Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil.

There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic diversity distribution and population structure of Anacardium occidentale L. (cashew) from the Brazilian Cerrado, one of the most economically important tropical crops in the world.

Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands.

Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands.

Community voices: sowing, germinating, flourishing as strategies to support inclusion in STEM.

Understanding gaps in academic representation while considering the intersectionality concept is paramount to promoting real progress towards a more inclusive STEM. Here we discuss ways in which STEM careers can be sown and germinated so that inclusivity can flourish.

Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species.

The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF.

RNA-Seq reveals different responses to drought in Neotropical trees from savannas and seasonally dry forests.

Background: Water is one of the main limiting factors for plant growth and crop productivity. Plants constantly monitor water availability and can rapidly adjust their metabolism by altering gene expression. This leads to phenotypic plasticity, which aids rapid adaptation to climate changes.

In situ radiation explains the frequency of dioecious palms on islands.

Background And Aims: Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type.

Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree.

Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree . We sampled adults and juveniles in 10 savanna remnants within five landscapes.

Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm.

Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events.

Higher evolutionary rates in life-history traits in insular than in mainland palms.

Isolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms.

Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae.

Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests.

Multi-Scale Landscape Influences on Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree.

Changes in landscape structure can affect essential population ecological features, such as dispersal and recruitment, and thus genetic processes. Here, we analyze the effects of landscape metrics on adaptive quantitative traits variation, evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree . Using a multi-scale approach, we sampled five landscapes with two sites of savanna in each.

Megafauna Seed Dispersal in the Neotropics: A Meta-Analysis Shows No Genetic Signal of Loss of Long-Distance Seed Dispersal.

Restricted gene flow may lead to the loss of genetic diversity and higher genetic differentiation among populations, but the genetic consequences of megafauna extinction for plant populations still remain to be assessed. We performed a phylogenetic-independent meta-analysis across 102 Neotropical plants to test the hypothesis that plant species with megafaunal seed dispersal syndrome have a lower genetic diversity and a higher genetic differentiation than those without it. We classified as megafauna-dependent plant species those that potentially relied only on megafauna to seed dispersal, and as megafauna-independent those that relied on megafauna and other seed dispersers.

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms.

Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests.

A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree.

The role of natural selection in shaping patterns of diversity is still poorly understood in the Neotropics. We carried out the first genome-wide population genomics study in a Neotropical tree, Handroanthus impetiginosus (Bignoniaceae), sampling 75,838 SNPs by sequence capture in 128 individuals across 13 populations. We found evidences for local adaptation using Bayesian correlations of allele frequency and environmental variables (32 loci in 27 genes) complemented by an analysis of selective sweeps and genetic hitchhiking events using SweepFinder2 (81 loci in 47 genes).

Diversification of the widespread neotropical frog Physalaemus cuvieri in response to Neogene-Quaternary geological events and climate dynamics.

Here we reconstructed the demographical history and the dispersal dynamics of Physalemus cuvieri through the Neogene-Quaternary periods by coupling DNA regions with different mutation rates, ecological niche modelling, reconstruction of spatio-temporal lineage dispersal and coalescent simulations. Still, to test alternative diversification scenarios we used approximate Bayesian computation. Molecular phylogenetic analysis recovered four deep and strongly supported clades, which we interpret as population lineages.

Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.

Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the species genome. This system identifies nearly 200,000 SNPs located inside or in close proximity to almost 14,000 annotated protein-coding genes, generating quality genotypic data in populations spanning wide geographic distances across the species native range.

Unravelling the genetic differentiation among varieties of the Neotropical savanna tree Hancornia speciosa Gomes.

Background And Aims: Spatial distribution of species genetic diversity is often driven by geographical distance (isolation by distance) or environmental conditions (isolation by environment), especially under climate change scenarios such as Quaternary glaciations. Here, we used coalescent analyses coupled with ecological niche modelling (ENM), spatially explicit quantile regression analyses and the multiple matrix regression with randomization (MMRR) approach to unravel the patterns of genetic differentiation in the widely distributed Neotropical savanna tree, Hancornia speciosa (Apocynaceae). Due to its high morphological differentiation, the species was originally classified into six botanical varieties by Monachino, and has recently been recognized as only two varieties by Flora do Brasil 2020.

The road to evolutionary success: insights from the demographic history of an Amazonian palm.

Evolutionary success, as demonstrated by high abundance and a wide geographical range, is related to genetic variation and historical demography. Here we assess how climatic change during the Quaternary influenced the demography and distribution of the Neotropical swamp palm Mauritia flexuosa. Using microsatellite loci and coalescent analyses we examined how demographical dynamics affected genetic diversity, effective population size and connectivity through time and space.

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree.

Background: Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica.

First description and evaluation of SNPs in the ADH and ALDH genes in a population of alcoholics in Central-West Brazil.

Worldwide, different studies have reported an association of alcohol-use disorder (AUD) with different types of Single Nucleotide Polymorphisms (SNPs) in the genes for aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH). In Brazil, there is little information about the occurrence of these SNPs in the AUD population and an absence of studies characterizing the population in the Central-West Region of Brazil. Actually, in Brazil, there are more than 4 million people with AUD.

Correction: Pollination Mode and Mating System Explain Patterns in Genetic Differentiation in Neotropical Plants.

[This corrects the article DOI: 10.1371/journal.pone.

Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters.

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability.