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Local extinctions have cascading effects on ecosystem functions, yet little is known about the potential for the rapid evolutionary change of species in human-modified scenarios. We show that the functional extinction of large-gape seed dispersers in the Brazilian Atlantic forest is associated with the consistent reduction of the seed size of a keystone palm species. Among 22 palm populations, areas deprived of large avian frugivores for several decades present smaller seeds than nondefaunated forests, with negative consequences for palm regeneration. Coalescence and phenotypic selection models indicate that seed size reduction most likely occurred within the past 100 years, associated with human-driven fragmentation. The fast-paced defaunation of large vertebrates is most likely causing unprecedented changes in the evolutionary trajectories and community composition of tropical forests.

Aim Future climate changes may affect species distribution and their genetic diversity, hampering species adaptation to a new climate or tracking the suitable conditions. Amphibians have high sensitivity to environmental degradation and changes in temperature and humidity. Thus, the expected climatic changes by the end‐of‐century (EOC 2100) may cause local or complete extinction of some species. Here, we address the effects of climate change on genetic and phylogeographical diversity, together with the geographical distribution of the South American treefrog Scinax squalirostris Lutz, 1925. Furthermore, we assess how protected areas will conserve its genetic variation. Location South America. Methods We combined Ecological Niche Modelling and genetic simulations to predict the effects of climate change on the geographical distribution, genetic diversity, structure and phylogeographical diversity of Scinax squalirostris, using two scenarios of CO2 emission. We also performed a spatial analysis to investigate the effectiveness of the current Protected Areas (PAs) to preserve the species’ genetic and phylogeographical diversity. Results Scinax squalirostris' geographical range will potentially increase in the future due to the expansion of suitable areas towards its southern distribution, despite the shrinking of suitable areas in the northern part of its current distribution. Besides the shifts in suitable areas, our findings point to a genetic homogenization across the geographical range of S. squalirostris due to the displacement and loss of genetic ancestry clusters. Although existing PAs are conserving the current genetic diversity, they conserve less phylogeographical diversity than expected by chance. Scinax squalirostris may shift its distribution into areas with lower number of PAs, compromising its future conservation. Main conclusions Climate change will potentially increase S. squalirostris range size, however, not towards regions where most of the current established PAs are located, hence driving to homogenization and loss of genetic diversity, and leading to a gap of conservation within PAs.

We studied genetic diversity and differentiation patterns in Neotropical plants to address effects of life history traits (LHT) and ecological attributes based on an exhaustive literature survey. We used generalized linear mixed models (GLMMs) to test the effects as fixed and random factors of growth form, pollination and dispersal modes, mating and breeding systems, geographical range and habitat on patterns of genetic diversity (HS, HeS, π and h), inbreeding coefficient (FIS), allelic richness (AR) and differentiation among populations (FST) for both nuclear and chloroplast genomes. In addition, we used phylogenetic generalized least squares (pGLS) to account for phylogenetic independence on predictor variables and verify the robustness of the results from significant GLMMs. In general, GLMM revealed more significant relationships among LHTs and genetic patterns than pGLS. After accounting for phylogenetic independence (i.e., using pGLS), FST for nuclear microsatellites was significantly related to pollination mode, mating system and habitat. Plants specifically with outcrossing mating system had lower FST. Moreover, AR was significantly related to pollination mode and geographical range and HeS for nuclear dominant markers was significantly related to habitat. Our findings showed that different results might be retrieved when phylogenetic non-independence is taken into account and that LHTs and ecological attributes affect substantially the genetic pattern in Neotropical plants, hence may drive key evolutionary processes in plants.

Studies based on contemporary plant occurrences and pollen fossil records have proposed that the current disjunct distribution of seasonally dry tropical forests (SDTFs) across South America is the result of fragmentation of a formerly widespread and continuously distributed dry forest during the arid climatic conditions associated with the Last Glacial Maximum (LGM), which is known as the modern-day dry forest refugia hypothesis. We studied the demographic history of Tabebuia rosealba (Bignoniaceae) to understand the disjunct geographic distribution of South American SDTFs based on statistical phylogeography and ecological niche modeling (ENM). We specifically tested the dry forest refugia hypothesis; i.e., if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the LGM. We sampled 235 individuals across 18 populations in Central Brazil and analyzed the polymorphisms at chloroplast (trnS-trnG, psbA-trnH and ycf6-trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. We performed coalescence simulations of alternative hypotheses under demographic expectations from two a priori biogeographic hypotheses (1. the Pleistocene Arc hypothesis and, 2. a range shift to Amazon Basin) and other two demographic expectances predicted by ENMs (3. expansion throughout the Neotropical South America, including Amazon Basin, and 4. retraction during the LGM). Phylogenetic analyses based on median-joining network showed haplotype sharing among populations with evidence of incomplete lineage sorting. Coalescent analyses showed smaller effective population sizes for T. roseoalba during the LGM compared to the present-day. Simulations and ENM also showed that its current spatial pattern of genetic diversity is most likely due to a scenario of range retraction during the LGM instead of the fragmentation from a once extensive and largely contiguous SDTF across South America, not supporting the South American dry forest refugia hypothesis.

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.

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. Here, we address phenotypic plasticity under drought stress by analyzing differentially expressed genes (DEG) in four phylogenetically related neotropical Bignoniaceae tree species: two from savanna, Handroanthus ochraceus and Tabebuia aurea, and two from seasonally dry tropical forests (SDTF), Handroanthus impetiginosus and Handroanthus serratifolius. To the best of our knowledge, this is the first report of an RNA-Seq study comparing tree species from seasonally dry tropical forest and savanna ecosystems. Results Using a completely randomized block design with 4 species × 2 treatments (drought and wet) × 3 blocks (24 plants) and an RNA-seq approach, we detected a higher number of DEGs between treatments for the SDTF species H. serratifolius (3153 up-regulated and 2821 down-regulated under drought) and H. impetiginosus (332 and 207), than for the savanna species. H. ochraceus showed the lowest number of DEGs, with only five up and nine down-regulated genes, while T. aurea exhibited 242 up- and 96 down-regulated genes. The number of shared DEGs among species was not related to habitat of origin or phylogenetic relationship, since both T. aurea and H impetiginosus shared a similar number of DEGs with H. serratifolius . All four species shared a low number of enriched gene ontology (GO) terms and, in general, exhibited different mechanisms of response to water deficit. We also found 175 down-regulated and 255 up-regulated transcription factors from several families, indicating the importance of these master regulators in drought response. Conclusion Our findings show that phylogenetically related species may respond differently at gene expression level to drought stress. Savanna species seem to be less responsive to drought at the transcriptional level, likely due to morphological and anatomical adaptations to seasonal drought. The species with the largest geographic range and widest edaphic-climatic niche, H. serratifolius , was the most responsive, exhibiting the highest number of DEG and up- and down-regulated transcription factors (TF).

[This corrects the article DOI: 10.1371/journal.pone.0158660.].

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. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.

Biodiversity can be quantified by taxonomic, phylogenetic, and functional diversity. Current evidence points to a lack of congruence between the spatial distribution of these facets due to evolutionary and ecological constraints. A lack of congruence is especially evident between phylogenetic and taxonomic diversity since the name and number of species are an artificial, yet commonly used, way to measure biodiversity. Here we hypothesize that due to evolutionary constraints that link phylogenetic and functional diversity, areas with higher phylogenetic and functional diversity will be spatially congruent in Neotropical cocosoid palms, but neither will be congruent with areas of high taxonomic diversity. Also, we hypothesize that any congruent pattern differs between rainforests and seasonally dry forests, since these palms recently colonized and diversified in seasonally dry ecosystems. We use ecological niche modeling, a phylogenetic tree and a trait database to test the spatial congruence of the three facets of biodiversity. Taxonomic and phylogenetic diversity were negatively correlated. Phylogenetic and functional diversity were positively correlated, even though their spatial congruence was lower than expected at random. Taken together, our results suggest that studies focusing solely on large-scale patterns of taxonomic diversity are missing a wealth of information on diversification potential and ecosystem functioning.

1. In many species, density-dependent processes regulate population size through size- and neighbourhood-dependent mortality. 2. If a kin structure exists in a particular population, mortality may be spatially clustered due to enhanced competition among relatives. 3. Demography, kin structure and genetic diversity, based on 10 microsatellite loci, of a local population of the Neotropical tree Caryocar brasiliense were studied for 23 years. Overall population growth was static (λ = 1.0) during this time, but some time intervals showed negative growth. 4. Mortality was spatially clustered and negatively correlated with spatial distance among pairs of individuals at distances lower than c. 13 m. Probability of death was related to individual genotypes, and seedlings and juveniles with lower proportion of heterozygous loci had the highest probability of mortality. 5. Kinship was significantly related to spatial distance among pairs of individuals at distance lower than 10 m and kinship structure did not change along the life stages, but the inbreeding coefficient was not significantly different from zero in adults. 6. Synthesis. We hypothesize that genetic clustering in C. brasiliense dissipates over time due to more intense competition among relatives. Thus, the kin structure in C. brasiliense is highly important in determining mortality patterns, driving the spatial pattern in plant recruitment.