Skip to main content
SpringerLink
Log in

Putative Local Adaptive SNPs in the Genus Avicennia

  • Original Article
  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

The genus Avicennia with eight species grow in intertidal zones of tropical and temperate regions, ranging in distribution from West Asia, to Australia, and Latin America. These mangroves have several medicinal applications for mankind. Many genetic and phylogenetic studies have been carried out on mangroves, but none is concerned with geographical adaptation of SNPs. We therefore, used ITS sequences of about 120 Avicennia taxa growing in different parts of the world and undertook computational analyses to identify discriminating SNPs among these species and to study their association with geographical variables. A combination of multivariate and Bayesian approaches such as CCA, RDA, and LFMM were conducted to identify the SNPs with potential adaptation to geographical and ecological variables. Manhattan plot revealed that many of these SNPs are significantly associated with these variables. The genetic changes accompanied by local and geographical adaptation were illustrated by skyline plot. These genetic changes occurred not under a molecular clock model of evolution and probably under a positive selection pressure imposed in different geographical regions in which these plants grow.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Data Availability

All data are available from the corresponding author on reasonable request.

Code Availability

Not applicable.

References

  • Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L). Front Plant Sci 6:813

    Article  PubMed  PubMed Central  Google Scholar 

  • Alongi DM (2014) Carbon cycling and storage in mangrove forests. Annu Rev Mar Sci 6:195–219. https://doi.org/10.1146/annurev-marine-010213-135020

    Article  Google Scholar 

  • Barbier EB, Hacker SD, Kennedy C, Koch EW, Stier AC, Silliman BR (2011) The value of estuarine and coastal ecosystem services. Ecol Monogr 81:169–193. https://doi.org/10.1890/10-1510.1

    Article  Google Scholar 

  • Carugati L, Gatto B, Rastelli E, Lo Martire M, Coral C, Greco S et al (2018) Impact of mangrove forests degradation on biodiversity and ecosystem functioning. Sci Rep 8:13298. https://doi.org/10.1038/s41598-018-31683-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charlesworth B, Nordborg M, Charlesworth D (1997) The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet Res 70:155–174

    Article  CAS  PubMed  Google Scholar 

  • Cheong SM, Silliman B, Wong PP, van Weesenbeeck B, Kim CK, Guannel G (2013) Coastal adaptation with ecological engineering. Nat Clim Chang 3:787–791. https://doi.org/10.1038/nclimate1854

    Article  Google Scholar 

  • Churchill DM (1973) the ecological significance of temperature tropical mangroves in the early Tertiary floras of southern Australia. Geol Soc Aust Spec Pub 4:79–86

    Google Scholar 

  • Danielsen F, Sørensen MK, Olwing MF, Selvam V, Parish F, Burgess ND et al (2005) The Asian tsunami: a protective role for coastal vegetation. Science 310:643. https://doi.org/10.1126/science.1118387

    Article  CAS  PubMed  Google Scholar 

  • Duarte CM, Middelburg JJ, Caraco N (2005) Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences 2:1–8. https://doi.org/10.5194/bg-2-1-2005

    Article  CAS  Google Scholar 

  • Duke NC (1991) A systematic revision of the mangrove genus Avicennia (Avicenniaceae) in Australasia. Aust Syst Bot 4(2):299–324. https://doi.org/10.1071/sb991029

    Article  Google Scholar 

  • Duke NC (1995) Genetic diversity, distributional barriers and rafting continents? More thoughts on the evolution of mangroves. Hydrobiologia 295:167–181

    Article  Google Scholar 

  • Duke NC (2017) Mangrove floristics and biogeography revisited: further deductions from biodiversity hot spots, ancestral discontinuities, and common evolutionary processes. In: Rivera-Monroy VH, Lee SY, Kristensen E, Twilley RR (eds) Mangrove Ecosystems: A Global Biogeographic Perspective. Springer, Berlin, pp 17–53

    Chapter  Google Scholar 

  • Duke NC, Lo E, Sun M (2002) Global distribution and genetic discontinuities of mangroves—emerging patterns in the evolution of Rhizophora. Trees 16:65–79

    Article  Google Scholar 

  • Ellison AM, Farnsworth EJ, Merkt RE (1999) Origins of mangrove ecosystems and the mangrove biodiversity anomaly. Glob Ecol Biogeogr 8:95–115

    Article  Google Scholar 

  • Estoque RC, Myint SW, Wang C, Ishtiaque A, Aung TT, Emerton L et al (2018) Assessing environmental impacts and change in Myanmar’s mangrove ecosystem service value due to deforestation (2000–2014). Glob Chang Biol 24:5391–5410. https://doi.org/10.1111/gcb.14409

    Article  PubMed  Google Scholar 

  • Ezcurra P, Ezcurra E, Garcillán PP, Costa MT, Aburto-Oropeza O (2016) Coastal landforms and accumulation of mangrove peat increase carbon sequestration and storage. Proc Natl Acad Sci 113(16):4404–4409. https://doi.org/10.1073/pnas.1519774113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Faridah-Hanum I et al (2019) Development of a comprehensive mangrove quality index (MQI) in Matang Mangrove: assessing mangrove ecosystem health. Ecol Ind 102:103–117

    Article  Google Scholar 

  • Figueroa-Rangel BL, Valle-Martíne A, Olvera-Vargas M, Liu KB (2016) Environmental History of MangroveVegetation in Pacific West-Central Mexico during the Last 1300 Years. Front Ecol Evol. https://doi.org/10.3389/fevo.2016.00101

    Article  Google Scholar 

  • Flenley JR (1998) Tropical Forests under the Climates of the Last 30,000 Years. In: Markham A (ed) Potential Impacts of Climate Change on Tropical Forest Ecosystems. Springer, Dordrecht, pp 37–57

    Chapter  Google Scholar 

  • Frichot E, Francois O (2015) LEA: An R package for landscape and ecological association studies. In. press.

  • Frichot E, Schoville SD, Bouchard G, Francois O (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30(7):1687–1699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garot E, Dussert S, Domergue F, Joët T, Fock-Bastide I, Combes MC, Lashermes P (2021) Multi-approach analysis reveals local adaptation in a Widespread Forest Tree of Reunion Island. Plant Cell Physiol 62(2):280

    Article  CAS  PubMed  Google Scholar 

  • Gee CT (2001) the mangrove palm Nypa in the geologic past of the new world. Wetl Ecol Manag 9(181–94):23

    Google Scholar 

  • Gruas-Cavagnetto C, Tambareau Y, Villatte J (1988) Graham, Donnees paleoecologiques nouvelles sur le Thanetien et l’Ilerdien de l’avant-pays pyreneen et de la Montagne Noire. Inst Francais Pondichery. Sect Sci Tech 25:219–235

    Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2012) PAST: Paleontological Statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  • Ingvarsson PK, Garcı´a MV, David Hall D, Luquez V, Jansson S, (2006) Clinal variation in phyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in. European Aspen (Populus tremula). Genetics 172:1845–1853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee SY, Primavera JH, Dahdou+h-Guebas F, McKee K, Bosire JO, Cannicci S, et al (2014) Ecological role and services of tropical mangrove ecosystems: a reassessment. Glob Ecol Biogeogr 23:726–743. https://doi.org/10.1111/geb.12155

    Article  Google Scholar 

  • Legendre P, Legendre L (2012) Numerical ecology. Elsevier, Amsterdam

    Google Scholar 

  • Leopold EB (1969) Miocene pollen and spore flora of Eniwetok Atoll, Marshall Islands. US Geol Surv Prof 59:330–342

    Google Scholar 

  • Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu XY (2017) Ten years of landscape genomics: challenges and opportunities. Front Plant Sci 8:2136

    Article  PubMed  PubMed Central  Google Scholar 

  • Lovelock CE, Cahoon DR, Friess DA, Guntenspergen GR, Krauss KW, Reef R et al (2015) The vulnerability of Indo-Pacific mangrove forests to sea-level rise. Nature 526:559–563. https://doi.org/10.1038/nature15538

    Article  CAS  PubMed  Google Scholar 

  • Lovelock CE, Feller IC, Reef R, Hickey S, Ball MC (2017) Mangrove dieback during fluctuating sea levels. Sci Rep 7:1680. https://doi.org/10.1038/s41598-017-01927-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manson FJ, Loneragan NR, Harch BD, Skilleter GA, Williams L (2005) A broad 1 scale analysis of links between coastal fisheries production and mangrove extent: a case-study for northeastern Australia. Fish Res 74:69–85. https://doi.org/10.1016/j.fishres.2005.04.001

    Article  Google Scholar 

  • Mazda Y, Kobashi D, Okada S (2005) Tidal scale hydrodynamics within mangrove swamps. Wetlands Ecol Manag 13:647–655

    Article  Google Scholar 

  • Mori GM, Zucchi MI, Sampaio I, Souza AP (2015) Species distribution and introgrossive hybridization of two Avicennia species from the Western Hemisphere unveiled by phylogeographic patterns. BMC Evol Biol 15:61

    Article  PubMed  PubMed Central  Google Scholar 

  • Muller J (1964) A palynological contribution to the history of the mangrove vegetation of Borneo. In: Cranwell LM (ed) Ancient Pacific floras: the pollen story. University of Hawaii Press, Honolulu, pp 33–42

    Google Scholar 

  • Nordborg M, Innan H (2003) the genealogy of sequences containing multiple sites subject to strong selection in a subdivided population. Genetics 163:1201–1213

    Article  PubMed  PubMed Central  Google Scholar 

  • Plaziat JC, Cavagnetto C, Koeniguer JC, Baltzer F (2001) History and biogeography of the mangrove ecosystem, based on a critical reassessment of the paleontological record. Wetl Ecol Manag 9:161–179

    Article  Google Scholar 

  • Podani J (2000) Introduction to the Exploration of Multivariate Data. Backhuyes, Leiden

    Google Scholar 

  • Polidoro BA, Carpenter KE, Collins L, Duke NC, Ellison AM, Ellison JC et al (2010) The los of species: mangrove extinction risk and geographic areas of global concern. PLoS One 5:e10095. https://doi.org/10.1371/journal.pone.0010095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rege AA, Ambaye RY, Deshmukh RA (2010) In vitro testing of anti-HIV activity of some medicinal plants. Indian J Nat Prod Resour 1:193–199

    Google Scholar 

  • Ricklefs RE, Schwarzbach AE, Renner SS (2006) Rate of lineage origin explains the diversity anomaly in the world’s mangrove vegetation. Am Natl 168:805–810

    Article  Google Scholar 

  • Schneider P (2011) the discovery of tropical mangroves in Graeco-Roman antiquity: science and wonder. J Hakluyt Soc 3:1–16

    Google Scholar 

  • Segovia NI, González-Wevar CA, Haye PA (2020) Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast. Sci Rep 10:14098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shafie M, Forghani A, Moshtaghiyan J (2013) Mangrove (Avicennia marina) and vitamin C on arthritic rats. Bul Environ Pharmacol Life Sci 2:32–37

    Google Scholar 

  • Sharief MN, Umamaheswararao V (2011) Antibacterial activity of stem and root extracts of Avicennia officinalis L. Int J Pharm App 2:231–236

    Google Scholar 

  • Suan G, Popescu SM, Suc JP, Schnyder J, Fauquette S et al (2017) Subtropical climate conditions and mangrove growth in Arctic Siberia during the early Eocene. Geology 45:539–542

    Article  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:595–595

    Article  Google Scholar 

  • Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526

    CAS  PubMed  Google Scholar 

  • Temmerman S, Meire P, Bouma TJ, Herman PMJ, Ysenbaert T, De Vriend HJ (2013) Ecosystem-based coastal defence in the face of global change. Nature 504:79–83. https://doi.org/10.1038/nature12859

    Article  CAS  PubMed  Google Scholar 

  • Thanikaimoni G (1987) Mangrove palynology Inst. Francais Pondichery. Sect Sci Tech 24:1–100

    Google Scholar 

  • Ward RD, Friess DA, Day RH, MacKenzie RA (2016) Impacts of climate change on mangrove ecosystems: a region-by-region overview. Ecosyst Health Sustain 2:e01211. https://doi.org/10.1002/ehs2.1211

    Article  Google Scholar 

  • Zhang K, Liu H, Li Y, Xu H, Shen J, Rhome J et al (2012) The role of mangroves in attenuating storm surges. Estuar Coast Shelf Sci 102–103:11–23. https://doi.org/10.1016/j.ecss.2012.02.021

    Article  Google Scholar 

  • Zhang XX, Liu BG, Li Y, Liu Y, He YX, Qian ZH, Li JX (2019) Landscape genetics reveals that adaptive genetic divergence in Pinus bungeana (Pinaceae) is driven by environmental variables relating to ecological habitats. BMC Evol Biol 19:160

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank the Iran National Science Foundation (INSF), for partial financial support of this project (No.4002299).

Funding

None.

Author information

Authors and Affiliations

  1. Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran

    Laleh Malekmohammadi, Masoud Sheidai & Fahimeh Koohdar

  2. Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran

    Farrokh Ghahremaninejad

  3. Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran

    Afshin Danehkar

Authors
  1. Laleh Malekmohammadi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masoud Sheidai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Farrokh Ghahremaninejad
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Afshin Danehkar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fahimeh Koohdar
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MS, Project manager and data scientist; FG and AD contributed to conceptualization of the project; FK and LM contributed to data collection and data analysis.

Corresponding author

Correspondence to Masoud Sheidai.

Ethics declarations

Conflict of interest

All authors have no conflict of interest.

Ethical Approval

Not applicable.

Consent to Participate

Not applicable.

Consent for Publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Malekmohammadi, L., Sheidai, M., Ghahremaninejad, F. et al. Putative Local Adaptive SNPs in the Genus Avicennia. Biochem Genet 61, 2260–2275 (2023). https://doi.org/10.1007/s10528-023-10362-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-023-10362-4

Keywords

Search

Navigation