Phylogeny of Davallia (Davalliaceae) from Sumatra and Mentawai Islands, Indonesia: evidence from trnL-F Intergenic Spacer
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Mildawati, Sobir, Sulistijorini, Chikmawati T. 2023. Phylogeny of Davallia (Davalliaceae) from Sumatra and Mentawai Islands, Indonesia: evidence from trnL-F Intergenic Spacer. Biodiversitas 24: 4589-4596. Davallia is a member of the family Davalliaceae, which has a wide distribution in the Malesia region. The classification of this genus based on morphological and molecular data shows differences that cause the relationship among species to be debated until now. This study aimed to examine the phylogeny of Davallia from Sumatra and Mentawai Islands, Indonesia based on trnL-F intergenic spacer (IGS) sequence data. A total of 26 accessions representing 10 Davallia species were selected as ingroup and Oleandra articulata (Sw.) C.Presl as an outgroup was downloaded from Gen-Bank (accession number KF667613.1). Data analysis using the Maximum Parsimony (MP) method confirmed Davallia into 2 clades with divided into 7 subclades. Results showed that trnL-F IGS sequence as a non-coding gene explains the grouping species in Davallia. trnL-F IGS sequence can estimate species identity caused by changes in nucleotide bases from mutation. The MP analysis showed each species was resolved as monophyletic. Based on the phylogenetic tree, the longest branching was found in D. corniculata, suggesting that this species is the most primitive in the genus of Davallia in this region. Thus, the trnL-F marker effectively showed the relationship among species in Davallia in Sumatra and Mentawai Islands.
##plugins.themes.bootstrap3.article.details##
References
Bauret L, Field AR, Gaudeul M, Selosse MA, Rouhan G. 2018. First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar. Mol Phylogenet Evol 127: 488-501. DOI: 10.1016/j.ympev.2018.05.004.
Bonatelli IAS, Zappi DC, Taylor NP, Moraes EM. 2013. Usefulness of cpDNA markers for phylogenetic and phylogeographic analyses of closely related cactus species. Genet Mol Res 12 (4): 4579-4585. DOI: 10.4238/2013.February.28.27.
Chen WC, Huang YM, Kuo LY, Nguyen QD, Luu HT, Callado JR, Farrar DR, Chiou WL. 2013. trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae). Ann Bot 111 (4): 663-673. DOI: 10.1093/aob/mct004.
Christenhusz MJM, Zhang XC, Schneider H. 2011. A linear sequence of extant families and genera of lycophytes and ferns. Phytotaxa 19: 7-54. DOI: 10.11646/phytotaxa.19.1.2.
Ding HH, Chao YS, Callado JR, Dong SY. 2014. Phylogeny and character evolution of the fern genus Tectaria (Tectariaceae) in the Old World inferred from chloroplast DNA sequences. Mol Phylogenet Evol 80: 66-78. DOI: 10.1016/j.ympev.2014.06.004. PMID: 25034727.
Fan XP, Thi Lu N, Li CX, Knapp R, He H, Zhou XM, Wan X, Zhang L, Gao XF, Zhang LB. 2022. Phylogeny, biogeography, and character evolution in the fern family Hypodematiaceae. Mol Phylogenet Evol 166: 107340. DOI: 10.1016/j.ympev.2021.107340.
Gaskin JF, Schwarzländer M, Gibson RD II, Gibson RD, Simpson H, Marshall DL, Gerber E, Hinz H. 2018. Geographic population structure in an outcrossing plant invasion after centuries of cultivation and recent founding events. AoB Plants 10 (2): 20. DOI: 10.1093/aobpla/ply020.
Gunawan. 2020. Biosystematics of Red Leatherback in Borneo and Natuna Island [Dissertation]. Graduate School of Institut Pertanian Bogor, Bogor. [Indonesian]
Harsono T, Pasaribu N, Sobir, Fitmawati, Prasetya E. 2017. Phylogenetic analysis of Indonesian Gandaria (Bouea) using molecular markers of cpDNA trnL-F intergenic spacer. Biodiversitas 18 (1): 51-57. DOI: 10.13057/biodiv/d180108.
Haufler CH, Pryer KM, Schuettpelz E, Sessa EB, Farrar DR, Moran R, Schneller JJ, Watkins Jr. JE, Windham MD. 2016. Sex and the single gametophyte: Revising the homosporous vascular plant life cycle in light of contemporary research. BioScience 66 (11): 928-937. DOI: 10.1093/biosci/biw108.
Huang J, Liu Y, Zhu T, Yang Z. 2021. The asymptotic behavior of bootstrap support values in molecular phylogenetics. Syst Biol 70 (4): 774-785. DOI: 10.1093/sysbio/syaa100.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35 (6): 1547-1549. DOI: 10.1093/molbev/msy096.
Kuo L-Y, Ebihara A, Shinohara W, Rouhan G, Wood KR, Wang C-N, Chiou W-L. 2016. Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy. Mol Phylogenet Evol 104: 123-134. DOI: 10.1016/j.ympev.2016.08.004.
Lestari DA, Azrianingsih R. 2019. Species identity and taxonomical position of selected species of Annonaceae based on trnL molecular marker. Biodiversitas 20 (4): 1012-1019. DOI: 10.13057/biodiv/d200411.
Li F-W, Kuo L-Y, Rothfels CJ, Ebihara A, Chiou W-L, Windham MD, Pryer KM. 2011. rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PLoS ONE 6 (10): e26597. DOI: 10.1371/journal.pone.0026597.
Li Y, Zhao H, Yan X, Li Meng, Chen P, Zhang S. 2017. A universal method for direct PCR ampli?cation of plant tissues. Anal Methods 9: 1800-1805. DOI: 10.1039/C6AY03156K.
Liu H, Schneider H. 2013. Evidence supporting Davallia canariensis as a late Miocene relict endemic to Macaronesia and Atlantic Europe. Austral Syst Bot 26: 378-385. DOI: 10.1071/SB13029.
Lukhtanov VA. 2019. Species delimitation and analysis of cryptic species diversity in the XXI century. Entomol Rev 99 (4): 463-472. DOI: 10.1134/S0013873819040055.
Ma X-D, Wang A-H, Wang F-G, He C-M, Liu D-M, Gerstberger P, Xing F-W. 2018. A revised classification of Chinese Davalliaceae based on new evidence from molecular phylogenetics and morphological characteristics. PLoS ONE 13 (11): e0206345. DOI: 10.1371/journal.pone.0206345.
Maideen H, Milne RI, Gibby M. 2009. Davalliaceae in Peninsular Malaysia, a preliminary study based on trnL-F region. Blumea J Plant Taxon Plant Geogr 54 (1-3): 203-206. DOI: 10.3767/000651909X476166.
Mildawati, Sobir, Sulistijorini, Chikmawati T. 2022. Diversity, distribution and ecology of Davallia in Sumatra (Indonesia) and the nearby small islands. Biodiversitas 23 (1): 33-42. DOI: 10.13057/biodiv/d230105.
Nooteboom HP. 1998. Davalliaceae. Flora Malesiana Ser II. Pteridophytes 2: 235-276.
Olejnik N, Celka Z, Szkudlarz P, Shevera MV. 2018. Taxonomic significance of morphological characters of spores in the family Ophioglossaceae (Psilotopsida). Rev Palaeobot Palynol 252: 77-85. DOI: 10.1016/j.revpalbo.2018.02.007.
Parris BS, Latiff A. 1997. Towards a Pteridophyte flora of Malaysia: A provisional checklist of taxa. Malay Nat J 50: 235-280.
Pirie MD, Vargas MPB, Botermans M, Bakker FT, Chatrou LW.2007. Ancient paralogy in the cpDNA trnL-F region in Annonaceae: Implications for plant molecular systematics. Am J Bot 94 (6): 1003-1016. DOI: 10.3732/ajb.94.6.1003.
Pteridophyte Phylogeny Group (PPG). 2016. A community - derived classification for extant lycophytes and ferns. J Syst Evol 54 (6): 563-603. DOI: 10.1111/jse.12229.
R Core Team. 2018. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. Available online at https://www.R-project.org/.
Reichenberger ER, Rosen G, Hershberg U, Hershberg R. 2015. Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biol Evol 7: 1380-1389. DOI: 10.1093/gbe/evv063.
Sargis EJ, Woodman N, Morningstar NC, Reese AT, Olson LE. 2014. Island history affects faunal composition: The treeshrews (Mammalia: Scandentia: Tupaiidae) from the Mentawai and Batu Islands, Indonesia. Biol J Linn Soc 111 (2): 290-304. DOI: 10.1111/bij.12195.
Smith AR, Pryer KM, Schuettpelz E, Korall P, Schneider H, Wolf PG. 2006. A classification for extant ferns. Taxon 55: 705-731. DOI: 10.2307/25065646.
Surya S, Hari N. 2017. Use of noncoding plastid marker trnL-F as DNA barcode for identification of true mangrove genus Rhizophora. Intl J Sci Res Sci Eng Technol 3 (8): 830-834.
Taberlet P, Gielly L, Pautou G, Bouvet J. 1991. Universal primer for amplification of three noncoding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109. DOI: 10.1007/BF00037152.
Tsutsumi C, Chen CW, Larsson A, Hirayama Y, Kato M. 2016. Phylogeny and classification of Davalliaceae on the basis of chloroplast and nuclear markers. Taxon 65 (6): 1236-1248. DOI: 10.12705/656.2.
Tsutsumi C, Kato M. 2005. Molecular phylogenetic study on Davalliaceae. Fern Gaz 17: 147-162.
Tsutsumi C, Zhang XC, Kato M. 2008. Molecular phylogeny of Davalliaceae and implications for generic classification. Syst Bot 33: 44-48. DOI: 10.1600/036364408783887492.
Vanderlaan TA, Ebach MC, Williams DM, Wilkins JS. 2013. De?ning and rede?ning monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of de?nition. Aust Syst Bot 26 (5): 347-355. DOI: 10.1071/SB13031.
Verstappen HT. 1973. A Geomorphological Reconnaisaance of Soematra and Adjacent Island (Indonesia). Wolters-Noordhoff, Groningen.
Wei R, Ebihara A, Zhu Y-M, Zhao C-F, Hennequin S, Zhang X-C. 2018. A total evidence phylogeny of the lady fern genera Athyrium Roth (Athyriaceae) with a new infrageneric classification. Mol Phylogenet Evol 119: 25-36. DOI: 10.1016/j.ympev.2017.10.019.
Xing FW, Wang FG, Nooteboom HP. 2013. Davalliaceae. In: Wu ZY, Raven PH, Hong DY (eds.) Flora of China (Pteridophytes). Science Press, Beijing; Missouri Botanical Garden Press, St. Louis.
Zhou X-M, Zhang L, Chen C-W, Li C-X, Huang Y-M, Chen D-K, Lu NT, Cicuzza D, Knapp R, Luong TT, Nitta J-H, Gao X-F, Zhang L-B. 2017. A plastid phylogeny and character evolution of the Old World fern genus Pyrrosia (Polypodiaceae) with the description of a new genus: Hovenkampia (Polypodiaceae). Mol Phylogenet Evol 114: 271-294. DOI: 10.1016/j.ympev.2017.06.02.
Most read articles by the same author(s)
- DENIA DWI CITRA RESMI, TATIK CHIKMAWATI, NINA RATNA DJUITA, MIFTAHUL HUDA FENDIYANTO, DEWI RAHMAWATI, Genetic diversity of mangoes (Mangifera indica L.) and its relatives in Seliu Island, Belitung District, Indonesia based on Inter-Simple Sequence Repeat markers , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 11 (2024)
- LUKITA DEVY, INDAH ANITA-SARI, AGUNG WAHYU SUSILO, ADE WACHJAR, SOBIR SOBIR, Genetic diversity and indirect selection of fine cacao (Theobroma cacao) based on bean color , Biodiversitas Journal of Biological Diversity: Vol. 19 No. 6 (2018)
- TATIK CHIKMAWATI, MIFTAHUDIN MIFTAHUDIN, J. PERRY GUSTAFSON, PCR-Based EST Mapping in Wheat (Triticum aestivum L.) , Biodiversitas Journal of Biological Diversity: Vol. 10 No. 2 (2009)
- TATIK CHIKMAWATI, SULISTIJORINI, NINA RATNA DJUITA, DIMAS PRASAJA, THOBIB HASAN AL YAMINI, MIFTAHUDIN, YULIAN FAKHRURROZI, Ethnobotany of food plants utilized by Malay Ethnic in Belitung District, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 5 (2023)
- TRI WAHONO DYAH AYU SAYEKTI, MUHAMAD SYUKUR, SRI HENDRASTUTI HIDAYAT, AWANG MAHARIJAYA, SOBIR, KARLIN AGUSTINA, EVRIANI MAREZA, ANUNG WAHYUDI, BAMBANG SUPRIYANTA, Performance and yield stability of cayenne peppers (Capsicum frutescens) in multilocation trials in the Indonesian lowlands , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 7 (2024)
- DOKI EFENDI, TATIK CHIKMAWATI, SULISTIJORINI, NINA RATNA DJUITA, Ethnoecology of home garden landscapes on Seliu Island, Belitung District, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 3 (2024)
- SOBIR SOBIR, SOALOON SINAGA, ROEDHY POERWANTO, RISMITASARI RISMITASARI, RUDY LUKMAN, Comparison Analysis of Genetic Diversity of Indonesian Mangosteens (Garcinia mangostana L.) and Related Species by Means Isozymes and AFLP Markers , Biodiversitas Journal of Biological Diversity: Vol. 10 No. 4 (2009)
- PUDJI WIDODO, ALEX HARTANA, TATIK CHIKMAWATI, Correlations between Degree of Petal Fusion, Leaf Size and Fruit Size: A Case in Syzygium (Myrtaceae) , Biodiversitas Journal of Biological Diversity: Vol. 10 No. 3 (2009)
- MIFTAHUDIN, RINI SYAHRAYNI HASIBUAN, TATIK CHIKMAWATI, Antioxidant activity of ethanolic extract of three Selaginella species from Java Island, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 12 (2019)
- MUHAMAD SYUKUR, ZULFIKAR DAMARALAM SAHID, SOBIR, AWANG MAHARIJAYA, ARYA WIDURA RITONGA, YUNANDRA, SULASSIH, MUHAMMAD RIDHA ALFARABI ISTIQLAL, ABDUL HAKIM, YUDIWANTI WAHYU, TOBIAS MONIZ VICENTE, MUKHLISIN, KARLIN AGUSTINA, YURSIDA, KUNCI MUSLIMIN, SITI HAFSAH, NURA, ANDRY SETYAWAN, Yield evaluation of curly chili lines in three lowland locations , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 6 (2022)