Landscape genetics reveal low diversity and adaptive divergence inPortulaca hatschbachii(Portulacaceae): an endangered species endemic to rocky outcrops of the Atlantic Forest

Abstract

Portulaca hatschbachii is endemic to the basaltic rocky outcrops that are distributed, in a discontinuous way, along the Third Plateau of Paraná State, Brazil, composing environments that form the Subtropical Highland Grasslands of the Atlantic Forest Biome. Considering the risk of extinction of the species and the massive anthropization of these outcrops, we applied AFLP, ITS and rps16 molecular markers in ten populations throughout the area of occurrence of the species to generate information about the genetic status of P. hatschbachii and contribute to the development of conservation strategies. Low rates of genetic diversity, high population structure, restricted gene flow and the presence of diversifying selection were observed for the populations. The analysis of variation partitioning (R2adj. = 63.60%) showed that environmental variables have a greater influence on the distribution of variation of loci under selection (R2adj. = 26.70%) than geographical isolation (R2adj. = 1.20%). The strong population structure, for both neutral and selected loci, suggests an isolation by adaptation mechanism (IBA) occurring in populations and highlights the need and urgency for in situ conservation plans for the species and its occurrence on rocky outcrops.

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

“…In this study, we applied RDA and GDM to quantify the contributions of spatial isolation and climate variables to patterns of genomic variation, and obtained concordant results. Both methods identified a larger proportion of SNP variation attributed to climate than to geography ( Figure 3 ), indicating that the assessed climate variables are more influential in driving the pattern of genetic variation in T. hemsleyanum , which has been frequently reported in plant species ( Shryock et al, 2017 ; Vidaller et al, 2020 ; Feliciano et al, 2022 ). When we isolate the effect of climate variables, geography alone explained a rather small portion (RDA: 2.5%; GDM: 8.1%; Figure 3 ), which potentially reflect the absence of unmeasured spatially structured climate variables ( Feliciano et al, 2022 ).…”

“…Both methods identified a larger proportion of SNP variation attributed to climate than to geography ( Figure 3 ), indicating that the assessed climate variables are more influential in driving the pattern of genetic variation in T. hemsleyanum , which has been frequently reported in plant species ( Shryock et al, 2017 ; Vidaller et al, 2020 ; Feliciano et al, 2022 ). When we isolate the effect of climate variables, geography alone explained a rather small portion (RDA: 2.5%; GDM: 8.1%; Figure 3 ), which potentially reflect the absence of unmeasured spatially structured climate variables ( Feliciano et al, 2022 ). Furthermore, our RDA and regional climatic differences revealed that climate predictors acting as key selective agents vary across specific geographic clusters ( Figure 2 ; Supplementary Figure S3 ).…”

Genome‐wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

“…Many studies have demonstrated that genetic diversity in species is influenced by multiple factors, including gene flow (Feliciano et al, 2022;Su, Richardson, et al, 2017), selection (Luo et al, 2022;Niu et al, 2019), evolutionary history (Guerra-Garcia et al, 2022;Roy et al, 2017), and the level of inbreeding (Dicks et al, 2023). For example, Feliciano et al (2022) found low population genetic diversity associated with restricted gene flow in the endemic and endangered species Portulaca hatschbachii in Brazil.…”

“…If the genetic diversity of ex situ populations is consistent with, similar to, or higher than that of wild populations, the ex situ conservation programs are considered to be preliminarily successful, and if not, further improvements are required. Many studies have demonstrated that genetic diversity in species is influenced by multiple factors, including gene flow (Feliciano et al, 2022 ; Su, Richardson, et al, 2017 ), selection (Luo et al, 2022 ; Niu et al, 2019 ), evolutionary history (Guerra‐Garcia et al, 2022 ; Roy et al, 2017 ), and the level of inbreeding (Dicks et al, 2023 ). For example, Feliciano et al ( 2022 ) found low population genetic diversity associated with restricted gene flow in the endemic and endangered species Portulaca hatschbachii in Brazil.…”

“…Many studies have demonstrated that genetic diversity in species is influenced by multiple factors, including gene flow (Feliciano et al, 2022 ; Su, Richardson, et al, 2017 ), selection (Luo et al, 2022 ; Niu et al, 2019 ), evolutionary history (Guerra‐Garcia et al, 2022 ; Roy et al, 2017 ), and the level of inbreeding (Dicks et al, 2023 ). For example, Feliciano et al ( 2022 ) found low population genetic diversity associated with restricted gene flow in the endemic and endangered species Portulaca hatschbachii in Brazil. A large‐scale genomic analysis of walnuts ( Juglans regia ) revealed the effect of selection on genetic diversity, and they found slower rates of linkage disequilibrium (LD) decay and lower levels of nucleotide diversity in domesticated cultivars and landraces compared with wild walnuts (Luo et al, 2022 ).…”