Biology subjects

Caetano, D. S.

Publications and source records attributed to Caetano, D. S..

7 recordsLinked to original sources

bioRxiv2025

A Unified Theory and Bayesian Framework for Phenological Inference from Biocollection Data: Resolving Paradoxes by Considering Phenophase Duration

O_LIPhenology, the study of recurring biological events, has gained increased attention with the rise of digitized biocollections. However, no general theoretical framework has linked variation in biocollection data to underlying phenological processes. C_LIO_LIWe present a unified statistical theory of phenological distributions that mathematically integrates phenological extremes, onset timing, phenophase duration, cessation, and peak activity and links these phenomena to variation in biocollection data. C_LIO_LIA key insight from this theory is that phenological sensitivity estimates from biocollection data are confounded by phenophase duration. Both onset and duration contribute to variation in collection dates, and standard regression methods cannot disentangle these effects. C_LIO_LITo address this, we develop a Bayesian inference framework based on Gaussian processes (GPs) that explicitly models onset and duration as latent variables. We assess its performance under various scenarios, including model misspecification and identifiability, and show that it outperforms three alternative methods. C_LIO_LIApplying the method to an empirical dataset of over 5,000 herbarium records, we find that phenophase duration frequently acts as a confounder, correlating with one or more covariates across all species examined. C_LIO_LIThese results highlight that phenophase duration is a critical but underappreciated factor in phenological studies using biocollection data. C_LI

ecology↗

bioRxiv2024

Gestation length drives brain size and litter size variation in eutherian mammals

The length of gestation in eutherian mammals, which is key to their reproductive success, is closely connected to other life history traits and with body mass and brain mass, but causal relationships between these variables are unclear. Here, we used an integrative analytical framework to evaluate the evolutionary relationships between gestation length and eight other traits on a dataset of 3,258 eutherian mammals and infer causality. We identify variation in generation length and litter size as the primary predictors of eutherian gestation length variation, whereas additional traits, such as brain mass, significantly predict gestation length only in specific mammalian orders. Using a structural equation modeling approach known as phylogenetic path analysis to infer causality, we find that gestation length variation positively influences brain mass variation and negatively influences litter size variation. Furthermore, body mass causally influences gestation length variation only in certain orders. Consistent with these causal inferences, examination of trait-trait coevolution reinforces that gestation length is strongly positively associated with brain mass, strongly negatively associated with litter size, and only moderately correlated with body mass. These findings reveal how gestation length directly and indirectly influences, and is influenced by, other key eutherian traits. Our study establishes a robust framework for identifying causal relationships within suites of correlated and co-evolving traits.

evolutionary biology↗

bioRxiv2024

The evolution of male weapons is associated with the type of breeding site in a clade of Neotropical frogs

Male weaponry evolution is often linked to resource or female defense polygyny. This pattern emerges from highly studied taxa, such as arthropods and mammals. However, whether factors such as breeding site type influence weaponry evolution remains an open question. We explore this question using frogs of the subfamily Leptodactylinae, where males of species spawning in exposed sites (water bodies) fight to hold oviposition sites or dislodge rivals during amplexus. Conversely, males of species spawning in concealed sites (ground nests and crevices) rarely engage in intense physical contests. We hypothesize that male weaponry evolution would be associated with reproduction in exposed sites. Using two complementary phylogenetic comparative methods, we first found a macroevolutionary correlation between male weapons and breeding site type. The presence of weapons is consistently associated with exposed sites, while their absence is linked to concealed sites. We explore how this macroevolutionary pattern can also be influenced by female mate choice. Second, we found that both gains and losses of weapons occurred more frequently in species spawning in exposed sites. This unexpected finding suggests that the dynamics of weapon evolution are more intricate than anticipated. We propose some explanations aspiring to stimulate further investigations with other external fertilizer species.

evolutionary biology↗

bioRxiv2022

How Important is Budding Speciation for Comparative Studies?

The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with three or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here we show that many PCMs assume that divergence happens as a symmetric split, even if these methods dont explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.

evolutionary biology↗

bioRxiv2020

Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past

The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian squamate communities an ideal system to investigate biogeographic patterns and their drivers. Here we reconstruct the phylogenetic relationships and the ancestral geographic distributions of several Afro-Arabian reptile clades (totaling 430 species) to estimate the number of dispersal, vicariance and range contraction events. We then compare the observed biogeographic history to a distribution of simulated biogeographic events based on the empirical phylogeny and the best-fit model. This allows us to identify periods in the past where the observed biogeographic history was likely shaped by forces beyond the ones included in the model. We find an increase in vicariance following the Oligocene, most likely caused by the fragmentation of the Afro-Arabian plate. In contrast, we did not find differences between observed and expected dispersal and range contraction levels. This is consistent with diversification enhanced by environmental processes and with the establishment of a dispersal corridor connecting Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show that our novel approach is useful to pinpoint events in the evolutionary history of lineages that might reflect external forces not predicted by the underlying biogeographic model.

evolutionary biology↗

bioRxiv2019

Comparative analyses of phenotypic sequences using phylogenetic trees

Phenotypic sequences are a type of multivariate trait organized structurally, such as teeth distributed along the dental arch, or temporally, such as the stages of an ontogenetic series. However, unlike other multivariate traits, the elements of a phenotypic sequence are arranged along a vector, which allows for distinct evolutionary patterns between neighboring and distant positions. In fact, sequence traits share many characteristics with molecular sequences. We implement an approach to estimate rates of trait evolution that explicitly incorporates the sequence organization of traits. We apply models to study the temporal pattern evolution of cricket calling songs. We test whether songs show autocorrelation of rates (i.e., neighboring positions along a phenotypic sequence have correlated rates of evolution), or if they are best described by rate variation independent of sequence position. Our results show that models perform well when used with sequence phenotypes even under small sample sizes. We also show that silent regions of the songs evolve faster than chirp regions, which suggests that macroevolutionary changes are faster when associated with axes of variation less constrained by multiple sources of selection. Our approach is flexible and can be applied to any multivariate trait with units organized in a sequence-like structure.

evolutionary biology↗

bioRxiv2017

Estimating correlated rates of trait evolution with uncertainty

Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration. Our approach incorporates the uncertainty related to phylogeny, ancestral state estimates and parameter estimates to produce posterior distributions using Bayesian Markov chain Monte Carlo. We implemented the use of summary statistics to test for regime shifts based on a series of attributes of the model that can be directly relevant to biological hypotheses. In addition, we extend Felsensteins pruning algorithm to the case of multivariate Brownian motion models with multiple rate regimes. We performed extensive simulations to explore the performance of the method under a series of scenarios. Finally, we provide two test cases; the evolution of a novel buccal morphology in fishes of the family Centrarchidae and a shift in the trajectory of evolution of traits during the radiation of anole lizards to and from the Caribbean islands.

evolutionary biology↗