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Eslami-Farouji, Atena, Khosravi, Ahmad Reza, Gholami, Mehdi, Mohsenzadeh, Sasan. (1402). A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study. , 12(4), 155-163. doi: 10.22099/mbrc.2023.47706.1842
Atena Eslami-Farouji; Ahmad Reza Khosravi; Mehdi Gholami; Sasan Mohsenzadeh. "A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study". , 12, 4, 1402, 155-163. doi: 10.22099/mbrc.2023.47706.1842
Eslami-Farouji, Atena, Khosravi, Ahmad Reza, Gholami, Mehdi, Mohsenzadeh, Sasan. (1402). 'A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study', , 12(4), pp. 155-163. doi: 10.22099/mbrc.2023.47706.1842
Eslami-Farouji, Atena, Khosravi, Ahmad Reza, Gholami, Mehdi, Mohsenzadeh, Sasan. A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study. , 1402; 12(4): 155-163. doi: 10.22099/mbrc.2023.47706.1842

A comparison of phylogenetic and distance-based approaches for the distinction of genetically closed species, Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji, and Draba aucheri Boiss. (Brassicaceae) as a case study

Molecular Biology Research Communications
دوره 12، شماره 4، 2023، صفحه 155-163    اصل مقاله (320.58 K)
نوع مقاله: Original article
شناسه دیجیتال (DOI): 10.22099/mbrc.2023.47706.1842
نویسندگان
Atena Eslami-Farouji* ؛ Ahmad Reza Khosravi؛ Mehdi Gholami؛ Sasan Mohsenzadeh
Department of Biology, School of Science, Shiraz University, Shiraz, Iran
چکیده
Circumscribing species boundries is necessary in systematic plant biology. Even a mistake in delimiting taxa may lead to incorrect scientific interpretations. Draba rimarum (Rech.f.) A.R. Khosravi & A. Eslami-Farouji is an endemic Iranian species with a narrow geographic distribution, and is genetically close to D. aucheri. The present study provided a phylogenetic review, time divergence, and planar network of both species to unravel the distinct position of both species along with the prediction of any conflicting or ambiguous signals. Regarding this purpose, here we represent that phylogenetic trees may fail to show reliable results toward the distinct position of genetically close species.
کلیدواژه‌ها
Cruciferae؛ Distance-based methods؛ Draba؛ Genetically close species
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مراجع
  1. Tripp EA, Hoagland KE. Typifying an era in biology through synthesis of biodiversity information: Achievements and impediments. Taxon 2013;62:899-911.
  2. Posso‐Terranova A, Andrés J. Multivariate species boundaries and conservation of harlequin poison frogs. Mol Ecol 2018;27:3432-3451.
  3. Shaw J, Lickey EB, Schilling EE, Small RL. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 2007;94:275-288.
  4. Wiens JJ. Species delimitation: new approaches for discovering diversity. Syst Biol 2007;56:875-878.
  5. Parolly G, Nordt B, Bleeker W, Mummenhoff K. Heldreichia Boiss. (Brassicaceae) revisited: a morphological and molecular study. Taxon 2010;59:187-202.
  6. Yüzbaşioğlu SI, Al-Shehbaz IA, Yüzbaşioğlu EL, Dalyan E. Berteroa physocarpa (Brassicaceae), a new species from NW Turkey based on morphological and molecular data. Phytotaxa 2017;305:87-96.
  7. Özgişi KU, Ocak A, Özüdoğru BA. Noccaea birolmutlui, a new crucifer species from south west Anatolia, Turkey. Phytotaxa 2018;345:59-67.
  8. Khosravi AR, Eslami-Farouji A, Sultani-Ahmadzai A, Mohsenzadeh S. Toward a better understanding of phylogenetic relationships within Conringieae (Brassicaceae). Mol Biol Res Commun 2022;11:37-54.
  9. Tripp EA, Lendemer JC. Sleepless nights: When you can't find anything to use but molecules to describe new taxa. Taxon 2014;63:969-971.
  10. Scotland RW, Olmstead RG, Bennett JR. Phylogeny reconstruction: the role of morphology. Syst Biol 2003;52:539-548.
  11. Müller T, Philippi N, Dandekar T, Schultz J, Wolf M. Distinguishing species. RNA 2007;13:1469-1472.
  12. Porter J. Fast NeighborNet: Improving the Speed of the Neighbor-Net Phylogenetic Network Algorithm with Multithreading and a Relaxed Search Strategy. bioRxiv 2018;283424.
  13. Thatcher DR. Reliability of molecular phylogenetic trees. Nature 1975;28, 256:698.
  14. Bandelt HJ, Dress AW. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1992;1:242-252.
  15. Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16:37-48.
  16. Huson DH, Rupp R, Scornavacca C. Phylogenetic networks: concepts, algorithms and applications. Camb Univ Press 2010.
  17. Morrison DA. Phylogenetic networks in systematic biology (and elsewhere). Adv Biol Res 2010;1:1-36.
  18. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006;23:254-267.
  19. Morozov AA, Galachyants YP, Likhoshway YV. Inferring phylogenetic networks from gene order data. BioMed Res Int 2013;2013:503193.
  20. Bryant D, Filimon F, Gray RD. Untangling our past: languages, trees, splits and networks. Routledge. 2016;77-93.
  21. Gauthier O, Lapointe FJ. Hybrids and phylogenetics revisited: a statistical test of hybridization using quartets. Syst Bot 2007;32:8-15.
  22. Kong S, Sánchez‐Pacheco SJ, Murphy RW. On the use of median‐joining networks in evolutionary biology. Cladistics 2016;32:691-699.
  23. Kong S. On the use of median-joining networks: A philosophical and empirical evaluation of its suitability in evolutionary biology. University of Toronto (Canada).
  24. Eslami-Farouji A, Khodayari H, Assadi M, Çetin Ö, Mummenhoff K. Özüdoğru B. Phylogeny and biogeography of the genus Hesperis (Brassicaceae, tribe Hesperideae) inferred from nuclear ribosomal DNA sequence data. Plant Syst Evol 2021;307:1-22.
  25. Khosravi AR, Eslami‐Farouji A. Gain a better understanding of the true entity of Arabis rimarum Rech. f., a misapplied plant under the name Draba aucheri Boiss.(Brassicaceae). Feddes Repert 2023;1-18.
  26. Jordon-Thaden I, Hase I, Al-Shehbaz IA, Koch MA. Molecular phylogeny and systematics of the genus Draba (Brassicaceae) and identification of its most closely related genera. Mol Phylogenet Evol 2010;55:524-540.
  27. Bastkowski S, Mapleson D, Spillner A, Wu T, Balvočiūtė M, Moulton V. SPECTRE: a suite of phylogenetic tools for reticulate evolution. Bioinformatics 2018;34:1056-1057.
  28. Forster P, Forster L, Renfrew C, Forster M. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci USA 2020;117:9241-9243.
  29. Liede-Schumann S, Grimm GW, Nürk NM, Potts AJ, Meve U, Hartmann HE. Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae). Peer J 2020;8:e8999.
  30. Huson DH. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 1998; 14:68-73.
  31. Bryant D, Moulton V. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. In: Guigó R, Gusfield D (eds) Algorithms in bioinformatics, WABI 2002, vol. LNCS 2002;2452:375-391.
  32. Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004;21:255-265.
  33. Buckley CD. Investigating cultural evolution using phylogenetic analysis: the origins and descent of the Southeast Asian tradition of warp Ikat weaving. PLoS One 2012;7:e52064.
  34. Bryant D, Moulton V. Consistency of the neighbornet algorithm for constructing phylogenetic networks. Montreal, McGill University, School of Computer Science. 2003.
  35. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol 2018;4:vey 016.
  36. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 14 Nov 2010;1-8.
  37. Couvreur TLP, Franzke A, Al-Shehbaz IA, Bakker FT, Koch MA, Mummenhoff K. Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol Biol Evol 2010;27:55-71.
  38. Karl R, Kiefer C, Ansell SW, Koch MA. Systematics and evolution of arctic‐alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean. Am J Bot 2012;99:778-794.
  39. Kropf M. Vergleichende Biogeographie europäischer Gebirgspflanzen: Molekulare und morphometrische Untersuchungen an der montan-subalpinen Anthyllis montana L. (Fabaceae) und der hochalpinen Pritzelago alpina (L.) O. Kuntze (Brassicaceae). Cuvillier, PhD Thesis, Mainz University. 2002.
  40. Kay KM, Whittall JB, Hodges SA. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol Biol 2006;6:1-9.
  41. Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A 2010;107:18724-18728.
  42. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006;4:e88.
  43. Akaike H. A new look at the statistical model identification. – IEEE Trans. Automat. Contr. 1974;19:716-723.
  44. Yule GU. A mathematical theory of evolution, based on the conclusions of Dr.J.C. Willis. Philosophical Transactions of the Royal Society of London, Series B, Biol Sci 1925;213:21-87.
  45. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007;7:214.
  46. Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 2006;172:2665-2681.
  47. Darwin C. On the origin of species, first ed. Cambridge University Press, Cambridge, UK. 1859.
  48. Koch MA, Al-Shehbaz IA. Molecular data indicate complex intra- and intercontinental differentiation of American Draba (Brassicaceae). Ann Mo Bot Gard 2002;89:88-109.
  49. Bailey CD, Koch MA, Mayer M, Mummenhoff K, O’Kane Jr SL, Warwick SI, Windham MD, Al-Shehbaz IA. Toward a global phylogeny of the Brassicaceae. Mol Biol Evol 2006;23:2142-2160.
  50. Segatto ALA, Reck-Kortmann M, Turchetto C, Freitas LB. Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex. BMC Evol Biol 2017;17:1-14.
  51. Sukumaran J, Knowles LL. Multispecies coalescent delimits structure, not species. Proc Natl Acad Sci U S A 2017;114:1607-1612.
  52. Eslahchi C, Habibi M, Hassanzadeh R, Mottaghi E. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. BMC Evol Biol 2010;10:1-10.
  53. Tan M, Long H, Liao B, Cao Z, Yuan D, Tian G, Zhuang J, Yang J. QS-net: reconstructing phylogenetic networks based on quartet and sextet. Front Genet 2019;10:607.
  54. Huson DH. What If I Don't Have a Tree?: Split Decomposition and Related Models. Curr Protoc Bioinformatics 2003;1:6-7.
  55. Beilstein MA, Windham MD. A phylogenetic analysis of western North American Draba (Brassicaceae) based on nuclear ribosomal DNA sequences from the ITS region. Syst Bot 2003;1:584-592.
  56. Jordon-Thaden I, Koch M. Species richness and polyploid patterns in the genus Draba (Brassicaceae): a first global perspective. Plant Ecol Divers 2008;1:255-263.
  57. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 2004;101:11030-11035.
  58. Tamura K, Stecher G, Kumar S. MEGA 11:Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021;38:3022-3027. 
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