Forest genetic monitoring: an overview of concepts and definitions

Population genomics of the neotropical palm Copernicia prunifera (Miller) H. E. Moore: Implications for conservation

Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.

Evaluation of the Current State of Preservation of Vaccinio uliginosi-Pinetum Kleist 1929 in Eastern Poland

The study assessed the genetic variability and the possibility of Scots pine regeneration in marshy forest. The genetic parameters were determined using the ISSR technique. The relationships between herbaceous plants, pine regeneration density, and their genetic variability were determined. On average, per 1 m2, three regenerated pine seedlings with a mean height of 27.56 cm were inventoried. Based on genetic analysis, it was found that the proportion of polymorphic loci was 60.46%. The average number of alleles at the locus was 1.345, and the effective number of alleles at the locus was 1.345. The values of the expected heterozygosity and Shannon index were 0.200 and 0.301, respectively. No species competing with pine regeneration were found. A significantly negative correlation of the number of pine regenerations with the area covered with an herbaceous plant layer and tree canopy closure was found. There was a relation to the insufficient amount of light under the stand canopy. In conclusion, the condition of marshy forests was satisfactory and the genetic variability of pine seedlings was moderate. The vegetation was typical for this habitat, but the significant presence of dry habitat species could indicate the beginning of habitat drainage. It seemed that the amount of light under the stand canopy was insufficient. Nevertheless, more light probably reached the inside of the stand in the terminal stage, as a result of upper layer tree separation, which in turn may facilitate the effective regeneration of Scots pine in this habitat.

Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies

The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.

Why European biodiversity reporting is not reliable

The Convention on Biological Diversity (CBD) aims to end the loss of biodiversity, which is one of the greatest ecological challenges of our time. The lack of success in biodiversity policy implementation is partly related to gaps in biodiversity monitoring. Our overall objective is to contribute to the preparation of the upcoming post 2020 period by a review of biodiversity indicator choices in European CBD reports and hence in national monitoring systems. Negative binary generalized models and poisson generalized linear models prove that through free indicator choice in CBD reporting, countries do not choose biodiversity indicators according to their national geographic and socioeconomic characteristics. Moreover, species and ecosystem diversity indicators were chosen with a disproportionate frequency compared to that of genetic diversity indicators. Consequently, trends derived from national CBD reports and monitoring systems in Europe are not reliable, which should be an alarming signal concerning biodiversity policy implementation. Finally, a flow chart to revise national biodiversity monitoring systems is proposed.

Integrated conservation of important plant taxa through the improvement of the original plant micro-reserve (PMR) approach: The intensive PMR monitoring case of Ophrys kotschyi

Developing a monitoring system and a conservation strategy against the negative impact of global change on threatened plant species, is nowadays the challenge for conservation experts. The Plant Micro-Reserve (PMR) approach became a highly effective approach in protecting plant species, since mild active management of vegetation plots and protection of plant populations takes place. The PMR has greatly evolved since its initial concept of managing a large network of PMRs, to having fewer protected areas subject to intensive scientific monitoring (e.g. Intensive Monitoring PMR; IM-PMR). This study further improved the IM-PMR approach by focusing on the threatened plant species of Ophrys kotschyi in Cyprus. The proposed IM-PMR enhances the available knowledge on the biology, physiology and ecology of the targeted plant species, through implementing an intensive monitoring system and assessing its genetic diversity. Within the framework of IM-PMR, the population size of O. kotschyi recorded statistically significant differentiation during the monitoring period, most likely due to the vegetative dormancy of the species. The subpopulation size and dormancy in O. kotschyi was correlated with precipitation and air temperature for specific months. In addition, the different local climatic conditions and the species dormancy between years seem to influence the flowers production among individuals, in the four monitoring years. Nevertheless, the low natural fecundity compared to the artificially pollinated plants and the absent correlation with any of the climatic parameters, might be closely related to the lack of pollinators at this site. The genetic diversity (H_T = 0.456) is higher compared to other endemic and short-lived perennial species, while the genetic differentiation among the subpopulations of O. kotschyi showed significant substructure (F_ST^FIS=0.5 = 0.097*). The subpopulation within IM-PMR showed relatively lower genetic diversity among the largest subpopulations of O. kotschyi, and the highest percentage of linked loci. Such observations support the non-random association of different loci in this subpopulation, and the ineffective pollen flow within this single subpopulation. The improvement of the original PMR approach in the current IM-PMR proposal denotes that different ecological aspects are taken into account towards gaining a holistic knowledge on a target species. The IM-PMR approach as implemented for O. kotschyi, could lead to the development of an integrated conservation approach for rare, threatened, or endangered species.

Next-generation metrics for monitoring genetic erosion within populations of conservation concern

Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.