Biology subjects

Soares, L. S.

Publications and source records attributed to Soares, L. S..

3 recordsLinked to original sources

bioRxiv2026

The Speciation Continuum in Bloom: Incomplete Lineage Sorting, Gene Flow, and Reticulate Evolution in Rapidly Diverging Plant Lineages

The remarkable diversity of life on Earth results from evolutionary processes functioning across different spatial and temporal scales. Species diversification occurs through various mechanisms and at widely varying rates, but identifying the conditions that trigger bursts of diversification over short timescales remains a central challenge in evolutionary biology. This difficulty is more pronounced when incomplete lineage sorting (ILS), hybridization, and ongoing gene flow obscure evolutionary relationships and complicate species delimitation. In this study, we investigated the evolutionary history and species boundaries within a group of recently diverged Petunia lineages shaped by pervasive gene flow. We integrated phylogenomic, population genetic, and species delimitation approaches to reconstruct lineage relationships and assess whether these lineages represent distinct species or stages along a speciation continuum. By applying methods that account for both ILS and gene flow, we revealed that most lineages are not fully independent evolutionary units but rather occupy intermediate positions along this continuum. Gene flow played a crucial role during diversification, blurring species boundaries and generating reticulate evolutionary patterns. Our findings demonstrate that traditional phylogenetic trees may oversimplify relationships in such systems, while phylogenetic networks offer a more accurate representation of evolutionary history. Comprehensive and integrative analyses, such as those employed here, are essential for capturing these complex dynamics. Ultimately, only four lineages could be confidently recognized as distinct species, whereas the remaining represent cases of ongoing divergence. These results emphasize the need to refine species delimitation frameworks for systems characterized by recent divergence and extensive reticulation.

evolutionary biology↗

bioRxiv2026

Reference genome choice impacts SNP recovery but not evolutionary inference in young species

Reduced-representation sequencing approaches such as RAD-seq are widely used in population genomics and phylogenetics, particularly for non-model organisms. However, bioinformatics choices during data processing can strongly influence downstream analyses. One key but underexplored factor is the reference genome used for read alignment and SNP discovery. Here, we evaluate the effects of reference genome choice on RAD-seq analyses using multiple datasets spanning recent radiations in Petunia and Calibrachoa, and reference genomes that differ in phylogenetic relatedness. When using congeneric reference genomes, we observed highly consistent mapping rates, SNP recovery, and downstream population genomic patterns. In contrast, mapping to more distantly related genomes resulted in lower mapping rates and stronger effects on summary statistics. Despite these quantitative reductions, broader patterns of genetic structure and diversity, as well as evolutionary relationships, remained largely congruent across reference genomes. Overall, our results indicate that reference genome choice matters most when genomes are distantly related or when analyses target fine-scale genomic signals. For recent radiations with largely conserved genome structure, closely related reference genomes yield comparable SNP datasets and lead to the same biological conclusions regarding population structure and phylogenetic relationships. These findings provide practical guidance for RAD-seq studies in non-model systems, showing that congeneric reference genomes are sufficient for robust population and phylogenetic inference, and that more distantly related genomes can remain informative when no close reference is available.

bioinformatics↗

bioRxiv2025

First record of the invasive red lionfish (Pterois volitans) in the Parcel de Manuel Luis Marine State Park, Brazilian Equatorial Margin

The red lionfish (Pterois volitans), native to the Indo-Pacific, is recognized as one of the most harmful invasive species in the marine ecosystems of the Western Atlantic. Since its accidental introduction, the species has rapidly expanded across the Caribbean, Gulf of Mexico, and Brazilian coast, reaching marine protected areas with high ecological value. This study documents the first confirmed occurrence of P. volitans in the reef environment of the Parcel de Manuel Luis Marine State Park, located on the Brazilian Equatorial Margin. The record was based on underwater footage collected during a scientific expedition in June 2025. Two individuals were observed near the wreck of the ship Ana Cristina at a depth of five meters. The specimens exhibited typical morphological features and behavioral patterns associated with foraging and habitat exploration. Physicochemical variables measured at the site confirmed stable tropical marine conditions, including high salinity and temperature, compatible with the ecological tolerance of the species. Additional measurements at eight surrounding stations revealed minimal stratification, reinforcing the environmental suitability for the species. Statistical analysis detected no significant differences in salinity or dissolved oxygen between surface and bottom waters, and a slight variation in temperature. The presence of P. volitans in a conservation unit raises concern about its potential expansion into other reef and coastal environments. Given its high reproductive capacity, absence of natural predators, and ecological plasticity, the species poses a serious threat to native biodiversity and trophic dynamics. The results highlight the urgency of establishing systematic monitoring programs and early-response strategies for invasive species in Brazilian reef systems.

ecology↗