Biology subjects

Quintero, I.

Publications and source records attributed to Quintero, I..

11 recordsLinked to original sources

bioRxiv2026

The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

The domestic dog is a powerful genetic model for complex traits, disease and behaviours relevant to human biology, yet the canine genome still lacks a systematic transcription-defined atlas of regulatory elements. Existing resources have improved annotation but largely infer regulatory activity from chromatin features rather than directly mapping transcription initiation at promoters and enhancers. Here, we address this gap using 114 CAGE-seq libraries spanning 56 tissues and developmental stages from 9 dogs. We identify 68,446 promoters and 46,661 active enhancers, and define their tissue-enriched activity across the canine body. Regulatory programmes are organized around shared transcription factor motif infrastructures, with prominent enrichment of KLF family motifs across tissues. The cerebellum emerges as a major regulatory hub, showing the highest density of enhancer-promoter interactions among brain regions. During embryogenesis, enhancer activity shifts from early neurodevelopmental patterning programmes, including OTX2 and ZIC1/4, towards regulators of functional maturation and synaptic organization, including AQP4 and NLGN3. Comparative analyses revealed 69 enhancers with highly similar regulatory structures linked to potential orthologous genes in dog and human. Together, these data establish a tissue-resolved transcription-based atlas of the canine regulatory genome that advances functional annotation and improves interpretation of non-coding variation in comparative and disease genomics.

genomics↗

bioRxiv2025

The Occurrence Birth-Death Diffusion Process: Unraveling Diversification Histories with Fossils and Heterogeneous Rates

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic diversification analyses often overlook the wealth of information contained in fossils that cannot be directly integrated into phylogenetic trees (called fossil occurrences), as well as fine-grained variations in speciation and extinction rates across lineages. Addressing both of these shortcomings, we develop the Occurrence Birth-Death Diffusion (OBDD) process. This process incorporates the sampling of fossil occurrences by extending the recently developed Fossilized Birth-Death Diffusion (FBDD) process, thereby taking advantage of a clades entire fossil record to infer its evolutionary history. To mitigate the computational challenges associated with the OBDD process, we employ Bayesian data augmentation methods. We illustrate our approach with an empirical analysis of cetacean diversification. Our analyses show that the integration of fossils is essential to recover diversification rates and richness trajectories. More specifically, all types of fossils are highly informative about past diversification dynamics, but fossil occurrences do not provide significant additional information when the phylogeny already contains many fossils. We make the OBDD available in the Julia package Tapestree.

evolutionary biology↗

bioRxiv2025

The rise, decline and fall of clades

How and why species diversity varies over geological time scales remains disputed. We analyzed the evolutionary history of 27 radiations with phylogenetic information incorporating extinct and extant species under a new fossilized birth-death diffusion model that provides a detailed characterization of past diversification and resulting diversity dynamics. Clade diversity trajectories follow rise and decline dynamics, with fast accumulation following recurrent speciation while slowdowns and losses are modulated primarily by changes in extinction. Diversity dynamics do not appear to be governed by clade-level processes expected from adaptive radiations or diversity equilibria. Rather, these patterns emerge from dynamics at the species-level, where lineages tend to become increasingly vulnerable to extinction and less likely to speciate with time. Those species that counteract this trend create and maintain biodiversity through deep time. One Sentence Summary

evolutionary biology↗

bioRxiv2025

Small and large extracellular vesicles from human preovulatory follicular fluid display distinct ncRNA cargo profile and differential effect on granulosa cell line KGN

Follicular fluid extracellular vesicles (FF EVs) facilitate communication between oocytes and somatic cells within the ovarian follicle, playing a pivotal role in follicular development. This study highlights the molecular and functional distinctions between small (SEV) and large (LEV) FF EV subpopulations, revealing their specialized regulatory roles in granulosa cell (GC) biology and their consequential impact on ovarian function. Single-EV profiling uncovered distinct tetraspanin distributions, with LEVs containing a lower proportion of CD9/CD63/CD81-positive particles compared to SEVs. Functionally, SEVs reduced estradiol secretion by GCs, whereas LEVs enhanced progesterone production, demonstrating their differential effects on steroidogenesis. Transcriptomic analysis revealed extensive SEV-induced changes in GC gene expression, affecting pathways involved in transcription, TGF-{beta} signaling, extracellular matrix (ECM) remodeling, and cell cycle regulation. In contrast, LEVs elicited minimal transcriptional changes, primarily modulating genes associated with immune regulation and oxidative stress defense. Small RNA sequencing further revealed distinct non-coding RNA (ncRNA) profiles, with SEVs enriched in miRNAs targeting pathways critical for GC differentiation, while LEVs carried higher levels of piRNAs implicated in maintaining genomic stability. These findings advance our understanding of FF EV-mediated intercellular communication and underscore the importance of investigating EV subpopulations independently.

cell biology↗

bioRxiv2024

Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation

The seasonality hypothesis posits that limited seasonal temperature variability in tropical mountains leads to greater climatic zonation along elevation gradients compared to temperate regions. This is predicted to result in narrow thermal tolerances and restricted dispersal for organisms, which may reduce gene flow and increase opportunities for climate-associated parapatric or allopatric speciation in tropical mountains relative to temperate-zone mountains. This hypothesis has been tested in various animal groups but not in plants. We examine the elevational and thermal ranges of pairs of sister species of angiosperms from mountains worldwide. Our findings indicate no significant difference in the breadth and overlap of elevational ranges between tropical and temperate species. However, tropical species have narrower thermal ranges and show greater similarity in these ranges between sister species compared to temperate ones. Such narrow thermal specialization in tropical plants facilitates population divergence and allopatric speciation within thermal zones more than in temperate species.

evolutionary biology↗

bioRxiv2022

The build-up of the present-day tropical diversity of tetrapods

The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatio-temporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.

evolutionary biology↗

bioRxiv2022

The birth-death diffusion leading to present-day Mammal diversity

Dramatic spatial, temporal and taxonomic variation in biodiversity is ultimately explained by differences in speciation and extinction rates. Mammals represent a [~]200 My old radiation that resulted in over 6500 extant species, with stark temporal, spatial and taxonomic heterogeneity in biodiversity. Throughout their history, every mammal lineage is expected to have undergone diversification rates that vary instantaneously in time resulting from the complex interplay of context-specific extrinsic factors (e.g., K-Pg mass extinction event, rise of angiosperms) with their evolving ecologies (e.g., body size, diet). When studying the diversification history of a clade, however, mathematical and computational limitations have hindered inference of such a flexible birth-death model where speciation and extinction rates evolve continuously along a phylogenetic tree. Here we overcome these challenges by implementing a series of phylogenetic models in which speciation and extinction rates are inherited and diffuse following a latent Geometric Brownian motion process. We enable full Bayesian inference using data augmentation techniques to sample from the posterior distribution of model parameters, including augmented phylogenetic trees and validate using simulations. Using a genome-informed time-calibrated tree for over 4000 Mammals species, we are able to estimate a complete and fine-grained picture of the variation in diversification rates that captures both global and lineage specific effects. We find that, contrary to the idea of a suppressed mammalian diversification before the K-Pg mass extinction event (i.e., explosive- or delayed-rise), mammal speciation rates dramatically increased around 10-20 My before the K-Pg. Our new model opens exciting possibilities in disentangling the drivers behind variation in diversification and assaying how small-scale processes scale-up to macroevolutionary dynamics.

evolutionary biology↗

bioRxiv2021

Macroevolutionary dynamics of climatic niche space

How and why lineages evolve along niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a comprehensive empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of external episodic and biotic factors remains poorly understood. Here we characterize species two-dimensional temperature and precipitation niche space occupied (i.e., species niche envelope) as complex geometries and assess their evolution across a large vertebrate radiation (all Aves) using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the K-Pg boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution as lineages diversify, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings share the limitations of all work based purely on extant taxa but highlight the growing ecological and conservation insights arising from the model-based integration of increasingly comprehensive and robust environmental and phylogenetic information.

evolutionary biology↗

bioRxiv2020

Allochronic Divergence Driven by Spatial Asynchrony in Precipitation in Neotropical Frogs?

The role of geographic barriers in promoting reproductive isolation across space is well understood. Isolation by the time of breeding, however, may also promote population divergence when populations reproduce asynchronically in space, even in the absence of geographic barriers. Few examples exist of divergence due to breeding allochrony, particularly in vertebrates. We tested whether in Neotropical frogs asynchrony in precipitation patterns promotes intraspecific genetic divergence, speciation, and regional accumulation of diversity. We assessed the relationship between spatial asynchrony in precipitation and genetic divergence controlling for ecological connectivity across 48 Neotropical frog species. In addition, we examined whether regions within which precipitation regimes are more asynchronous across space have higher species richness and have experienced greater speciation rates. Beyond a generalized expected effect of ecological connectivity on intraspecific genetic divergence, we found that asynchrony in precipitation is positively associated with genetic differentiation in 31% of the species tested, resulting in a significantly positive cross-species effect of asynchrony in precipitation on genetic divergence in a meta-analysis. However, the effect of asynchrony in precipitation on population divergence seems not to scale to macroevolutionary patterns because spatial asynchrony in precipitation was not associated with geographical patterns of species richness or speciation rates. Our results indicate that genetic divergence can be promoted by asynchronous breeding lag in the absence of geographic barriers in species where breeding is associated with water availability, but such effects may not be stable enough through time to influence macroevolutionary patterns.

ecology↗

bioRxiv2019

Functional community assembly and turnover along elevation and latitude

The drivers of community coexistence are known to vary with environment, but their consistency across latitudes and scales, and resulting conservation implications, remain little understood. Here, we combine functional and phylogenetic evidence along elevations to document strong biotic constraints on coexistence in avian communities in both benign (tropical low elevations) and severely harsh (temperate/polar highlands) environments. Assemblages in both are marked by high assemblage functional uniqueness, whereas in tropical highlands and temperate/polar low elevations there is strong functionally redundancy and pronounced environmental constraints. Only in harsh environments is phylogeny an effective surrogate for functional assemblage structure, reflecting nuanced shifts in the position, shape, and composition of measured multivariate trait space along gradients. Independent of scale and latitude, high elevation assemblages emerge as exceptionally susceptible to functional change.

ecology↗

bioRxiv2019

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions

Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and co-evolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwins finches--a classic example of adaptive divergence--and find support for in situ trait divergence in beak size, convergence in traits such as beak shape and tarsus length, and strong competitive exclusion throughout their evolutionary history. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters.

evolutionary biology↗