Landscape conservation genetics of Dipteryx alata (“baru” tree: Fabaceae) from Cerrado region of central Brazil

Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies

Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.

Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account

The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.

Dispersal analysis of three Peltigera species based on landscape genetics data

Lichens can either disperse sexually through fungal spores or asexually through vegetative propagules and fragmentation. Understanding how genetic variation in lichens is distributed across a landscape can be useful to infer dispersal and establishment events in space and time as well as the conditions needed for this establishment. Most studies have sampled lichens across large spatial distances on the order of hundreds of kilometers, while here we sequence the internal transcribed spacer (ITS) for 113 samples of three Peltigera species sampling at a variety of small spatial scales. The maximum distance between sampled lichens was 3.7 km and minimum distance was approximately 20 cm. We find significant amounts of genetic diversity across all three species. For P. praetextata, two out of the three most common ITS genotypes exhibit spatial autocorrelation supporting short-range dispersal. Using rarefaction we estimate that all ITS genotypes in our sampling area have been found for P. praetextata and P. evansiana, but not P. canina. Comparing our results with other ITS data in the literature provides evidence for global dispersal for at least one sequence followed by the evolution of endemic haplotypes with wide dispersal and rare haplotypes with more local dispersal.

Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas

Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species' paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence.

Genetic structure in fragmented populations of Solanum lycocarpum A. St.-Hil. with distinct anthropogenic histories in a Cerrado region of Brazil

Solanum lycocarpum is a woody tree widely distributed in the Cerrado that reaches high population densities in disturbed environments. We examined the genetic diversity and population differentiation of six S. lycocarpum populations with different degrees of human disturbance in order to determine if they are negatively affected by anthropogenic activity. Three populations located in southern and three located in southeastern regions of Goiás State, Central Brazil, were genotyped with five microsatellite markers. The population located in a protected area had higher number of alleles (26) than the remaining populations (19 to 21 alleles). It indicates that extensive and continuous areas of preserved native vegetation contribute positively to the conservation of genetic diversity, even with S. lycocarpum that easily adapts to disturbed environments. The three southeastern populations, although fragmented, had preserved native vegetation and were not significantly different from each other (θp = 0.002). All other population pairs compared were significantly divergent (θp varied from 0.03 to 0.11 between pairs, P < 0.05). We found three distinct sets of allele frequencies. The three southeastern populations shared similar gene pools, as well as the two disturbed southern populations, which are secondary vegetation. The southern population located in protected area had the most dissimilar gene pool. In conclusion, populations showing a higher degree of human disturbance tends to show a larger population differentiation than expected from the isolation by distance model, which in the current scenario of the Cerrado destruction points out to a threat to the long-term conservation of the species.

Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations

The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F(ST) (or related statistics, such as ϕ(ST) from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation. Moreover, the relative magnitude of these components and their spatial patterns can help identifying microevolutionary processes driving population differentiation. Here we show how recent methodological advances in ecological community analyses that allows partitioning dissimilarity into turnover (turnover) and richness differences, or nestedness-resultant dissimilarity, can be applied to allelic variation data, using an endemic Cerrado tree (Dipteryx alata) as a case study. Individuals from 15 local populations were genotyped for eight microsatellite loci, and pairwise dissimilarities were computed based on presence-absence of alleles. The turnover of alleles among populations represented 69 % of variation in dissimilarity, but only the richness difference component shows a clear spatial structure, appearing as a westward decrease of allelic richness. We show that decoupling richness difference and turnover components of allelic variation reveals more clearly how similarity among populations reflects geographical patterns in allelic diversity that can be interpreted in respect to historical range expansion in the species.

Random amplified marker technique for plants rich in polyphenols

More than 10,000 publications using the random amplified polymorphic DNA (RAPD) or related arbitrary marker techniques have been published in two decades of its inception in 1990. Despite extensive use, RAPD technique has also attracted some criticisms, mainly for lack of reproducibility. In the light of its widespread applications, the objective of this chapter is to (1) provide a protocol for RAPD assay, (2) identify the potential factors affecting the optimization of the RAPD assays, and (3) provide proper statistical analysis to avoid false positives. It is suggested that after proper optimization, the RAPD is a reliable, sensitive, and reproducible assay having the potential to detect a wide range of DNA variations. Analyses of the relevant fragments generated in RAPD profile allow not only to identify some of the molecular events implicated in the genomic instability but also to discover genes playing key roles in genetic evolution and gene mapping. RAPD markers will continue to be boon for genetic studies of those organisms where yet no sequence information or scanty information is available.

Landscape genetics of plants

Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.

Genetic characterization of natural populations of the medicinal plant Palicourea coriacea (Rubiaceae) with molecular markers

Palicourea coriacea (Rubiaceae) is a herbaceous, perennial species typical of the Cerrado; it is popularly known as "douradinha", because of its yellow flowers. It is utilized in popular medicine, mainly for the treatment of renal diseases. We used RAPD markers to evaluate the genetic structure of nine natural populations of P. coriacea, totaling 168 individuals, collected in the States of Goiás and Bahia. This species showed a high level of genetic diversity, with He values varying between 0.259 and 0.338, with an overall mean of 0.296. Analysis by AMOVA revealed that 23% of the total variability was between populations and 77% was within populations. The estimate of apparent gene flow (Nm) was 0.83. Analyses of the fixation index (f ) using a Bayesian approach yielded a mean value of 0.98, suggesting that this is an autogamous species. Analyses of genetic divergence and spatial pattern of the populations utilizing theta(B) and Phi(ST) matrices, pair to pair, revealed no correlation between geographic distance and genetic distance; the nine populations grouped randomly, without relation to their geographic origin. The hypothesis that geographically close populations should be genetically close was discarded based on the Mantel test; the correlation was 0.155 (P = 0.23). The degree of interpopulational differentiation was relatively high, which allows us to recommend a strategy of sampling for the ex situ conservation of genetic variability, utilizing a larger number of populations. For in situ conservation, we suggest preservation of a larger number of areas in the Cerrado, where this species naturally occurs.

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.

A review of techniques for spatial modeling in geographical, conservation and landscape genetics

Most evolutionary processes occur in a spatial context and several spatial analysis techniques have been employed in an exploratory context. However, the existence of autocorrelation can also perturb significance tests when data is analyzed using standard correlation and regression techniques on modeling genetic data as a function of explanatory variables. In this case, more complex models incorporating the effects of autocorrelation must be used. Here we review those models and compared their relative performances in a simple simulation, in which spatial patterns in allele frequencies were generated by a balance between random variation within populations and spatially-structured gene flow. Notwithstanding the somewhat idiosyncratic behavior of the techniques evaluated, it is clear that spatial autocorrelation affects Type I errors and that standard linear regression does not provide minimum variance estimators. Due to its flexibility, we stress that principal coordinate of neighbor matrices (PCNM) and related eigenvector mapping techniques seem to be the best approaches to spatial regression. In general, we hope that our review of commonly used spatial regression techniques in biology and ecology may aid population geneticists towards providing better explanations for population structures dealing with more complex regression problems throughout geographic space.