mangrove canopy that feed the mangrove flower of Sonneratia alba, Avicennia alba and Lumnitzera racemosa. Internodes with P > 95% were considered to be statistically significant. All gene segments we obtained satisfied the stationarity test (P > 5%) for base composition at the variable sites and were retained for further analysis. The HKY85+G model was used with different transition/transversion rate ratios (kappa) and different shape parameters (alpha) among the loci. Using nuclear gene sequences sampled in this study, we were able to resolve phylogenetic relationships among five species of the IWP region. Two primer pairs produced PCR products with two bands, widely spaced in size. Sequencing reactions were conducted with amplification primers in an ABI 3730 DNA automated sequencer with BigDye chemistry (Applied Biosystems, Foster City, CA, USA). Library News Use cases. integra subclade is more closely related to the A. marina complex than to the A. alba/A. IWP: Indo-West Pacific region; AEP: Atlantic-East Pacific region. Vienna, Austria: R Foundation for Statistical Computing; 2015. activities. 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. Bark Seedlings of various ages. The coding and its meaning were showed in legend. Diagnostic characters Botany & morphology Regeneration Reproductive biology Ecology Distribution Uses. Richard Morris. The overall substitution rate (rgene_gamma) was assigned by a gamma distribution with prior G(14, 40), which is a mean of 0.35×10−8 substitutions per site per year, based on the substitution rate from nuclear genes in genus Avicennia (He et al., in review). eucalyptifolia). The divergence time for species in the Indo-Western Pacific (IWP) region was calibrated by mcmctree 4.8a . Useful Tropical Plants Database 2014 by Wide sampling and population-genomic studies are necessary to reveal the demography of Avicennia marina and to understand the causes of evolution and diversification of Avicennia species. Akar nafas biasanya tipis, berbentuk jarum yang ditutupi oleh lentisel. 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. The remaining trees were used to calculate the posterior probabilities (P) through the construction of a majority rule consensus tree. Among them, the first three are endemic to the Atlantic-East Pacific (AEP) region; the remaining five are in the Indo-West Pacific region (IWP) . Avicennia alba forms a low, dense bushy crown often branching near the base of the trunk. In our phylogenetic tree, the crown age of the A. marina subclades was dated at 2.8 MYA (95% HPD: 1.2~4.6 MYA; Fig 2), which is consistent with the age estimated for this subclade based on allozyme data (approximately 2 MYA, ). 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. We estimated species divergence time with fossil calibration using coding sequences (CDS). State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, Guangdong, China, 2 Fig 1 shows divergence time estimates. Sorenson L, Allen GR, Erdmann MV, Dai C-F, Liu S-YV. Phoenix paludosa; Nypa. These have been sequenced in our lab or have published in genomes or transcriptomes [28, 29], as well as a fossil record . No specific permission was required for sampling these species in this study. Avcenia alba and Avicennia marina were distributed the shoreline, Aegiceras corniculatum, Avcenia alba and Bruguiera parviffora were distributed the seaward and then Avicennia officianalis, Cerops dencandra, C.tagal, Heritiera forms, H.littoralis, Sonneratia alba , S.graffithii, Xylocarpus granatum and X.moluccensis were distributed the landward. All characteristics were weighted equally, and gaps were treated as missing data. Giesen, Wim and Stephan Wulffraat, Max Zieren and Liesbeth Scholten. (Lamiales), A rapid DNA isolation procedure for small quantities of fresh leaf tissue. We conducted further phylogenetic analyses among the IWP species using concatenated sequences of 25 nuclear genes, with Avicennia germinans as an outgroup. The mangrove genus Avicennia (Avicenniaceae) in Australasia Cerbera oddloam fruit on the tree. We selected two morphologically important characters (stigma position and style length; S3 Table; [2, 31]) and reconstructed their ancestral states. AvicenniaL. However, the divergence between var. R: A language and environment for statistical computing Specifically, we address the following questions: (1) Do molecular data support a phylogenetic grouping based on geographical distributions of AEP and IWP lineages? For the chloroplast matrix, the best-fit model was a general time reversible model with a gamma correction for rate variation among sites (GTR + G). 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). Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China. Prior to using model-based analytical approaches (BI and ML), nucleotide substitution models were selected based on the Akaike information criterion, as determined by jModelTest 2.1.4 . Phoenix. marina) from those on the east (var. eucalyptifolia near the Strait of Torres, may experienced several rounds of isolation, dispersal and admixture. Manual; media. The greatest number of known species of marine fungi are found growing in mangrove swamps where A. alba is one of a number of species colonised. Minobe S, Saiki R, Kajita T, Changtragoon S, Shukor NAA, Latiff A, et al. Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle, Major Genetic Differences between Crown-of-Thorns Starfish (Acanthaster planci) Populations in the Indian and Pacific Oceans, The genetic legacy of the Quaternary ice ages, South Alligator River, North Territory, Australia. The forward and reverse primers of each pair were located in different exons of the same gene to amplify a segment with introns. It has a common name Api-api putih, in the Malay language ¹. It plays a significant role in supporting the coastal ecosystem and holds unique potential for studying molecular mechanisms underlying ecological adaptation. The assumed range of divergence time (from 10 to 50 million years ago, MYA) between the IWP and AEP lineages was estimated by a previous study based on fossil records and molecular dating . mcmctree employs two strategies to model the change in evolutionary rate among lineages: independent rates and auto-correlated rates . Highly differentiated population structure of a Mangrove species, Bruguiera gymnorhiza (Rhizophoraceae) revealed by one nuclear GapCp and one chloroplast intergenic spacer trnF–trnL. We used our molecular phylogeny to study evolution of flower morphology in Avicennia. Distributions of species are color coded on the map (modified from ). To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. 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 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. The field studies did not affect endangered or protected species. T ermasuk tingkatan pohon yang tumbuh menyebar dengan ketinggian mencapai 25 m. Kumpulan pohon membentuk perakaran horizontal dan akar nafas. 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. Nypa fruticans; Acanthaceae. Red rectangle shows the earliest fossil records of mangrove lineages while gray one shows that of inland relatives. 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. 1 Reported number of nodes produced annually along the main axis by different mangrove species around the world. Yang Y, Yang S, Li J, Deng Y, Zhang Z, Xu S, et al. A number of invertebrates are associated with A. alba. Avicennia bicolor and A. schaueriana were not sampled in this study. The sample of A. germinans was collected from La Paz, Mexico. 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 are grateful to David E. Bufford and Anthony Greenberg for English proofreading. Avicennia L. is one of the most diverse mangrove genera, comprising eight species: A. germinans (L.) Stearn, A. schaueriana Stapf & Leechm. Renema W, Bellwood D, Braga J, Bromfield K, Hall R, Johnson K, et al. To evaluate the phylogenetic tree and to capture the major clusters of Avicennia species , a multi-dimensional scaling (MDS) analysis based on the matrix of the average pairwise genetic divergence value among all Avicennia species calculated using our sample of 2 chloroplast genes was conducted using the command "cmdscale" in R package stats . Subsequently, bootstrap analyses were performed on 500 replicates  using the options described above. 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. Hewitt (2000)  proposed that sea level oscillations would lead to many changes in distribution of marine and coastal species in IWP. However, their phylogenetic relationships were determined based on morphological and allozyme data. Home; about. 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. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. The distribution of ancestral Avicennia was likely to have been similar to its present location, extending from Japan to Borneo and from the Marshall Islands to the Red Sea [40, 41]. The result was also supported by two morphological traits in floral structure: stigma position in relation to the anthers and the length of the styles. A recent systematic revision of Avicennia  based on morphological studies  divided the five IWP species into three groups: (i) A. marina; (ii) A. officinalis and A. integra; and (iii) A. rumphiana and A. alba . Analysis of 142 genes resolves the rapid diversification of the rice genus, Molecular phylogenetics and morphological evolution of Thunbergioideae (Acanthaceae), Toward a comprehensive understanding of phylogenetic relationships among lineages of Acanthaceae s.l. If you have any useful information about this plant, please leave a comment. Prior to combining the sequences, congruence was examined using the partition–homogeneity test by PAUP* 4b10 [17, 18]. marina is closer to A. marina var. Population genetic data have revealed the role of land barriers in shaping genetic structure across IWP in many species, such as Kandelia candel [48, 49], Ceriops spps., [50–52], Bruguiera gymnorhiza , Rhizophora apiculata , reef fish  and starfish . Plot of the first and second axis of a multidimensional scaling matrix based on pairwise genetic divergence value among all Avicennia species of two chloroplast genes. Avicennia alba on Total Vascular Flora of Singapore Online: photos and fact sheet. Orange yellow flowers, borne in a racemose inflorescence, have a diameter of 3 to 4 mm when expanded. Ajna Fern For the detailed phylogenetic analyses of the IWP species, 25 pairs of primers were designed to amplify targeted nuclear genes from genomic DNA, based on the EST library of A. marina obtained from GenBank. Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, et al. 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. We infer the ancestral of two important traits: stigma position and style length (S5 and S6 Figs). Our phylogeny reveals with high confidence that Avicennia is divided into two distinct clades, consistent with our expectations based on geography and systematics. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. A number of studies of marine species have also suggested a diversification surrounding the IWP oceans in that period (late Miocene-Pliocene), such as wrasse (Halichoeres in 3.5–8 MYA ), Pomacentrus coelestis species complex (within 2.8 MYA ) and mangrove snails (Cerithidea, within Plio-Pleistocene ). Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, et al. 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. All sequences data for this study are available from the GenBank database (accession numbers is listed in S2 Table). This split is in line with biogeographic distribution of the clade. 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). Phylogenetic analyses of this dataset using the BI, ML and MP methods yielded identical topologies (Fig 1; see detail in S2 Fig). This species is accepted, and its native range is Tropical Asia to N. Australia. Trop WATER, James Cook University, Townsville, Queensland, Australia, 3 Li XX, Zou Y, Xiao CL, Gituru RW, Guo YH, Yang CF. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Guo Z, Huang YJ, Chen Y, Duke NC, Zhong C, Shi S. Genetic discontinuities in a dominant mangrove Rhizophora apiculata (Rhizophoraceae) in the Indo‐Malesian region. Farris JS, Källersjö M, Kluge AG, Bult C. Swofford D. PAUP*: phylogenetic analysis using parsimony, version 4.0 b10. Among the three varieties, A. marina, var. Home; Mangroves . However, detailed evolutionary relationships among the species of Avicennia, such as chronological speciation order and divergence time, have not been clearly described so far. The phylogenetic positions of A. alba and A. rumphiana were still unclear in the chloroplast tree (P < 0.5 and BS < 50%). Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. Avicennia alba and A. rumphiana were grouped into one subclade (P = 1.00 and BS = 100% for both ML and MP). Interestingly, these subclades can be clearly differentiated using two morphological traits in floral structure, i.e. eucalyptifolia, and A. marina var. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. Avicennia marina is a widely distributed mangrove species that thrives in high-salinity habitats. Our analyses indicate that the ancestral stigma position in Avicennia from IWP is between anthers, and the ancestral style length is over 1.0 mm. Kulit kayu berwarna keabu-abuan atau gelap kecoklatan, beberapa ditumbuhi tonjolan kecil, sementara yang lain kadang-kadang â¦ 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). Although the first fossil record of Avicennia in the IWP region dates back to the late Eocene of southwest Australia, significant flourishing of Avicennia in this region has occurred since the Miocene [39–41]. 10 images. Attached are cropped pics of the above flower and of Avicennia officinalis that I had observed in Konkan around the same period. Vierh, A. alba Blume, A. officinalis L., A. integra N. C. Duke, and A. rumphiana Hallier f . Brazil M, Thomas DA, Nielsen BK, Winter P, Wulff‐Nilsen C, Zachariasen M. A novel approach to phylogenetic trees: d‐Dimensional geometric Steiner trees. The fieldwork was outside protected areas or natural reserves, and no specific permission was required for these collection activities. The map was modified from the 1:110m coastline map of Natural Earth (http://www.naturalearthdata.com). australasica (P = 1.00, BS = 96% for ML and BS = 100% MP). Both species have an elongate flask- or ampulla-shape style exerted above or equal to the upper edge of anthers. Raw sequences were aligned and manually edited using SeqMan 7.1 (Madison, WI, USA). For Avicennia bicolor and Avicennia alba, only mature ï¬owers were studied, and selected features deviating from those of A. germinans are described. Structural attributes of the floral organs of A. rumphiana and A. alba differ from those of the A. marina complex. 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). marina, A. marina var. INTRODUCTION Mangroves are unique salt-tolerant species which grow in the intertidal zone between terrestrial and marine systems along tropical and subtropical shorelines of the world. Mapper Data access Data quality Contribute data Data policy External sources Indicators. We included Thunbergia grandiflora as the outgroup, since a close relationship between Thunbergioideae and Avicennia has been suggested based on recent molecular and morphological data [3, 12, 13]. 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). Two selected morphological characters of taxonomic importance (source from ) have been mapped on the tree. 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). We then calculated substitution rates for our sequences using weighted means of introns and CDS values. kingdom Plantae > subkingdom Viridiplantae â¦ Considering repeated oscillations of sea level, Avicennia marina populations, especially var. 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]. Three distinct subclades were identified within the IWP group with high bootstrap support: (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex. ex Moldenke, A. bicolor Standley, A. marina (Forssk.) Key words: Avicennia alba, mangrove, survival, growth, excessive sedimentation. 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. Where seen? The leaves are eaten by beetles, Monolepta spp. The larvae of certain small moths, Euopoicillia spp., feed on the flower buds and those of another moth, Autoba alabastrata, feed on the fruits. The flowers range from white to a golden yellow colour, are less than 1 cm across, and occur in clusters of three to five. Avicennia Alba subscribed to a channel 9 months ago Le Monde - Channel. Table 2. Sequencing multiple loci has been a successful strategy used to resolve phylogenetic relationships among numerous species [10, 11]. Trouver la graines de mangrove photo idéale Une vaste collection, un choix incroyable, plus de 100 millions dâimages LD et DG abordables de haute qualité. Avicennia marina, commonly known as grey mangrove or white mangrove, is a species of mangrove tree classified in the plant family Acanthaceae (formerly in the Verbenaceae or Avicenniaceae). Api-api nama ilmiahnya Avicennia alba Blume. A gamma prior G (2.6, 2) was assigned for kappa and G (1, 1) was assigned for alpha. rumphiana lineage and the A. marina complex exhibit independent degeneration. For most genes, only one band was amplified from all species. Herkogamy. The accession numbers are listed in S2 Table. The partition–homogeneity test indicated that the trnT-trnD and psbA sequences could be combined for phylogenetic analyses (P = 1.0). We would like to thank Chung-I Wu for his critical evaluation of the manuscript. Habit of Avicennia alba The pneumatophores of arise from lateral root growing out of the sand Fruiting branch Flowers. Photo about Young Leaves of Cnidoscolus aconitifolius or chaya plants and blur bud flower on nature background. (3) When did the IWP Avicennia species diversify and what was the possible driving force behind this divergence? 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 . General Information Avicennia alba is an evergreen shrub or small tree that can grow up to 30 metres tall but is usually much smaller eucalyptifolia than to A. marina var. 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]. (2) What are the phylogenetic relationships of the five IWP Avicennia species and what do they tell us about evolution of flower characters? However, their phylogenetic relationships were determined based on morphological and allozyme data. The ePub format is best viewed in the iBooks reader. We had low power to resolve the sub-clade relationships, but our results suggest that the A. officinalis/A. eucalyptifolia, and var. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. The study was conducted during February 2008âApril 2010. Mida creek. Molecular phylogenies can shed light on evolution of morphological traits. Bayesian inference was performed using MrBayes 3.2.6  with the models mentioned above. integra lineage, with style length about 2mm and stigma level in the middle of the variety anthers (Fig 2). Avicennia alba is a common mangrove tree, widely distributed throught the tropical and subtropical areas of the World. Avicennia marina (Forssk.) Multiple-sequence alignments were performed using ClustalW 2.1  by leaving the default parameters unchanged and visually adjusting as necessary. Our molecular phylogenetic analyses strongly support a subclade with A. officinalis and A. integra (Fig 2). The style is about 0.5mm . The length of style is about 2mm (Fig 2, ). The Officinalis lineage includes A. officinalis and A. integra, while the latter includes all other species. 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.
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