Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests

Abstract

The rapid pace of deforestation and fragmentation that took place in the Brazilian Atlantic Forest and other global hotspots for biodiversity conservation has motivated ecosystem restoration efforts. The genetic viability of restored tree populations and their potential to conserve genetic diversity remains, however, unclear. Here, we assessed the genetic viability and potential to conserve the genetic diversity of restored populations of Centrolobium tomentosum, a native legume tree, in the Brazilian Atlantic Forest, based on a genotyping by sequencing (GBS). We have successfully generated a total of 2877 single nucleotide polymorphism (SNP) markers across the whole C. tomentosum genome. Surprisingly, restoration sites presented overall higher levels of genetic diversity compared to natural remnant areas and negative inbreeding coefficient (FIS), mainly in juveniles’ trees from newer restored areas, indicating an excess of heterozygotes probably due to the founding event. The most likely number of genetic clusters found was two (K = 2), suggesting that diverse seed sources were used to produce seedlings for restoration. Clear signs of gene flow from restored to natural remnants areas had also been detected when diversity values of adults and juveniles were contrasted. Even though we did not find any clear relation of the genetic diversity and landscape composition, the low percentage of forest and high levels of fragmentation are likely reducing patch connectivity in some areas. LOSITAN detected 88 SNP outliers under positive selection, but analysis with Bayescan failed to support this evidence. In conclusion, our post hoc evaluation of restored tree populations indicated that the old restored area is stable and new areas have great potential to contribute to conserving genetic diversity and increasing the chances of the natural populations to persist over time.

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Data availability

All data necessary to reproduce this study was provided as supplementary material and at FigShare (https://figshare.com/s/96123894ecc44d2ef24c). Any additional data or information are available from the corresponding author upon request.

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Acknowledgements

We want to FAPESP (Industry) for the postdoc assistantships: CMM (FAPESP; Grant #2011/50296-8), EMGC (FAPESP; Grant #2017/02393-0), doctorate: KDS (FAPESP; Grant #2015/06349-0), EAS (FAPESP; Grant #2015/15536-9), and PSB (FAPESP; Grant #2014/01364-9). MIZ and PHSB thank the National Council for Scientific and Technological Development of Brazil (CNPq; Grant #310446/2015-5, CNPq; Grant #304817/2015-5).

Funding

This study was fully funded by the São Paulo Research Foundation (FAPESP, Portuguese: Fundação de Amparo à Pesquisa do Estado de São Paulo) and The Brazilian National Council for Scientific and Technological Development (CNPq, Portuguese: Conselho Nacional de Desenvolvimento Científico e Tecnológico). Sponsors have no role in the study design, data collection, and data analysis, or manuscript preparation.

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Correspondence to Erick M. G. Cordeiro.

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Cordeiro, E.M.G., Macrini, C.M., Sujii, P.S. et al. Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests. Conserv Genet 20, 1073–1085 (2019). https://doi.org/10.1007/s10592-019-01195-z

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Keywords

  • Active restoration
  • Conservation genetics
  • Ecological restoration
  • Landscape genetics
  • Forest restoration
  • Restoration plantations