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Integration of Modern Molecular Tools with Geological Processes to Reveal Species Phylogeny, Biogeographical Niche Prediction, and Bio-Evolution

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Proceedings of the National Academy of Sciences, India Section B: Biological Sciences Aims and scope Submit manuscript

Abstract

Nature is integrated, being simultaneously controlled by different natural aspects. Genetics, bioinformatics, biostatistics and geology are four diverse and broad scientific disciplines. But we believe that these can offer important insights into species distribution and evolution, if integrated. This perspective is grounded on a case study of the family Salvadoraceae, where species distribution and phylogeny show high correlation with the geological records. The results obtained from published and ongoing research indicate that we are pointing toward better visualizing the overlapping boundaries of these specific disciplines, which will be able to more accurately answer key evolutionary questions. We highlight: (1) the combined application of bedrock-soil geological data and bioinformatics to resolve evolutionary questions regarding species eco-distribution, niche prediction and bio-evolution; and (2) signifies the importance of relaxing boundaries between the disciplines to come to a better conclusion on species diversity and distribution-driven controls. Overall, we express and briefly explain our hypothesis to integrate modern analytical tools, viz., statistical correlation of geological data via. geo-statistics (Geo), and spatiotemporal biostatistics via. geo-informatics (Geo), with gene-based paleontological shreds of evidence, and sequence-based bioinformatics, to devise a practical analysis tool, namely “Geo2 gene-bioinformatics”. We invoke the development of algorithms through computational-based programs that can provide useful correlations to understand evolutionary systematics and phylogeny, species distribution, and niche prediction.

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References

  1. Matson PA, Dietz T, Abdalati W et al (2010) What we know about climate change and its interactions with people and ecosystems. National research council. Advancing the science of climate change. The National Academies Press, Washington, DC

    Google Scholar 

  2. Hessler AM (2011) Earth’s Earliest Climate. Nature Education Knowledge. 3:24. https://www.nature.com/scitable/knowledge/library/earth-s-earliest-climate-24206248/

  3. Mergeay J, Santamaria L (2012) Evolution and biodiversity: the evolutionary basis of biodiversity and its potential for adaptation to global change. Evol Appl 5:103–106. https://doi.org/10.1111/j.1752-4571.2011.00232.x

    Article  PubMed  PubMed Central  Google Scholar 

  4. Swenson NG (2008) The past and future influence of geographic information systems on hybrid zone, phylogeographic and speciation research. J Evol Biol 21:421–434. https://doi.org/10.1111/j.1420-9101.2007.01487.x

    Article  CAS  PubMed  Google Scholar 

  5. Singh JK, Yadav KK, Gupta N, Kumar V (2016) Remote Sensing and Geographical Information System (GIS) and its application in various fields. National Conference on Energy and Environment: Threats and Remedies.

  6. Rogers JJW, Santosh M (2004) Continents and Supercontinents, Oxford: Oxford University Press, pp 146, ISBN 978-0-19-516589-0.

  7. Carpenter EM (2020) Five Types of Isolation in Biology. Sciencing.com, https://sciencing.com/five-types-isolation-biology-8501726.html.

  8. FSI (2017) Uttarakhand. In: India State of Forest Report 2017. Forest Survey of India, Dehradun, Uttarakhand, India, pp. 1–367.

  9. Malik SK, Chaudhury R, Dhariwal OP, Bhandari DC (2010) Salvadora Species (Pilu and Miswak). In: Genetic Resources of Tropical Underutilized Fruits in India. NBPGR, New Delhi. pp 168.

  10. Kutner L (2019) NatureServe Network Species Occurrence Data. Version 8.4. NatureServe. Occurrence dataset. https://doi.org/10.15468/lysaex. Accessed via GBIF.org on 2020-04-23.

  11. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Vavilov NI (1926) Studies on the origin of cultivated plants. Leningrad* Dobzhansky, Th. (1951): Genetics and the origin of species.

  13. Chiarucci A, Bacaro G, Scheiner SM (2011) Old and new challenges in using species diversity for assessing biodiversity. Philos Trans Royal Soc B: Biol Sci 366:2426–2437. https://doi.org/10.1098/rstb.2011.0065

    Article  Google Scholar 

  14. Brockerhoff EG, Barbaro L, Castagneyrol B, Forrester DI, Gardiner B, González-Olabarria JR, Lyver POB, Meurisse N, Oxbrough A, Taki H, Thompson ID (2017) Forest biodiversity, ecosystem functioning and the provision of ecosystem services. Biodivers Conserv 26:3005–3035. https://doi.org/10.1007/s10531-017-1453-2

    Article  Google Scholar 

  15. Saini S, Yadav JP (2013) Genetic variation in natural population of Salvadora oleoides: An important medicinal plant that need conservation. Asian J Plant Sci Res 3:20–27

    Google Scholar 

  16. Yadav JP, Manila SK, Yadav SK, Yadav S (2014) Assessment of Genetic Diversity using RAPD marker among different accessions of Salvadora oleoides of North-West India. Bioresearch Bulletin, 4.

  17. Bast F, Kaur N (2017) Nuclear and plastid DNA sequence-based molecular phylogeography of Salvadora oleoides (Salvadoraceae) in Punjab, India reveals allopatric speciation in anthropogenic islands due to agricultural expansion. J Phylogenetics Evolut Biol 5:1–7. https://doi.org/10.4172/2329-9002.1000180

    Article  CAS  Google Scholar 

  18. Goncalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK (2019) Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol 138:219–232. https://doi.org/10.1016/j.ympev.2019.05.022

    Article  CAS  PubMed  Google Scholar 

  19. Bhandari MS, Shamoon A, Meena RK, Saroj S, Pandey S, Kant R (2020) First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora. Mol Biol Rep 47:6997–7008. https://doi.org/10.1007/s11033-020-05758-z

    Article  CAS  PubMed  Google Scholar 

  20. Quandt D, Muller KF, Hilu K, Frahm J (2004) Molecular evolution of the chloroplast TRNL-F region in land plants. Monogr Syst Bot Missouri Bot Gard 98:13–37

    Google Scholar 

  21. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of the chloroplast DNA. Plant Mol Biol 17:1105–1109

    Article  CAS  PubMed  Google Scholar 

  22. Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC (2018) Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. Am J Bot 105:463–469. https://doi.org/10.1002/ajb2.1040

    Article  PubMed  Google Scholar 

  23. Hao DC, Huang BL, Chen SL, Mu J (2009) Evolution of the chloroplast trnL-trnF region in the gymnosperm lineages taxaceae and cephalotaxaceae. Biochem Genet 47:351–369. https://doi.org/10.1007/s10528-009-9233-7

    Article  CAS  PubMed  Google Scholar 

  24. De Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, Erkens RHJ (2011) Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective. PLoS ONE 6:e16371. https://doi.org/10.1371/journal.pone.0016371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chen CW, 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 111:663–673. https://doi.org/10.1093/aob/mct004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Ramoliya PJ, Pandey AN (2002) Effect of increasing salt concentration on emergence, growth and survival of seedlings of Salvadora oleoides (Salvadoraceae). J Arid Environ 51:121–132. https://doi.org/10.1006/jare.2001.0908

    Article  Google Scholar 

  27. Vaghela PM, Patel AD, Pandey IB, Pandey AN (2009) Implications of calcium nutrition on the response of Salvadora oleoides (Salvadoraceae) to soil salinity. Arid Land Res Manag 23:311–326. https://doi.org/10.1080/15324980903232080

    Article  CAS  Google Scholar 

  28. Bhandari MS, Shankhwar R, Maikhuri S, Pandey S, Meena RK, Ginwal HS, Kant R, Rawat PS, Martins-Ferreira MAC, Silveira LHC (2021) Prediction of ecological and geological niches of Salvadora oleoides in arid zones of India: causes and consequences of the global warming. Arab J Geosci. https://doi.org/10.1007/s12517-020-06384-6

    Article  Google Scholar 

  29. Sousa C (2016) Bridging darwin’s origin of species & wegener’s origin of continents and oceans: using biogeography, phylogeny, geology & interactive learning. Am Biol Teach 78:24–33. https://doi.org/10.1525/abt.2016.78.1.24

    Article  Google Scholar 

  30. CAJG (Conference of the Arabian Journal of Geosciences). 2019. 2nd—Springer CAJG. Sousse, Tunisia. 25th—28th November. https://www.cajg.org/

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Acknowledgements

The financial support by the Ministry of Environment, Forest and Climate Change (MoEF&CC), Government of India, New Delhi under grant code 0265 entitled ‘Research and Development for Conservation and Development’ (No. 14/8/2013-RE; dated 09th May 2016) is gratefully acknowledged. The corresponding author is highly obliged to the travel support received to attend the Conference of the Arabian Journal of Geosciences (CAJG). 2019. 2nd—Springer CAJG. Sousse, Tunisia. 25th—28th November by the Uttarakhand State Council for Science & Technology (UCOST), Dehradun, India, with vide reference No. UCS&T/TRAVEL-10/19-20/17190/1, dated 10/12/2019. The authors are thankful to the Director, FRI for providing the research facilities.

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Authors and Affiliations

  1. Division of Genetics and Tree Improvement, Forest Research Institute (FRI), Dehradun, Uttarakhand, 248195, India

    Maneesh S. Bhandari, Arzoo Shamoon & Rajendra K. Meena

  2. Faculdade de Ciências e Tecnologia, Universidade Federal de Goiás (UFG), Rua Mucuri, Setor Conde dos Arcos, Aparecida de Goiânia, GO, Brazil

    Marco Antonio Caçador Martins-Ferreira

  3. Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute (FRI), Dehradun, Uttarakhand, 248006, India

    Shailesh Pandey

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  1. Maneesh S. Bhandari
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Contributions

M.S.B. conceived the ideas, designed the map, did the analysis, interpretation and led the writing; M.A.C.M.F. conceived the integration of geology in modern distribution biology of forestry tree species, i.e., Salvadora oleoides. S.P. and R.K.M. gave an overview and conceived the idea of integrating molecular biology tools with evolutionary phylogeny of the forestry tree species. A.S. did the phylogenetic analysis of species under the family Salvadoracae. All authors critically edited the draft.

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Correspondence to Maneesh S. Bhandari.

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Significance statement: Technological integration may lead to a new outlet for comprehensively describing the ecological distribution of biological species, which not only elaborates the clarity of the thought process but also marks authentication of the cause for the scientific event.

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Bhandari, M.S., Martins-Ferreira, M.A.C., Shamoon, A. et al. Integration of Modern Molecular Tools with Geological Processes to Reveal Species Phylogeny, Biogeographical Niche Prediction, and Bio-Evolution. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 93, 119–125 (2023). https://doi.org/10.1007/s40011-022-01417-4

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