Biology subjects

Sanmartin, I.

Publications and source records attributed to Sanmartin, I..

7 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

On the utility of Deep Learning for model classification and parameter estimation on complex diversification scenarios.

Birth-Death models applied to dated phylogenies are a useful tool to study past diversification dynamics. Parameters in these stochastic models are typically inferred using likelihood-based methods such as Maximum Likelihood Estimation (MLE) or Bayesian Inference. However, these approaches exhibit computational tractability issues in the case of models of moderate to high complexity. One approach to increase model complexity while remaining computationally tractable in the context of birth-death modelling is machine learning. So far, these techniques have been explored in the context of serially-sampled phylogenies (phylodynamics) and trait-dependent birth-death models. Here, we explored the power of Convolutional Neural Networks (CNNs), a type of Deep Learning (DL) method, to solve classification and regression (parameter estimation) tasks under constant-rate and time-homogeneous, rate-variable birth-death models. In particular, we compared six diversification scenarios: Constant Birth-Death, High-Extinction, Mass-Extinction, Diversity-Dependent, Stasis-and-Radiate, and Waxing-and-Waning. We simulated 10, 000 phylogenetic trees under each diversification scenario, which were encoded using a vectorization procedure that captures the topology and branch length information. The encoded trees were used to train or test a set of CNNs models that were designed to tailor three empirical case studies differing in the number of tips. We compared CNNs performance with MLE inference. Our results show that CNNs exhibited classification accuracy levels of 93-78%, whereas maximum likelihood estimation achieved levels of 74-70%. The most difficult scenarios to predict for the CNNs were the high-extinction and mass-extinction scenarios, which were often misidentified as one another. For the regression tasks, mean average errors were comparable between CNNs models and MLE inference, and they also coincided in their difficulty estimating ratio parameters such as mass extinction survival and turnover. Finally, we applied our CNNs to three empirical studies (eucalypts, conifers and cetaceans) and discussed potential shortcomings and future avenues for improvement in the application of deep-learning birth-death modelling approaches.

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↗

bioRxiv2024

Evolutionary macroecology: Incorporating phylogenetic information more explicitly into process-based, forward time, simulation models

AO_SCPLOWBSTRACTC_SCPLOWA conceptual and mechanistic approach for bridging the fields of macroecology (ecological biogeography) and historical biogeography has been a long-term aim in Evolutionary Biology. Such a bridge could increase our understanding on the processes governing the spatial and temporal generation of biodiversity distribution patterns. This aim has been recently approached from the perspective of evolutionary biogeographic inferential statistical models, within a maximum likelihood or Bayesian framework, which incorporates the contribution of environmental factors as scaling parameters. Here, we describe a new approach that builds on a spatially-explicit, forward-time, computer simulation ("automat") model. The model sets a series of rules by which speciation, extinction, and dispersal of lineages are governed within an environmentally heterogeneous, two-dimensional gridded landscape. Unlike some previous approaches, niche conservatism is assumed but the model allows for environmental conditions to vary both spatially and temporally, by letting the model run over three time-series of actual palaeoclimate data, spanning the last 20 million years of geological history. Speciation is governed by a global speciation rate, whereas the background extinction rate is made dependent on abiotic (palaeoenvironmental conditions) and biotic (species density per grid cell) factors, hence giving a local background extinction rate. Also, we propose a novel mechanistic approach in which species are not the result of unique, independent events but linked through evolutionary history from a single evolutionary origin. We set different rules to generate the resulting phylogenies to test different factors (time, environment) that govern the inheritance of range distributions. Dispersal follows a simple Poisson kernel model, with higher probability of migration to contiguous grid cells and rare long-distance movements to distant cells. We also describe ways in which the presence of temporal dispersal barriers could modify the resultant spatial patterns. Evaluation of model accuracy and fit is based on comparison of simulated spatial patterns with observed, empirical ones. We use statistic dependent variables such as the spatial distribution of species in the landscape, species geographic range size and location, and the shape of the resultant phylogenies. Finally, we propose that this spatially-explicit simulation model could be used to evaluate the role played by niche conservatism, ecological vicariance and climatic-driven extinction in the generation of disjunct continental patterns, such as the presence of sister-lineages in numerous families of angiosperms forming a ring in the continental margins of the African continent, the Rand Flora pattern.

evolutionary biology↗

bioRxiv2021

Diversification dynamics of hypermetamorphic blister beetles (Meloidae): Are homoplastic host shifts and phoresy key factors of a rushing forward strategy to escape extinction?

Changes in life history traits, including reproductive strategies or host shifts, are often considered triggers of speciation, affecting diversification rates. Subsequently, these shifts can have dramatic effects on the evolutionary history of a lineage. In this study, we examine the consequences of changes in life history traits, in particular host-type and phoresy, within the hypermetamorphic clade of blister beetles (Meloidae). This clade exhibits a complex life cycle involving multiple metamorphoses and parasitoidism. Most tribes within the clade are bee-parasitoids, phoretic or non-phoretic, while two tribes feed on grasshopper eggs. Species richness differs greatly between bee and grasshopper specialist clades, and between phoretic and non-phoretic genera. We generated a mitogenomic phylogeny of the hypermetamorphic clade of Meloidae, including 21 newly generated complete mitogenomes. The phylogeny and estimated lineage divergence times were used to explore the association between diversification rates and changes in host specificity and phoresy, using State-Dependent Speciation and Extinction (SSE) models, while accounting for hidden factors and phylogenetic uncertainty within a Bayesian framework. The ancestor of the hypermetamorphic Meloidae was a non-phoretic bee-parasitoid, and independent transitions towards phoretic bee-parasitoidism or grasshopper specialization occurred multiple times. Bee-parasitoid lineages that are non-phoretic have significantly higher relative extinction rates and lower diversification rates than grasshopper specialists or phoretic bee-parasitoids, while no significant differences were found between the latter two strategies. This suggests that these two life strategies contributed independently to the evolutionary success of Nemognathinae and Meloinae, allowing them to escape from the evolutionary constraints imposed by their hypermetamorphic life-cycle, and that the "bee-by-crawling" strategy may be an evolutionary "dead end". We show how SSE models can be used not only for testing diversification dependence in relation to the focal character but to identify hidden traits contributing to the diversification dynamics. The ability of blister beetles to explore new evolutionary scenarios including the development of homoplastic life strategies, are extraordinary outcomes along the evolution of a single lineage: the hypermetamorphic Meloidae.

evolutionary biology↗

bioRxiv2017

Reconstructing deep-time paleoclimate legacies unveil the demise and turnover of the ancient (boreo)tropical flora

AimSince the Late Cretaceous, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration or persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH), and the genus Hypericum as test cases.\n\nLocationHolarctic.\n\nTime periodLate Cretaceous-Cenozoic\n\nMajor taxa studiedangiosperms\n\nMethodsWe use paleoclimate simulations, species distribution models and phylogenetic comparative approaches calibrated with fossils.\n\nResultsAncestral CPH lineages could have been distributed in the Holarctic 100 Ma, occupying tropical subhumid assemblages, a finding supported by the fossil record. Expansion to closed-canopy tropical rain forests occurred after 60 Ma, in the Cenozoic, in agreement with earlier ideas of a post-Cretaceous origin of current tropical rain forest. Cooling during this period triggered diversification declines on CPH tropical lineages, and was associated with a climatic shift towards temperate affinities in Hypericum. Hypericum subsequently migrated to tropical mountains where it encountered different temperate conditions than in the Holarctic.\n\nMain conclusionsWe hypothesize that most clusioid CPH lineages failed to adapt to temperate regimes during periods of Cenozoic climate change, and thus went extinct in the Holarctic. In contrast, boreotropical descendants including Hypericum that underwent niche evolution demonstrated selective advantages as climates became colder. Our results points toward macroevolutionary trajectories involving the altering fates of closely related clades that adapt to periods of global climate change versus those that do not. Moreover, they suggest the hypothesis that potentially many clades, particularly inhabitants of boreotropical floras, were likely extirpated from the Holarctic and persist today (if at all) in more southern tropical locations.

evolutionary biology↗

bioRxiv2017

Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies

In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid development of new macroevolution models that tie diversification rates to changes in paleoenvironmental (extrinsic) and/or biotic (intrinsic) factors. We inferred a robust and fully-sampled species-level phylogeny, as well as divergence times and ancestral geographic ranges, and related these to the radiation of Apollo butterflies (Parnassiinae) using both extant (molecular) and extinct (fossil/morphological) evidence. We tested whether their diversification dynamics are better explained by a RQ or CJ hypothesis, by assessing whether speciation and extinction were mediated by diversity-dependence (niche filling) and clade-dependent host-plant association (RQ) or by large-scale continuous changes in extrinsic factors such as climate or geology (CJ). For the RQ hypothesis, we found significant differences in speciation rates associated with different host-plants but detected no sign of diversity-dependence. For CJ, the role of Himalayan-Tibetan building was substantial for biogeography but not a driver of high speciation, while positive dependence between warm climate and speciation/extinction was supported by continuously varying maximum-likelihood models. We find that rather than a single factor, the joint effect of multiple factors (biogeography, species traits, environmental drivers, and mass extinction) is responsible for current diversity patterns, and that the same factor might act differently across clades, emphasizing the notion of opportunity. This study confirms the importance of the confluence of several factors rather than single explanations in modeling diversification within lineages.

evolutionary biology↗