Climatic stability and contemporary human impacts affect the genetic diversity and conservation status of a tropical palm in the Atlantic Forest of Brazil

Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree

Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E. edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.

Juçara Fruit (Euterpe Edulis Martius) Valorization Combining Emergent Extraction Technologies and Aqueous Solutions of Alkanediols

Anthocyanins from juçara fruits were extracted by pressurized liquid extraction (PLE) or ultrasound-assisted extraction (UAE), using aqueous solutions of 1,2-alkanediols and glycerol ethers as biobased solvents. The PLE (100 bar, 13 min, 1 mL/min flow rate) in the optimal extraction conditions originated 23.1 mg_anthocyanins·g_{dry biomass}^-1. On the other hand, the UAE was 10 min long, and the optimal conditions using 1,2-propanediol were 42.6 wt%, 160 W, and pH 7.0, leading to 50 mg_anthocyanins·g_{dry biomass}^-1. Extractions at the UAE optimized conditions, with aqueous solutions of five different 1,2-alkanediols and three glycerol ethers were performed, and compared to water and ethanolic extracts. The biobased solvent solutions presented anthocyanin yields up to 33% higher than water, and were shown to be as efficient as ethanol/water, but generated extracts with higher antioxidant capacity. The anthocyanin-rich extract of juçara, obtained with 1,2-propanediol, was used in the production of a natural soap and incorporated into a cream, showing that the addition of the juçara extract resulted in an antioxidant capacity in both products.

Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest

The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.

Gene Flow and Genetic Structure Reveal Reduced Diversity between Generations of a Tropical Tree, Manilkara multifida Penn., in Atlantic Forest Fragments

The Atlantic Forest remnants in southern Bahia, Brazil, contain large tree species that have suffered disturbances in recent decades. Anthropogenic activities have led to a decrease in the population of many tree species and a loss of alleles that can maintain the evolutionary fitness of their populations. This study assessed patterns of genetic diversity, spatial genetic structure, and genetic structure among Manilkara multifida Penn. populations, comparing the genetic parameters of adult and juvenile trees. In particular, we collected leaves from adults and juveniles of M. multifida in two protected areas, the Veracel Station (EVC) and the Una Biological Reserve (UBR), located in threatened Atlantic Forest fragments. We observed a substantial decay in genetic variability between generations in both areas i.e., adults’ H_O values were higher (EVC = 0.720, UBR = 0.736) than juveniles’ (EVC = 0.463 and UBR = 0.560). Both juveniles and adults showed genetic structure between the two areas (θ = 0.017 for adults and θ = 0.109 for juveniles). Additionally, forest fragments indicated an unexpectedly short gene flow. Our results, therefore, highlight the pervasive effects of historical deforestation and other human disturbances on the genetic diversity of M. multifida populations within a key conservation region of the Atlantic Forest biodiversity hotspot.

Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species

BACKGROUND

Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated.

RESULTS

Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains.

CONCLUSIONS

The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.

Genetic diversity of North American vertebrates in protected areas

Protected areas play a crucial role in the conservation of biodiversity; however, it is unclear if these areas have an influence on genetic diversity. As a first step towards addressing this issue, we compare the genetic diversity inside and outside of protected areas. We tested the null hypothesis that there is no difference between genetic diversity inside compared to outside of protected areas in 44 vertebrate species. By automatically skimming the Global Biodiversity Information Facility (GBIF) and the National Center for Biotechnology Information (NCBI) GenBank we obtained genetic and geographical data to be repurposed and reanalysed. Novel pipelines were used to automate the process of assigning individuals to inside or outside of protected areas and then used to calculate different measures of intraspecific diversity. Forty-eight percent of examined species showed a significant difference in the amount of nucleotide diversity they contained inside compared to outside of protected areas, with similar numbers of species containing more or less genetic diversity inside compared to outside. Although our simulation testing suggests that this result is not an artefact of sampling, it is unclear what factors influence the relative amount of genetic diversity in protected areas across species.

The differential genetic signatures related to climatic landscapes for jaguars and pumas on a continental scale

Modern and paleoclimate changes may have altered species dynamics by shifting species' niche suitability over space and time. We analyze whether the current genetic structure and isolation of the two large American felids, jaguar (Panthera onca) and puma (Puma concolor), are mediated by changes in climatic suitability and connection routes over modern and paleoclimatic landscapes. We estimate species distribution under 5 climatic landscapes (modern, Holocene, last maximum glaciations [LMG], average suitability, and climatic instability) and correlate them with individuals' genetic isolation through causal modeling on a resemblance matrix. Both species exhibit genetic isolation patterns correlated with LMG climatic suitability, suggesting that these areas may have worked as "allele refuges." However, the jaguar showed higher vulnerability to climate changes, responding to modern climatic suitability and connection routes, whereas the puma showed a continuous and gradual transition of genetic variation. Despite differential responsiveness to climate change, both species are subjected to the climatic effects on genetic configuration, which may make them susceptible to future climatic changes, since these are progressing faster and with higher intensity than changes in the paleoclimate. Thus, the effects of climatic changes should be considered in the design of conservation strategies to ensure evolutionary and demographic processes mediated by gene flow for both species.

Genetic structure among morphotypes of the endangered Brazilian palm Euterpe edulis Mart (Arecaceae)

Euterpe edulis (Arecaceae) Mart has high ecological and economic importance providing food resources for more than 58 species of birds and 20 species of mammals, including humans. E. edulis is the second most exploited nontimber product from Brazilian Atlantic Forest. Due to overexploitation and destruction of habitats, E. edulis is threatened by extinction. Euterpe edulis populations have large morphological variations, with individuals having green, red, or yellow leaf sheath. However, no study has related phenotypic distinctions between populations and their levels of genetic structure. Thus, this study aimed to evaluate the diversity and genetic structure of different E. edulis morphotypes. We sampled 250 adult individuals in eight populations with the different morphotypes. Using 14 microsatellite markers, we access genetic diversity through population genetic parameters calculated in the GenAlex program and the diveRsity package in R. We used the Wilcoxon test to verify population bottlenecks and the genetic distance of Nei and Bayesian analysis for genetic clusters. The eight populations showed low allele richness, low observed heterozygosity, and high inbreeding values (f). In addition, six of the eight populations experienced genetic bottlenecks, which would partly explain the low genetic diversity in populations. Cluster analysis identified two clusters (K = 2), with green morphotype genetically distinguishing from yellow and red morphotypes. Thus, we show, for the first time, a strong genetic structure among E. edulis morphotypes even for geographically close populations.

Gene pool sharing and genetic bottleneck effects in subpopulations of Eschweilera ovata (Cambess.) Mart. ex Miers (Lecythidaceae) in the Atlantic Forest of southern Bahia, Brazil

Forest loss and fragmentation are the main threats to the maintenance of the Atlantic Forest, an important global biodiversity hotspot. Because of the current critical level of deforestation, ecological corridors are needed to facilitate species dispersion and gene flow among fragments. This study was conducted to investigate the genetic variability and gene pool sharing of Eschweilera ovata in five forest remnants in southern Bahia, Brazil using nuclear simple sequence repeat (nSSR) and plastid simple sequence repeat (cpSSR) microsatellite markers. cpSSR marker analysis revealed the domains of four haplotypes, showing that 80% of the individuals had only four maternal origins, reflecting a founder effect and/or genetic bottleneck. The results of cpSSR and nSSR analyses indicated moderate genetic diversity, particularly in conservation units with full protection, which showed the best parameters of all areas evaluated. Another indication of the susceptibility of these populations to forest loss and fragmentation was the strong genetic bottleneck observed. In contrast, genetic structure analyses (FST and discriminant analysis of principal components) revealed gene pool sharing between the subpopulations, which may reflect the historical gene flow that occurred before forest fragmentation.

Ecological niche modeling and a lack of phylogeographic structure in Vriesea incurvata suggest historically stable areas in the southern Atlantic Forest

PREMISE

Despite the efforts to understand the processes that shape neotropical biodiversity, the complexity of certain biomes, such as the Atlantic Forest (AF), prevents the generalization of patterns. Initially, ecological niche modeling (ENM), with phylogeographic studies, identified past stable areas in the central and northern portions of the AF, while the southern portion was thought to be highly fragmented. Here, we examined the phylogeography, historical patterns, genetic diversity, and population structure of Vriesea incurvata, an endemic species of the southern portion of the AF.

METHODS

We evaluated 149 individuals using two plastid DNA regions (cpDNA) and 13 nuclear microsatellite markers (nuSSRs) to access the historical patterns, genetic diversity, and structure of V. incurvata populations. We also conducted historical demography and ENM analyses.

RESULTS

We found moderate to high genetic diversity and low population structure for both genomes. The cpDNA network revealed high haplotype sharing. The ENM suggested no drastic changes in suitable areas for V. incurvata occurrence, corroborating the finding of no phylogeographic structure.

CONCLUSIONS

Contrary to some studies, our results indicate that the southern AF was a historically stable climate region for V. incurvata occupation after southward colonization by the species. Past climatic changes probably did not cause structuring among its populations.

Estimating seed and pollen dispersal kernels from genetic data demonstrates a high pollen dispersal capacity for an endangered palm species

PREMISE OF THE STUDY

Seed and pollen dispersal are key processes shaping plant population dynamics and maintaining genetic diversity. The essence of these processes is the movement of propagules from a parental tree to the site of propagule establishment. The estimation of plant dispersal kernels has remained challenging due to the difficulty of making direct observations. We estimated the dispersal capacity of the endangered palm Euterpe edulis, whose seeds are dispersed by vertebrates and pollen by insects.

METHODS

We used a hierarchical Bayesian model with genetic data from reproductive plants, juveniles, and embryos to estimate dispersal kernels. Our analyses account for genotyping error and uncertainty in parental assignment.

KEY RESULTS

We found that seeds were dispersed at most a few hundred meters, but pollen was dispersed up to several kilometers. We hypothesize that this long-distance pollen dispersal is generated mainly by euglossine bees, whereas the main dispersal vectors for short-distance seed dispersal are thrushes. The long-distance dispersal of pollen suggests a high level of gene flow that should maintain genetic diversity of E. edulis. Despite the relation between long-distance dispersal and genetic diversity, we observed low genetic diversity and inbreeding within the local population, which are probably due to restricted gene flow due to the low density of this population and its aggregated spatial distribution.

CONCLUSIONS

We conclude that if conservation actions are able to restore the population density of E. edulis, the recovery of its genetic diversity will be facilitated because of its high dispersal capacity, especially with regard to pollen.

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. Mauritia flexuosa presents significant genetic differentiation between the Amazonian and Cerrado biomes and among different river basins. Amazonian lineages are ancient compared to lineages from the Cerrado, a pattern corroborated using the fossil pollen record, where the species was absent from the Cerrado during the cold and dry periods of the last glacial cycles, then returned during the wet, interglacial phases. Coalescent simulations show that the pattern of observed genetic diversity for M. flexuosa is most likely due to a range retraction during the Last Glacial Maximum, leading to multiple refugia and resulting in high differentiation between Amazonian and Cerrado biomes. Isolation-by-distance and by-environment also shaped the distribution and evolutionary success of M. flexuosa. Our study provides new insights into the historical factors that affected geographical distribution and structure genetic diversity, contributing to long-term evolutionary success.

Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high-latitude B. huntii habitats exhibit low ENS when compared to low-latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low-latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.