Shong Huang

Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan.

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 atpB‐rbcL 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.

Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs.

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) atpB‐rbcL spacer, cpDNA trnL‐trnF 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 (ΦCT = 0.015, ΦSC = 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 trnL‐trnF spacer within the northern region. Instead, relative ages of alleles contributed to nonrandom chlorotype–mitotype associations and tree inconsistency. Widespread distribution and random associations (χ2 = 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.

Contrasting selection modes at the Adh1 locus in outcrossing Miscanthus sinensis vs. inbreeding Miscanthus condensatus (Poaceae)

We estimated DNA sequence variation of the Adh1 locus in the outcrossing Miscanthus sinensis (Poaceae) and its close selfing relative, M. condensatus. Tajimas test of selection is significantly negative for both overall exons and replacement sites in M. sinensis. Among its entire sample, nucleotide diversity of nonsynonymous sites is higher than that of synonymous sites. A McDonald and Kreitman test of neutrality indicates an excess of intraspecific replacement polymorphisms, suggesting possible directional selection toward advantageous mutants. However, frequent intragenic recombination suggests both purifying and positive selection is unlikely. Recent demographic expansions coupled with relaxation of purifying selection may have resulted in elevated genetic diversity at the Adh1 locus as well as the trnL-trnF intergenic spacer of cpDNA in this outcrossing species. In contrast, low levels of genetic diversity were detected at both the Adh1 locus and the cpDNA spacer in M. condensatus, consistent with bottlenecks associated with selfing in all populations. While Tajimas D and Fu and Lis F statistics did not reveal deviation from neutrality at the Adh1 locus in M. condensatus, 12 replacements vs. 10 synonymous changes were detected. Based on pairwise comparisons of the d(N)/d(S) ratio, lineages of closely related populations of the species distributed along saline habitats appeared to be under directional selection.

Phylogeography of Ceriops tagal (Rhizophoraceae) in Southeast Asia: the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea

The genetic structure of mangrove species is greatly affected by their geographic history. Nine natural populations of Ceriops tagal were collected from Borneo, the Malay Peninsula, and India for this phylogeographic study. Completely different haplotype compositions on the east versus west coasts of the Malay Peninsula were revealed using the atpB-rbcL and trnL-trnF spacers of chloroplast DNA. The average haplotype diversity (Hd) of the total population was 0.549, nucleotide diversity (θ) was 0.030, and nucleotide difference (π) was 0.0074. The cladogram constructed by the index of population differentiation (GST) clearly separated the South China Sea populations from the Indian Ocean populations. In the analysis of the minimum spanning network, the Indian Ocean haplotypes were all derived from South China Sea haplotypes, suggesting a dispersal route of C. tagal from Southeast Asia to South Asia. The Sunda Land river system and surface currents might be accountable for the gene flow directions in the South China Sea and Bay of Bengal, respectively. The historical geography not only affected the present genotype distribution but also the evolution of C. tagal. These processes result in the genetic differentiation and the differentiated populations that should be considered as Management Units (MUs) for conservation measurements instead of random forestation, which might lead to gene mixing and reduction of genetic variability of mangrove species. According to this phylogeographic study, populations in Borneo, and east and west Malay Peninsula that have unique genotypes should be considered as distinct MUs, and any activities resulting in gene mixing with each other ought to be prevented.

Phylogeny of hagfish based on the mitochondrial 16S rRNA gene.

The phylogenetic relationships among the species belonging to the family Myxinidae are still debatable. The mitochondrial DNA sequences from the large ribosomal RNA gene may be of great value for systematic and phylogenetic studies within families. Partial sequences of the 16S rRNA gene were obtained for comparisons among the following hagfish species, Paramyxine nelsoni, Paramyxine sheni, Paramyxine taiwanae, Paramyxine yangi, Paramyxine cheni, Eptatretus burgeri, Eptatretus stouii, Eptatretus cirrhatus, Myxine glutinosa, Myxine formosana, Myxine circifrons, Myxine sp1, and Myxine sp2. The boundary of four Paramyxine species (P. sheni, P. taiwanae, P. nelsoni, and P. yangi) from 16S rRNA sequences is ambiguous, however, they are valid based on our unpublished isozyme data as well as the gill aperture arrangement pattern. Both NJ and MP trees constructed from the present molecular data indicate that the genus Paramyxine is diphyletic and Eptatretus paraphyletic. The complexity of Eptatretus and Paramyxine in the clade would not be solved until the farther departed P. cheni is included to form a new clade under the genus Eptatretus. The other clade of Myxininae contains but single genus Myxine.

Allozyme Variation and the Genetic Structure of Populations of Trochodendron aralioides, a Monotypic and Narrow Geographic Genus

Trochodendron aralioides Siebold & Zucc., a primitive angiosperm that is insect-pollinated, has wind-dispersed seeds and grows only in eastern Asia. Nineteen populations were analyzed, including 16 from Taiwan, two from the main islands of Japan and one from Iriomote Island in the Ryukyu Islands. Genetic variability (0.133) at the species level was more similar to that of a narrow geographic species than an endemic species. Based on genotype frequencies, mating within populations was non-random (FIs=0.065) and there was significant genetic differentiation (FST=0.164) among populations. Genetic diversity was largely within, rather than among, populations (Hs=0.132, 85.14%). Bisexual flowers of T. aralioides exhibit synchronized dimorphism. The protogynous and protandrous morphs are self-incompatible, which probably promotes outcrossing and contributes to the high levels of heterozygosity within populations. Using a maximum likelihood tree, populations of T. aralioides were separated into two distinct clusters: Japan and Taiwan/ Iriomote Island. Populations of T. aralioides on Iriomote Island and in northern Taiwan exhibited a high degree of genetic similarity. The isolation-by-distance model does not fit populations in Taiwan, but suitably describes the relationship between populations of T. aralioides in Japan and Taiwan.

Patterns of Genetic Variation and Demography of Cycas taitungensis in Taiwan

Cycas taitungensis Shen, Hill, Tsou & Chen is an endemic species remaining in two remnant populations in southeastern Taiwan. Ecological studies showed that the sex ratio between female and male of the main population is approximately 1.7:1. Leaf production was found to be correlated with tree height before reaching 1 m in length (r = 0.95). The annual reproduction rate of female plants is highly variable, with seed numbering between 80 and 400 in each tree. The site study revealed a significant difference in vegetative growth and age structure between the subpopulations collected in two opposite microhabitats. Genetic studies using isozyme analysis showed low genetic variability (HE = 0.039) and little genetic differentiation between the populations (FST = 0.051). The genetic data are well correlated with the ecological observation that the differences reflect various microhabitat effects within a very local environment and that the impact influenced the extent of the degree of genetic differentiation within local populations. This work presents extensive genetic information forC. taitungensis that give rise to more ecological and genetic insights into the plant for better establishment of in situ and ex situ conservation programs.

Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata

Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end of the last glacial maximum, which obstructed gene flow, differentiated the Taiwanese and Chinese populations. Founders that colonized from both outlets of the Taiwan Strait were sourced from the northern South China Sea and the Ryukyus, thereby creating a melting pot in the Taiwan Strait. Inner-strait currents played roles as vectors for propagule dispersal among populations. Upon examination of the allele-frequency distributions of outlier loci, most negative outliers reflected the widespread polymorphisms shared by common ancestors. Furthermore, significant differentiation in the genetic components of positive outliers between this and other populations and the negative correlation with geographic distance suggested the presence of geography- or latitude-independent population divergence. Restored populations were compared with their sources and revealed biased sampling of nursery seedlings, which caused within-population substructures and reduced effective population sizes. This study indicated that multiple factors affect the population structure of the mangroves off southeast China.

Contrasting demographic patterns of Ceriops tagal (Rhizophoraceae) populations in the South China Sea

Demographic history and dispersal ability are significant factors in determining the genetic composition of a population.Inthisstudy,weexaminedthephylogeographicpatternsofCeriopstagalfromtheHainanIslandandtheGulfof ThailandintheSouthChinaSea,wherethereareabundantmangrovespecies.NucleotidevariationsintwochloroplastDNA spacers were compared with trace Ceriops propagule dispersal routes and demographic history. An analysis of Templeton, Crandall and Sings (TCS) parsimonious networks and population demographics suggests that the Ceriops population graduallyexpandedfromthenorthernpartsoftheSouthChinaSeatothesouth-westernpopulationsintheGulfofThailand. Such phylogeographic inferences reflect a postglacial southward shift in the mangrove genetic diversity centre and a connection between the demographic dynamics and the coastal range expansion caused by the sea-level rise in the Pleistocene. Therefore, the phylogeographic pattern and historical demography of mangrove species were affected by glaciations during the Pleistocene such as temperate biota.

Microgeographic genetic structure of the fidller crab, Uca arcuata De Haan (Ocypodidae) in Taiwan

The genetic structure of Uca arcuata in Tanshui mangrove swamp of northern Taiwan was examined. Using as genetic markers, isozymes identified through starch gel electrophoresis indicate that there was moderate genetic differentiation among subpopulations within the population (FST = .085). Gene flow appeared high when estimated indirectly (Nm = 2.69). The results suggest that the patterns of genetic structure of Uca arcuata were influenced by the interaction of local selection due to microhabitat differences and gene flow among fiddler crab colonies in the mangrove swamp.