Research Article: Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.

Date Published: March 7, 2018

Publisher: Public Library of Science

Author(s): João Paulo Gomes Viana, Marcos Vinícius Bohrer Monteiro Siqueira, Fabiano Lucas Araujo, Carolina Grando, Patricia Sanae Sujii, Ellida de Aguiar Silvestre, Mariana Novello, José Baldin Pinheiro, Marcelo Mattos Cavallari, Pedro H. S. Brancalion, Ricardo Ribeiro Rodrigues, Anete Pereira de Souza, Julian Catchen, Maria I. Zucchi, Tzen-Yuh Chiang.


The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (AR = 1.72 ± 0.005; HO = 0.135 ± 0.005; HE = 0.167 ± 0.005; FIS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.

Partial Text

Increasing environmental degradation has led to the promotion of ecological restoration worldwide, particularly for forest ecosystems [1–3]. Forest restoration methods are selected based upon the degree of ecosystem degradation [4,5], the availability of native forest fragments to act as seed sources in the landscape [6,7] the goals of restoration interventions [4], and funding constraints [8,9]. For all restoration approaches, forest succession must proceed in time, which is the primary ecological process controlling the recovery of forest ecosystems [10]. However, several factors drive tropical forest succession. Although some of these factors are unpredictable and difficult to manipulate at the site level, such as dispersal by fauna, others can be controlled at some level during restoration planning, implementation, or adaptive management; these are the factors that receive special attention from practitioners. Genetic diversity of reintroduced populations is a key factor for the long-term persistence of native species in forest restoration sites that can be manipulated by practitioners, based on the selection of natural populations and seed-trees for producing planting stocks [9,11,12].

The value of research involving population genetics in a genomic scale using non-model species without previous knowledge of the genome size and complexity has been previously demonstrated in conservation genomics. With the advent of inexpensive sequencing and the advancement of techniques that reduce genome complexity, such as GBS, the study of genetic diversity and structure in natural populations can be based on hundreds of SNPs [56,57]. Here, we demonstrate the usefulness of this approach for restoration genetics.




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