Sceura marina Forssk. Home; about. These have been sequenced in our lab or have published in genomes or transcriptomes [28, 29], as well as a fossil record . Key words: Avicennia alba, mangrove, survival, growth, excessive sedimentation. http://www.nsfc.gov.cn/), the Science Foundation of State Key Laboratory of Biocontrol (SKLBC16A35 to SS), and the Chang Hungta Science Foundation of Sun Yat-sen University. Introduction to botany. Gaither MR, Bowen BW, Bordenave TR, Rocha LA, Newman SJ, Gomez JA, et al. Giang LH, Geada GL, Hong PN, Tuan MS, Lien NTH, Ikeda S. Genetic Variation of Two Mangrove Species in Kandelia (Rhizophoraceae) in Vietnam and Surrounding Area Revealed by Microsatellite Markers, 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 distribution of the major biogeographic barriers and the shallow seas in the IWP region has not changed significantly since that time . In previous studies, species of Avicennia in the IWP region were divided into two lineages, the Officinalis lineage and the Marina lineage, based on the main types of corolla . Thus, we set out to re-evaluate the phylogenetic relationships among species in Avicennia based on a robust approach involving wide sampling and sequencing of a number of DNA segments. The time range of fossils are the earliest and most conformed fossil was from Spain and dated to Middle Bartonia (38.3–39.4 MYA, ). Within the subclades, the initial split between A. alba and A. rumphiana was estimated to be c. 3.6 MYA, whereas the split between A. officinalis and A. integra was estimated to have occurred c. 2.4 MYA. Townsville Queensland: James Cook University; 1988. Some studies on phylogeographic patterns of this genus based on a few nuclear and chloroplast DNA markers have been conducted for three AEP species of Avicennia [8, 9]. Red rectangle shows the earliest fossil records of mangrove lineages while gray one shows that of inland relatives. Our results indicated the ancestral flower structure is preserved in the A. officinalis/A. Based on genetic diversity of three A. marina varieties, Duke et al., (1998)  suggested that the split occurred during the ice age, when the emerged land barrier between New Guinea and Australia isolated the populations on the west coast (var. Voucher specimens were deposited in the Herbarium of Sun Yat-Sen University (SYS). mcmctree employs two strategies to model the change in evolutionary rate among lineages: independent rates and auto-correlated rates . Avicennia alba Blume - AVICENNIACEAE - Dicotyledon Common name in Tamil : Vellai kandai Common name in Telugu : Gundu mada, vilava mada. In the combined chloroplast tree, species of Avicennia fell into two clades: five in the IWP region forming one clade and the remaining three in the AEP region forming the other (S2 and S3 Figs; Posterior Probability P = 1.00 for BI; Bootstraps BS = 100% and 99% for ML and MP, respectively). (3) When did the IWP Avicennia species diversify and what was the possible driving force behind this divergence? The length of style is about 2mm (Fig 2, ). The shrub does not grow more than 20 m. The dark green leaves, 15 cm long by 5 cm wide, have a silvery gray under leaf and grow in opposites. Comments have to be approved before they are shown here. All sequences were deposited in GenBank. Despite the wide range of ecological and socio- economic benefits provided by mangrove ecosystem (Lewis, 2005; Bosire et al., â¦ In this study, diversification of the species of Avicennia in the IWP region was dated at approximately 6.0 MYA (95% HPD: 2.8~9.7 MYA; Fig 2). Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bayesian posterior probabilities for Bayesian Inference (BI), Likelihood bootstrap values from the maximum likelihood analysis (ML) and Parsimony bootstrap values from maximum parsimony analysis (MP) are indicated at nodes (BI/ML/MP). Our results shed fresh light on the evolution of this important mangrove clade and should enable further studies of this group’s remarkable adaptation to the intertidal environment. As with other mangroves, it occurs in the intertidal zones of estuarine areas. The leaves are eaten by beetles, Monolepta spp. australasica and var. State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China, 2 This species is accepted, and its native range is Tropical Asia to N. Australia. integra subclade is more closely related to the A. marina complex than to the A. alba/A. Bayesian posterior probabilities for Bayesian Inference (BI), Likelihood bootstrap values for maximum likelihood (ML) and Parsimony bootstrap values for maximum parsimony (MP) are indicated at nodes (BI/ML/MP), respectively. rumphiana lineage and the A. marina complex exhibit independent degeneration. Our phylogenetic tree suggests that A. rumphiana and A. alba are closely related to each other and form a basal subclade in the IWP lineage. No specific permission was required for sampling these species in this study. We obtained samples from eight accessions of Avicennia, including A. germinans, A. officinalis, A. integra, A. alba, A. rumphiana, and three varieties of A. marina (A. marina var. 10 images. The diversification of the IWP lineage was dated to late Miocene (c. 6 MYA) and may have been driven largely by fluctuating sea levels since that time. â¦ Avicennia alba; Avicennia marina We used the trnT-trnD intergenic spacer region and the psbA gene for the phylogenetic reconstruction of all species of Avicennia because they are the only available sequence data from the two AEP species. Avicennia rumphiana. In contrast, the stigma is positioned level with the middle or the lower edge of the anthers in the A. marina complex. Giesen, Wim and Stephan Wulffraat, Max Zieren and Liesbeth Scholten. It is found mainly in sandy or firm silt substrate of the mid to high water mark. Based on concatenated sequences of 25 nuclear genes, with A. germinans as the outgroup. eucalyptifolia). Moreover, Avicennia marina node production is below that for the cognatic Asian species Avicennia alba . We infer the ancestral of two important traits: stigma position and style length (S5 and S6 Figs). The style of A. rumphiana and A. alba is minute and narrow, ending well below the anthers. Fig 1 shows divergence time estimates. mangrove canopy that feed the mangrove flower of Sonneratia alba, Avicennia alba and Lumnitzera racemosa. (Lamiales), A rapid DNA isolation procedure for small quantities of fresh leaf tissue. The HKY85+G model was used with different transition/transversion rate ratios (kappa) and different shape parameters (alpha) among the loci. This produces a large, fleshy seed, often germinating on the tree and falling as a seedling. Long branches between the crown node and the roots of both the IWP and AEP clades indicated that the two clades had evolved independently over a long period since the initial split from the common ancestor. Photo about Young Leaves of Cnidoscolus aconitifolius or chaya plants and blur bud flower on nature background. Both species have an elongate flask- or ampulla-shape style exerted above or equal to the upper edge of anthers. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Confidence limits on phylogenies: an approach using the bootstrap. We re-designed allele-specific primers for these genes based on the sequences of isolated single bands that corresponded to the brightest-staining product that corresponded to the size of products from other taxa. The ePub format uses eBook readers, which have several "ease of reading" features Watamu, Kenya. Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang J, et al. Avicennia L. is one of the most diverse mangrove genera, comprising eight species: A. germinans (L.) Stearn, A. schaueriana Stapf & Leechm. Avicennia alba on NParks Flora and Fauna website: photos and fact sheet. To infer the phylogeny of Avicennia from all available data, we retrieved four sequences from two taxa, A. bicolor and A. schaueriana from GenBank (Table 1). Using nuclear gene sequences sampled in this study, we were able to resolve phylogenetic relationships among five species of the IWP region. Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Phylogenetic trees were reconstructed using Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) methods. Sea levels, however, began to fluctuate because of climate change . Plaziat J-C, Cavagnetto C, Koeniguer J-C, Baltzer F. History and biogeography of the mangrove ecosystem, based on a critical reassessment of the paleontological record, Southeast Asia's changing palaeogeography. Sequencing multiple loci has been a successful strategy used to resolve phylogenetic relationships among numerous species [10, 11]. This study was supported by grants from the National Natural Science Foundation of China (Grant Numbers: 41130208 and 91331202 to SS, 41276107 to YH. Farris JS, Källersjö M, Kluge AG, Bult C. Swofford D. PAUP*: phylogenetic analysis using parsimony, version 4.0 b10. This might help in validation. Where seen? The best model for the nuclear gene matrix was the Hasegawa-Kishino-Yano model, with a gamma correction for rate variation among sites (HKY+G). The partition–homogeneity test indicated that the trnT-trnD and psbA sequences could be combined for phylogenetic analyses (P = 1.0). Highly differentiated population structure of a Mangrove species, Bruguiera gymnorhiza (Rhizophoraceae) revealed by one nuclear GapCp and one chloroplast intergenic spacer trnF–trnL. Habit of Avicennia alba The pneumatophores of arise from lateral root growing out of the sand Fruiting branch Flowers. These estimates support the conclusion that varieties of A. marina diverged more recently, in the Pleistocene, possibly during periods of lowered sea levels during periods of glaciation . Attached are cropped pics of the above flower and of Avicennia officinalis that I had observed in Konkan around the same period. Tree growing in native habitat Photograph by: Fagg, M. Image credit to Australian National Botanic Gardens. (2) What are the phylogenetic relationships of the five IWP Avicennia species and what do they tell us about evolution of flower characters? Home; Mangroves . Purified PCR products were subjected to direct sequencing. However, the divergence between var. PCR was conducted with the following conditions: 94°C for 4 min, followed by 30 cycles of 94°C for 30 seconds, 48–58°C for 30 seconds, 72°C for 2 minutes, and a final extension of 8 minutes at 72°C. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Bootstrapping of the datasets was performed with 500 replications, and all node values for the ML trees are represented as the proportion of replicates in which that clade was recovered. Avicennia consists of two monophyletic clades: Atlantic-East Pacific (AEP) lineage and Indo-West Pacific (IWP) lineage. To estimate substitution rates per year for dating purpose, we constructed a phylogenetic tree using 2,326 orthologous genes from the following species: Sesamum indicum, Avicennia officinalis, Avicennia marina, Acanthus leucostachyus and Acanthus ilicifolius (S1 Fig). Avicennia officinalis, api-api daun lebar, api-api ludat. If you have any useful information about this plant, please leave a comment. We then calculated substitution rates for our sequences using weighted means of introns and CDS values. marina is closer to A. marina var. The concatenated sequences of 25 nuclear genes were used to estimate the divergence times within Avicennia, with gaps treated as missing data. The flowers range from white to a golden yellow colour, are less than 1 cm across, and occur in clusters of three to five. The three varieties of A. marina formed another subclade (P = 1.00, BS = 100% for ML and MP). Manual; media. The calibration point at the basal position of Avicennia was set as B (0.1, 0.5), with 100 million years as one time unit. Genetic diversity, distributional barriers and rafting continents–more thoughts on the evolution of mangroves, Floral biology and reproductive phenology of Avicennia marina in south-eastern Australia. We further concatenated the sequences of 25 nuclear genes to infer the phylogenetic relationship among the IWP species, with Avicennia germinans as the outgroup. The total genomic DNA of each individual was extracted by the modified CTAB method . This is an open access article distributed under the terms of the, A systematic revision of the mangrove genus Avicennia (Avicenniaceae) in Australasia, Phylogenetic relationships of the mangrove family Avicenniaceae based on chloroplast and nuclear ribosomal DNA sequences, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. The change of relative positions of anthers and stigma indicates that these species might have evolved herkogamy as a supplemental mechanism for selfing avoidance [37, 38]. Previous morphological analyses produced conflicting results regarding their affinity to other species of Avicennia. The sample of A. germinans was collected from La Paz, Mexico. All gene segments we obtained satisfied the stationarity test (P > 5%) for base composition at the variable sites and were retained for further analysis. Raw sequences were aligned and manually edited using SeqMan 7.1 (Madison, WI, USA). Xinnian Li, Norman C. Duke, [...], and Suhua Shi. Api-api nama ilmiahnya Avicennia alba Blume. Moreover, Avicennia marina node production is below that for the cognatic Asian species Avicennia alba (Table 2). It has a common name Api-api putih, in the Malay language ¹. The crypto-viviparous Avicennia alba, A. marina and A. officinalis (Avicenniaceae) occurring in Godavari mangrove forest (16030ââ17 00âN & 82010ââ 80023âE) in the state of Andhra Pradesh, India, were used for the present study. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time. We next investigated the evolution of the flower characters among Avicennia species in IWP. The resulting log-likelihood and number of generations were plotted to determine the point after which the log-likelihoods had stabilized. See the S4 Fig) MDS analysis of the mean pairwise genetic divergence among IWP species, again based on our sample of 25 nuclear genes, revealed a consistent pattern, with A. officinalis and A. integra, A. alba and A. rumphiana, and the three varieties of A. marina forming clear groups identical to those revealed by our phylogenetic analyses (Fig 3). integra subclade and is not grouped with the other two species, A. rumphiana and A. alba, which were included in the Marina lineage by Tomlinson (1986) . All sequences data for this study are available from the GenBank database (accession numbers is listed in S2 Table). We saved 40,000 samples every two steps after discarding the initial 10,000 samples as the burn-in in mcmctree. Those two species were close to the three varieties of the A. marina complex (P = 0.99; BS = 70% and 65%). Phoenix. About OBIS Partnerships sponsor Governance. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. Maximum parsimony (MP) analyses were conducted using PAUP* 4.0b10  with a “heuristic search”: tree bisection–reconnection branch swapping, MULPARS option on, and 1,000 random taxon additions. Avicennia marina (Forssk.) The field studies did not affect endangered or protected species. PCR products were purified using an agarose gel purification kit (QIAGEN, Hilden, Germany). Since our data set included introns as well as CDS, we adjusted the substitutions rate (μ) by inferring the μ intron/μCDS using Kintron/KCDS, where K is the number of segregating sites between A. marina and A. alba from 24 nuclear genes. Avicennia L., an important component of forests worldwide in tropical and subtropical intertidal zones [1, 2], is currently thought to be derived from within the Acanthaceae based on recent phylogenetic studies (APG III, [3, 4]), although it has been placed in Verbenaceae or Avicenniaceae in some classifications. The ePub format is best viewed in the iBooks reader. eucalyptifolia along the coast of East Australia is difficult to explain without positing an additional barrier in this region. Avicennia integra and A. officinalis were grouped into the third subclade (P = 1.00, BS = 100% for ML and BS = 96% for MP), which was consistent with results based on the chloroplast segments (S2 Fig). Avicennia alba is a common mangrove tree, widely distributed throught the tropical and subtropical areas of the World. Previous morphological analyses produced conflicting results regarding their affinity to other species of Avicennia. The style degenerated and the stigma became positioned under the anthers in the other IWP Avicennia species, especially for A. abla and A. rumphiana. with help from PAML 4: phylogenetic analysis by maximum likelihood, Inferring speciation times under an episodic molecular clock, A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions. Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, et al. We are grateful to David E. Bufford and Anthony Greenberg for English proofreading. Prior to combining the sequences, congruence was examined using the partition–homogeneity test by PAUP* 4b10 [17, 18]. Based on the phylogenetic tree reconstructed with 25 nuclear genes, we performed our analyses using maximum parsimony in Mesquite v. 3.04 . The fieldwork was outside protected areas or natural reserves, and no specific permission was required for these collection activities. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Plot of the first and second axis of a multidimensional scaling matrix based on pairwise genetic divergence value among IWP species of 25 nuclear genes.
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