Skip to main content

Computational Approach to Study Ecophysiology

  • Chapter
  • First Online:
Advances in Plant Ecophysiology Techniques

Abstract

Ecophysiology is the study of how the environmental cues affect the functional aspects of an organism. This aspect is vital for the adaptation of living organisms to the ever changing surrounding, and regulates the distribution and richness of the organisms in the natural habitat. This interaction of ecosystem with an organism and its physiological status are governed by the genomic structure and time period of environmental impact. The duration and dose or intensity of the environmental impact determines the functional and genomic stability of organisms, both at individual and community level. Genome performs as unified system displaying intricate and dynamic behavior (Zhu et al. 2008). Ecophysiological genomics deciphers the alterations in gene structure and function in a specific environment. The study of such alterations in the genome, which are pivotal for the functional integrity of an organism, can be well documented through bioinformatics tools (Aubin-Horth and Renn 2009). In silico experimental strategies can ease sighting of core genomic elements, regulatory networks and conserved sequences across species and the variations in biotic and abiotic components of the environmental (McCarroll et al. 2004; Ragland et al. 2010). These studies will bring out comparative schemes didactic to the variations arising from ecological variations, leading to adaptation, speciation and evolution, as such.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Albertson RC, Yan YL, Titus TA, Pisano E, Vacchi M, Yelick PC, Detrich HW, Postlethwait JH (2010) Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes. BMC Evol Biol 10:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Arbona V, Manzi M, Ollas C, Gomez-Cadenas A (2013) Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci 14:4885–4911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aubin-Horth N, Renn SCP (2009) Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity. Mol Ecol 18:3763–3780

    Article  CAS  PubMed  Google Scholar 

  • Barik BP (2013a) Computational visualization of biomolecular structures. Int J Atoms Mol 3:576–578

    Google Scholar 

  • Barik BP (2013b) In silico observations and analysis of metabolic pathways. Int J Sci Res 2:44–48

    Google Scholar 

  • Barik BP (2015) Animal actin phylogeny and RNA secondary structure study. Int J Knowl Discov Bioinf 5:47–63

    Article  Google Scholar 

  • Berkelmans R, Willis BL (1999) Seasonal and local spatial patterns in the upper thermal limits of corals on the inshore central great barrier reef. Coral Reefs 18:219–228

    Article  Google Scholar 

  • Cheviron ZA, Whitehead A, Brumfield RT (2008) Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichiacapensis) along an altitudinal gradient. Mol Ecol 17:4556–4569

    Article  CAS  PubMed  Google Scholar 

  • Claydon AJ, Beynon R (2012) Proteome dynamics: revisiting turnover with a global perspective. Mol Cell Proteomics 11:1551–1565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK et al (2011) The ecoresponsive genome of Daphnia pulex. Science 331:555–561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cork JM, Purugganan MD (2004) The evolution of molecular genetic pathways and networks. Bioassays 26:479–484

    Article  CAS  Google Scholar 

  • Denny MW, Gaylord B (2010) Marine ecomechanics. Annu Rev Mar Sci 2:89–114

    Article  Google Scholar 

  • Diz AP, Martinez-Fernandez M, Rolan-Alvarez E (2012) Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 21:1060–1080

    Article  CAS  PubMed  Google Scholar 

  • Eastman JT (2005) The nature of the diversity of Antarctic fishes. Polar Biol 28:93–107

    Article  Google Scholar 

  • Edmeades GO, McMaster GS, White JW (2004) Genomics and the physiologist: bridging the gap between genes and crop response. Field Crops Res 90:5–18

    Article  Google Scholar 

  • Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 107:1–15

    Article  CAS  Google Scholar 

  • Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1–15

    Article  Google Scholar 

  • Galperin M, Koonin E (1999) Functional genomics, enzyme evolution, homologous and analogous enzymes encoded in microbial genomes. Genetica 106:159–170

    Article  CAS  PubMed  Google Scholar 

  • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Green JL, Hastings A, Arzberger P, Ayala FJ, Cottingham KL et al (2005) Complexity in ecology and conservation: mathematical, statistical, and computational challenges. Bioscience 55:501–510

    Article  Google Scholar 

  • Hagenblad J, Tang CL, Molitor J, Werner J, Zhao K, Zheng HG, Marjoram P, Weigel D, Nordborg M (2004) Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics 168:1627–1638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harvey PH, Pagel MD (1991) The comparative method in evolutionary biology. Oxford University Press, Oxford/New York

    Google Scholar 

  • Haubold B, Wiehe T (2004) Comparative genomics: methods and applications. Naturwissenschaften 91:405–421

    PubMed  CAS  Google Scholar 

  • Hofmann GE, Barry JP, Edmunds PJ, Gates RD, Hutchins DA, Klinger T, Sewell MA (2010) The effect of ocean acidification on calcifying organisms in marine ecosystems: an organism-to-ecosystem perspective. Annu Rev Ecol Evol Syst 41:127–147

    Article  Google Scholar 

  • Kaur C, Kumar G, Kaur S, Ansari MW, Pareek A, Sopory SK, Singla-Pareek SL (2015) Molecular cloning and characterization of salt overly sensitive gene promoter from Brassica juncea (BjSOS2). Mol Biol Rep 42:1139–1148

    Article  CAS  PubMed  Google Scholar 

  • Kearney MR, Helmuth B, Matzelle A (2012) Biomechanics meets the ecological niche: the importance of temporal data resolution. J Exp Biol 215:922–933

    Article  PubMed  Google Scholar 

  • Kim TY, Kim HU, Lee SY (2010) Data integration and analysis of biological networks. Curr Opin Biotechnol 21:78–84

    Article  CAS  PubMed  Google Scholar 

  • Kvitek DJ, Will JL, Gasch AP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4:e1000223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai Z, Kane NC, Zou Y, Rieseberg LH (2008) Natural variation in gene expression between wild and weedy populations of Helianthus annuus. Genetics 179:1881–1890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lockwood BL, Somero GN (2011) Transcriptomic responses to salinity stress in invasive and native blue mussels (genus Mytilus). Mol Ecol 20:517–529

    Article  PubMed  Google Scholar 

  • Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994

    Article  CAS  PubMed  Google Scholar 

  • Mandic M, Sloman KA, Richards JG (2009) Escaping to the surface: a phylogenetically independent analysis of hypoxia-induced respiratory behaviors in sculpins. Physiol Biochem Zool 82:730–738

    Article  PubMed  Google Scholar 

  • McCarroll SA, Murphy CT, Zou SG, Pletcher SD, Chin CS, Jan YN, Kenyon C, Bargmann CI, Li H (2004) Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet 36:197–204

    Article  CAS  PubMed  Google Scholar 

  • Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney RK (2012) Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. TAG Theor Appl Genet 125:625–645

    Article  CAS  PubMed  Google Scholar 

  • Near TJ, Pesavento JJ, Cheng CHC (2004) Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA. Mol Phylogenet Evol 32:881–891

    Article  CAS  PubMed  Google Scholar 

  • Nelson CD, Johnsen KH (2008) Genomic and physiological approaches to advancing forest tree improvement. Tree Physiol 28:1135–1143

    Article  PubMed  Google Scholar 

  • Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86:641–647

    Article  CAS  PubMed  Google Scholar 

  • Nongpiur RC, Singla-Pareek SL, Pareek A (2016) Genomics approaches for improving salinity stress tolerance in crop plants. Curr Genomics 17:343–357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • OʼDonnell MJ, Todgham AE, Sewell MA, Hammond LM, Ruggiero K, Fangue NA, Zippay ML, Hofmann GE (2010) Ocean acidification alters skeletogenesis and gene expression in larval sea urchins. Mar Ecol Prog Ser 398:157–171

    Article  CAS  Google Scholar 

  • Palmer M, Bernhardt ES, Chornesky EA, Collins SL, Dobson AP et al (2005) Ecological science and sustainability for the 21st century. Front Ecol Environ 3:4–11

    Article  Google Scholar 

  • Parmesan C (2006) Ecological and evolutionary responses to recent climate change. Annu Rev Ecol Evol Syst 37:637–669

    Article  Google Scholar 

  • Podrabsky JE, Somero GN (2006) Inducible heat tolerance in Antarctic notothenioid fishes. Polar Biol 30:39–43

    Article  Google Scholar 

  • Ragland GJ, Denlinger DL, Hahn DA (2010) Mechanisms of suspended animation are revealed by transcript profiling of diapause in the flesh fly. Proc Natl Acad Sci U S A 107:14909–14914

    Article  PubMed  PubMed Central  Google Scholar 

  • Real LA, Brown JH (eds) (1991) Foundations of Ecology: Classic Papers with Commentaries. University of Chicago Press, Chicago, USA, pp. 920

    Google Scholar 

  • Rees BB, Andacht T, Skripnikova E, Crawford DL (2011) Population proteomics: quantitative variation within and among populations in cardiac protein expression. Mol Biol Evol 28: 1271–1279

    Google Scholar 

  • Schlichting C, Pigliucci M (1998) Phenotypic evolution: a reaction norm perspective. Sinauer Associates, Sunderland

    Google Scholar 

  • Schwenk K, Padilla DK, Bakken GS, Full RJ (2009) Grand challenges in organismal biology. Integr Comp Biol 49:7–14

    Article  PubMed  Google Scholar 

  • Smith EN, Kruglyak L (2008) Gene-environment interaction in yeast gene expression. PLoS Biol 6:810–824

    CAS  Google Scholar 

  • Somero GN (2000) Unity in diversity: a perspective on the methods, contributions, and future of comparative physiology. Annu Rev Physiol 62:927–937

    Article  CAS  PubMed  Google Scholar 

  • van Helden P (2013) Data-driven hypotheses. EMBO Rep 14:104

    Article  CAS  PubMed  Google Scholar 

  • Weinig C, Ewers BE, Welch SM (2014) Ecological genomics and process modeling of local adaptation to climate. Curr Opin Plant Biol 18:66–72

    Article  PubMed  Google Scholar 

  • Whitehead A, Crawford DL (2006) Neutral and adaptive variation in gene expression. Proc Natl Acad Sci U S A 103:5425–5430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Whitehead A, Pilcher W, Champlin D, Nacci D (2012) Common mechanism underlies repeated evolution of extreme pollution tolerance. Proc R Soc B 279:427–433

    Article  PubMed  Google Scholar 

  • Yin X, Struik PC, Kropff MJ (2004) Role of crop physiology in predicting gene-to-phenotype relationships. Trends Plant Sci 9:426–432

    Article  CAS  PubMed  Google Scholar 

  • Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40:854–861

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Barik, B.P., Mishra, A.N. (2018). Computational Approach to Study Ecophysiology. In: Sánchez-Moreiras, A., Reigosa, M. (eds) Advances in Plant Ecophysiology Techniques. Springer, Cham. https://doi.org/10.1007/978-3-319-93233-0_28

Download citation

Publish with us

Policies and ethics