; 10(5):1377-1380. · 1.61 Impact Factor
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ABSTRACT: Ludwigia polycarpa is the only species of section Microcarpium occurring north of 37°N in the central midwest of the United States. Recently, the loss of wetlands in North America reduced
the population number and size of L. polycarpa dramatically. In this study, for the purpose of the conservation of the endangered species, we described eight microsatellite
DNA loci. High variabilities enable these molecular markers to assess the population structure. The number of alleles per locus ranged from 8 to 23. The expected (H
E) and observed (H
O) heterozygosities ranged from 0.86 to 0.96 and 0.00 to 1.00, respectively. Seven of the eight microsatellite loci displayed
significant departures from Hardy–Weinberg expectations, likely due to the loss of habitats and the small population size.
No linkage disequilibrium was observed in the pairwise comparisons of loci. The application of these microsatellite loci in
L. polycarpa may provide a tool for understanding its demography and population structure.
Conservation Genetics 04/2012; 10(5):1381-1383. · 1.61 Impact Factor
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ABSTRACT: • Premise of the study: Fifteen microsatellite loci were developed in an endangered species, Amentotaxus formosana, and were tested in an additional three species, A. argotaenia, A. yunnanensis, and A. poilanei, to evaluate the population structure for conservation efforts and reconstruct the phylogeographic patterns of this ancient lineage. • Methods and Results: Polymorphic primer sets were developed from A. formosana; the number of alleles ranged from two to 10, with an observed heterozygosity ranging from 0 to 0.60. All of the loci were found to be interspecifically amplifiable. • Conclusions: These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct genetic units within species and establishing the phylogeographic patterns and the process of speciation among closely related species.
American Journal of Botany 03/2012; 99(4):e157-9. · 2.66 Impact Factor
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ABSTRACT: Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.
Gene 03/2012; 499(1):194-201. · 2.34 Impact Factor
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Chao-Li Huang,
Cheng-Yu Hung,
Yu-Chung Chiang,
Chi-Chuan Hwang,
Tsai-Wen Hsu,
Chi-Chun Huang, Kuo-Hsiang Hung,
Kun-Chan Tsai,
Kuo-Hsiung Wang,
Naoki Osada,
Barbara Anna Schaal,
Tzen-Yuh Chiang
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ABSTRACT: Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
The Plant Journal 01/2012; 70(5):769-82. · 6.16 Impact Factor
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ABSTRACT: Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central-marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population.
We examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central-marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.
The marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.
PLoS ONE 01/2012; 7(8):e43717. · 4.09 Impact Factor
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ABSTRACT: Nouelia insignis, an endangered species, is distributed in the Jinsha and Nanpan drainage areas in southwestern China. In this study, we examined the genetic diversity and population structure based on the sequences of the cpDNA rpL 16 intron. Low levels of genetic variation were detected within all populations of the endemic species. A gene genealogy of 11 haplotypes recovered two major lineages I and II, with haplotypes H1 and H6 nested as interior nodes, respectively. Haplotype H1 was widespread in all populations, while haplotype H6 was restricted to populations southern of the Jinsha River. Low levels of genetic differentiation were detected, as most F (st) values between populations were zero. This result, however, contradicts previous studies based on allozymes and fingerprinting. Genetic analyses suggested that coancestry due to low evolutionary rates resulted in the lack of geographical subdivision. Molecular dating estimated that the two lineages split about 3.224 MYA (95% CI 1.070-6.089 MYA). Maintenance of ancestral polymorphisms was possibly attributable to a long-standing large effective population size until recently. Postglacial demographic expansion was supported by a unimodal mismatch distribution and star-like phylogenies.
Journal of Plant Research 03/2011; 124(2):221-30. · 1.75 Impact Factor
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ABSTRACT: A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the Rhododendron pseudochrysanthum s. l.
Systematic inconsistency was detected between gene genealogies of the cpDNA and nrDNA. Rooted at R. hyperythrum and R. formosana, both trees lacked reciprocal monophyly for all members of the complex. For R. pseudochrysanthum s.l., the spatial distribution of the cpDNA had a noteworthy pattern showing high genetic differentiation (FST=0.56-0.72) between populations in the Yushan Mountain Range and populations of the other mountain ranges.
Both incomplete lineage sorting and interspecific hybridization/introgression may have contributed to the lack of monophyly among R. hyperythrum, R. formosana and R. pseudochrysanthum s.l. Independent colonizations, plus low capabilities of seed dispersal in current environments, may have resulted in the genetic differentiation between populations of different mountain ranges. At the population level, the populations of Central, and Sheishan Mountains may have undergone postglacial demographic expansion, while populations of the Yushan Mountain Range are likely to have remained stable ever since the colonization. In contrast, the single population of the Alishan Mountain Range with a fixed cpDNA haplotype may have experienced bottleneck/founder's events.
BMC Evolutionary Biology 01/2011; 11:108. · 3.52 Impact Factor
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ABSTRACT: Tetraena mongolica (Zygophyllaceae), an endangered endemic species in western Inner Mongolia, China. For endemic species with a limited geographical range and declining populations, historical patterns of demography and hierarchical genetic structure are important for determining population structure, and also provide information for developing effective and sustainable management plans. In this study, we assess genetic variation, population structure, and phylogeography of T. mongolica from eight populations. Furthermore, we evaluate the conservation and management units to provide the information for conservation.
Sequence variation and spatial apportionment of the atpB-rbcL noncoding spacer region of the chloroplast DNA were used to reconstruct the phylogeography of T. mongolica. A total of 880 bp was sequenced from eight extant populations throughout the whole range of its distribution. At the cpDNA locus, high levels of genetic differentiation among populations and low levels of genetic variation within populations were detected, indicating that most seed dispersal was restricted within populations.
Demographic fluctuations, which led to random losses of genetic polymorphisms from populations, due to frequent flooding of the Yellow River and human disturbance were indicated by the analysis of BEAST skyline plot. Nested clade analysis revealed that restricted gene flow with isolation by distance plus occasional long distance dispersal is the main evolutionary factor affecting the phylogeography and population structure of T. mongolica. For setting a conservation management plan, each population of T. mongolica should be recognized as a conservation unit.
BMC Genetics 01/2011; 12:1. · 2.47 Impact Factor
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ABSTRACT: • Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
New Phytologist 10/2010; 188(2):488-500. · 6.64 Impact Factor
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ABSTRACT: Ludwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of the Ludwigia sect. Isnardia, which is a polyploid complex (x = 8) of five species distributed in North America. The phylogeny of L. sect. Isnardia was reconstructed based on sequences of cpDNA atpB-rbcL intergenic spacer and nrITS (internal transcribed spacer). Most L. sect. Isnardia species are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted at L. sect. Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploid L. spathulata are nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. Allopolyploid L. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggesting L. palustris as the paternal genome donor. Ludwigia brevipes may have arisen via bi-directional hybridization between L. palustris and L. arcuata followed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species of L. sect. Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution in L. sect. Isnardia.
Taxon 10/2009; 58(4):1216-1226. · 2.70 Impact Factor
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ABSTRACT: Betel nut (Areca nut, Areca catechu L.) is a conspicuous and important cultivated plant of tropical and subtropical habitats throughout Southeast Asia and Oceania. As a significant cultural and social offering, the migration of betel nut associated with human dispersal is an important issue in ethnobotany and anthropology. In this study, we described the development of nine microsatellite loci from A. catechu. The number of alleles per locus ranged from 5 to 15. The expected and observed heterozygosities ranged from 0.71to 0.94 and from 0 to 0.88, respectively. All microsatellite loci, except for AC30, significantly deviated from Hardy-Weinberg equilibrium possibly due to artificially selected cultivation or the existence of excessive null alleles. No linkage disequilibrium was observed from pairwise comparisons of loci, except for AC06 and AC08.
Molecular Ecology Resources 03/2009; 9(2):658-60. · 3.06 Impact Factor
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ABSTRACT: This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China.
The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic.
Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.
BMC Evolutionary Biology 02/2009; 9:161. · 3.52 Impact Factor
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ABSTRACT: Abstract
Background
This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis , species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas . Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China.
Results
The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atp B and rbc L genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales . The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic.
Conclusion
Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.
BMC Evolutionary Biology. 01/2009;
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ABSTRACT: Several hepatitis B virus (HBV) subgenotypes, HBV/A1, A2, Bj and Ba, have been reported with respect to clinical differences among patients infected with these subgenotypes. The population genetics and phylogeography of HBV were investigated based on the complete genome sequences of 484 isolates with 108 from our chronic hepatitis B patients and the remaining from the GenBank database. Besides genotypes A-H (HBV/A-H), five subgenotypes were identified among 169 HBV/B isolates by phylogenetic analysis and nucleotide divergence. There were 27 isolates of subgenotype B(1) (HBV/B(1)) restricted to Japan, 104 isolates of HBV/B(2) with the widest distribution in most Asian countries, 4 isolates of HBV/B(3) restricted to Indonesia, 32 isolates of HBV/B(4) restricted to Vietnam, and 7 isolates of HBV/B(5) restricted to Philippines. HBV/B(2)-B(5) isolates carried a recombination with HBV/C over the precore and core genes. In addition to the characteristics of HBV/B(1)-B(5) at some cis-acting elements, the precore stop-codon mutant (G1896A) was significantly different among HBV/B(1), HBV/B(2), and HBV/B(4) (70.3%, 31.7%, 53.0%, P=0.001), while no such mutation was found in HBV/B(3) and B(5). Among characteristics of the HBV/B(1)-B(5) amino acid sequences, serotype adw (K(122)) was exclusive among HBV/B(1), HBV/B(2), and HB V/B(3) isolates, while serotype ayw (R(122)) was among the HBV/B(4) and HBV/B(5) isolates. Furthermore, distinct variations of T cell and B cell recognition epitopes within surface and core proteins were also found among these subgenotypes. In conclusion, subgenotypes HBV/B(1)-B(5) exhibited distinct geographical distributions, virologic characteristics, and probable clinical implications.
Virus Research 12/2007; 129(2):212-23. · 2.94 Impact Factor
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ABSTRACT: Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.
Proceedings of the National Academy of Sciences 07/2006; 103(25):9578-83. · 9.68 Impact Factor
