Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae)

One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.

Persisting while changing over time: modelling the historical biogeographic of cave crickets (Orthoptera, Grylloidea) in Neotropics

Using species distribution modelling (SDMs) techniques, we predicted the biogeographic history of crickets commonly found in Neotropical caves as a way to detect potential long-term environmental refuges in South America. Our models were built based on a thorough investigation of existing database regarding the genus Endecous Saussure, 1878 (Ensifera: Phalangopsidae) occurrences. The predictions of their distribution were obtained for two paleoclimate scenarios (LGM — 21 ka and Mid-Holocene — 6 ka), the current climate scenario (0 ka) and one future global warming climate scenario (RCP8.5, 2080–2100). Our findings suggest that in the past, the potential distribution of the crickets was wider, with potential forest corridors connecting different karst areas with caves within their occupancy area. The future prediction indicates a drastic reduction in their spatial distribution with an increased potential for isolation in subterranean ecosystems. Atlantic humid forest patches and caves represent the main environmental refuges for these crickets. Considering the ongoing impacts on surface environments and future climate change, the conservation of caves and karst landscapes has become one of the main strategies for the maintenance of these crickets and all the correlated subterranean communities.

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. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.

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. 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).

The Program for Biodiversity Research in Brazil: The role of regional networks for biodiversity knowledge, dissemination, and conservation

The Program for Biodiversity Research (PPBio) is an innovative program designed to integrate all biodiversity research stakeholders. Operating since 2004, it has installed long-term ecological research sites throughout Brazil and its logic has been applied in some other southern-hemisphere countries. The program supports all aspects of research necessary to understand biodiversity and the processes that affect it. There are presently 161 sampling sites (see some of them at Supplementary Appendix), most of which use a standardized methodology that allows comparisons across biomes and through time. To date, there are about 1200 publications associated with PPBio that cover topics ranging from natural history to genetics and species distributions. Most of the field data and metadata are available through PPBio web sites or DataONE. Metadata is available for researchers that intend to explore the different faces of Brazilian biodiversity spatio-temporal variation, as well as for managers intending to improve conservation strategies. The Program also fostered, directly and indirectly, local technical capacity building, and supported the training of hundreds of undergraduate and graduate students. The main challenge is maintaining the long-term funding necessary to understand biodiversity patterns and processes under pressure from global environmental changes.

Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan

The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For Jacaranda copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (>59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for Handroanthus impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.

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. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

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. Thus, H. speciosa is a good biological model for learning about evolution of phenotypic plasticity under genetic and ecological effects, and predicting their responses to changing environmental conditions.

Methods

We sampled 28 populations (777 individuals) of Monachino's four varieties of H. speciosa and used seven microsatellite loci to genotype them.

Key Results

Bayesian clustering showed five distinct genetic groups (K = 5) with high admixture among Monachino's varieties, mainly among populations in the central area of the species geographical range. Genetic differentiation among Monachino's varieties was lower than the genetic differentiation among populations within varieties, with higher within-population inbreeding. A high historical connectivity among populations of the central Cerrado shown by coalescent analyses may explain the high admixture among varieties. In addition, areas of higher climatic suitability also presented higher genetic diversity in such a way that the wide historical refugium across central Brazil might have promoted the long-term connectivity among populations. Yet, FST was significantly related to geographic distances, but not to environmental distances, and coalescent analyses and ENM predicted a demographical scenario of quasi-stability through time.

Conclusions

Our findings show that demographical history and isolation by distance, but not isolation by environment, drove genetic differentiation of populations. Finally, the genetic clusters do not support the two recently recognized botanical varieties of H. speciosa, but partially support Monachino's classification at least for the four sampled varieties, similar to morphological variation.