Biology subjects

Riina, R.

Publications and source records attributed to Riina, R..

4 recordsLinked to original sources

bioRxiv2025

The conquest and diversification of leafy spurges across the Holarctic and beyond: biogeography and evolution of life-history of Euphorbia subgenus Esula

Euphorbia subgenus Esula is one of four main lineages within the megadiverse angiosperm genus Euphorbia. It comprises 490 species, including herbs, shrubs, dendroid shrubs, and succulents. The subgenus is a northern temperate lineage, most diverse in the Irano-Turanian and Mediterranean regions. We assembled the largest taxon sampling of subg. Esula to date (321 spp.), using DNA sequences from nuclear ITS and plastid ndhF regions, and updated previous phylogenetic analyses and sectional classification of the group. We used Bayesian methods to estimate divergence times and reconstruct ancestral ranges, characterising the tempo and mode of lineage diversification that shaped the present distribution and extant diversity of the subgenus. We tested whether changes in life-history (annual vs. perennial) played a role in the diversification and current elevational distribution of subg. Esula. Our results show that subg. Esula diverged from its sister clade in the Mid-Eocene and started to diversify in the Late Eocene. The Western Palearctic was inferred to be the ancestral area of the subgenus, where the first diversification events began 41 Mya. Expansion to other continents was dated as occurring in the last 10 million years. This coincided with an increase in the diversification rate and with clade-specific rate shifts coupled with changes from annual to perennial life-histories. We found a positive correlation between perenniality and high elevations. These results support that the recent rapid diversification of subg. Esula could be associated with an evolutionary shift to perenniality, allowing colonisation of montane habitats and global range expansion beyond the Western Palearctic.

evolutionary biology↗

bioRxiv2025

Integrative taxonomy using traits and genomic data for Species Delimitation with Deep learning

Recognizing species boundaries in complex speciation scenarios, including those involving gene flow and demographic fluctuations, remains a challenge, particularly given the diversity of existing species concepts. Promising recent approaches adopt an integrative taxonomy that combines multiple sources of evidence (e.g., genetic, morphology, geographic distributions), reflecting different properties associated with the dynamics of the speciation continuum. The use of statistical inference methods for model comparison, such as approximate Bayesian computation, approximate likelihood approaches, and machine learning, has improved the better assessment of species boundaries in such contexts. However, most existing approaches involve analyzing genetic and phenotypic/geographical information separately, followed by visual/qualitative comparison. Methods that integrate genetic information with other sources of evidence remain limited to simple evolutionary models and are typically unable to analyze more than a few hundred loci across a maximum of a few tens of samples. Here, we present a deep learning approach (DeepID) that combines two convolutional neural networks to integrate genomic data (thousands of loci or single nucleotide polymorphisms, SNPs) and trait information into a unified framework. Using both simulated and empirical data sets, we evaluate the power and accuracy of this approach for discriminating among competing divergence speciation scenarios (with minimal ongoing gene flow) across a varying number of SNPs and traits, as well as different levels of missing data. Analyses based on genomic or trait data alone yielded a slight lower accuracy, whereas integrating genomic and trait data resulted in improved performance. When we violated the speciation model by including extensive migration, approaches incorporating trait data were less affected than those relying solely on genomic information. Together, these results suggest that combining genomic and trait data may capture complementary signals associated with different stages of the speciation process. Moreover, our approach successfully recovered the expected delimitation scenarios in empirical data sets from a plant (Euphorbia balsamifera) and a fish (Lepomis megalotis) species complex. We argue that our method is a flexible and promising approach, allowing for complex scenario comparison and the use of multiple types of data. Combining genomic and trait data likely captures complementary signals associated with different stages of the speciation process, reflecting the fact that speciation is a continuum in which genetic and phenotypic divergence may proceed at different rates.

evolutionary biology↗

bioRxiv2023

Phylogenetics and phylogeography of Euphorbia canariensis reveal an extreme Canarian-Asian disjunction and limited inter-island colonization

Euphorbia canariensis is an iconic endemic species of the Canary Islands and one of the most characteristic species of lowland xerophytic communities known, in Spanish, as cardonal-tabaibal. This species is widely distributed in the archipelago, which contrasts with the theoretically low dispersal abilities suggested by its unspecialized diasporas. Furthermore, the phylogenetic relationships of this species are unclear, although it is thought to be related to the Indian E. epiphylloides and not to other cactus-like Euphorbia of the Canary Islands (E. handiensis) and Africa. Here we aimed to reconstruct the evolutionary history of E. canariensis at two levels: (i) a phylogenetic approach aimed at unravelling relationships of this species and large-scale biogeographic patterns, and (ii) a phylogeographic approach focused on the history of colonization between islands of the Canarian archipelago in relation to habitat availability for this species through time. Based on previous phylogenetic studies of Euphorbia, we sequenced the ITS region for E. canariensis and several potentially related species to build a phylogenetic framework. We also sequenced two cpDNA regions for 92 individuals from 29 populations of E. canariensis representing its distribution range. We estimated the number of inter-island colonization events using PAICE, a recently developed method that includes a sampling effort correction. Additionally, we used species distribution modelling (SDM) to project current habitat availability for E. canariensis to past periods. Phylogenetic results supported the Canarian E. canariensis as closely related to the Southeast Asian E. epiphylloides and E. sessiliflora. In the Canarian archipelago, E. canariensis displayed a surprising west-to-east colonization pattern. The estimated number of inter-island colonization events was c. 20 - 50, and SDM suggested an increase in habitat availability in recent times. In summary, in this study we confirmed an extreme biogeographic disjunction between Macaronesia and Southeast Asia, described only for a small number of plant species, and estimated relatively low dispersal capabilities for E. canariensis, with a west-to-east colonization pattern in the Canary Islands. HighlightsO_LIThe Canarian Euphorbia canariensis is sister to Southeast Asian species. C_LIO_LIThis lineage shows one of the widest disjunctions affecting Macaronesian plants. C_LIO_LIThe lack of intermediate relatives could be the result of extinction events. C_LIO_LIE. canariensis displays low colonization ability in the Canarian archipelago. C_LI

evolutionary biology↗

bioRxiv2021

The origin and drivers of Neotropical plant and tetrapod diversification

The origins and evolution of the outstanding Neotropical biodiversity are still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we evaluate four evolutionary scenarios assuming different diversification trajectories and drivers of Neotropical diversification, and assess their variation across Neotropical regions and taxa. Our analysis of 150 phylogenies (12,512 species) of seed plants and tetrapods reveals that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity also account for 21% and 9% of Neotropical diversity, respectively. We identify five biogeographic areas that represent distinctive units of long-term Neotropical evolution (Pan-Amazonia, Dry Diagonal, Bahama-Antilles, Galapagos, and an elsewhere region) and find that diversity dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ substantially across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with climate change, with potential implications for future adaptation and ecosystem resilience.

evolutionary biology↗