Biology subjects

Falcon-Cortes, A.

Publications and source records attributed to Falcon-Cortes, A..

3 recordsLinked to original sources

bioRxiv2025

Quantifying the influence of genetic context on duplicated mammalian genes

Gene duplication is a fundamental part of evolutionary innovation. While single-gene duplications frequently exhibit asymmetric evolutionary rates between paralogs, the extent to which this applies to multi-gene duplications remains unclear. In this study, we investigate the role of genetic context in shaping evolutionary divergence within multi-gene duplications, leveraging microsynteny to differentiate source and target copies. Using a dataset of 193 mammalian genome assemblies and a bird outgroup, we systematically analyze patterns of sequence divergence between duplicated genes and reference orthologs. We find that target copies, those relocated to new genomic environments, exhibit elevated evolutionary rates compared to source copies in the ancestral location. This asymmetry is influenced by the distance between copies and the size of the target copy. We also demonstrate that the polarization of rate asymmetry in paralogs, the "choice" of the slowly evolving copy, is biased towards collective, block-wise polarization in multi-gene duplications. Our findings highlight the importance of genetic context in modulating post-duplication divergence, where differences in cis-regulatory elements and co-expressed gene clusters between source and target copies may be responsible. This study presents a large-scale test of asymmetric evolution in multi-gene duplications, offering new insight into how genome architecture shapes functional diversification of paralogs. Significance statementAfter a gene is duplicated, reduced selective constraints can lead the two copies to rapidly diverge, with one copy often evolving faster and occasionally gaining a new function. We quantify the influence of genetic context in choosing which copy of a duplicated gene has an elevated substitution rate. In a representative dataset of 193 mammalian genomes, we found strong evidence that gene copies pasted into new genomic locations tend to evolve faster than the corresponding copies in ancestral locations, suggesting an important role for the regulatory environment. The asymmetry in evolutionary rates of duplicated genes persists even for very large multigenic duplications, up to the scale of megabases, indicating that regulatory interactions frequently reach farther than previously thought.

evolutionary biology↗

bioRxiv2023

Levy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers

Many animal species benefit from spatial learning to adapt their foraging movements to the distribution of resources. Learning involves the collection, storage and retrieval of information, and depends on both the random search strategies employed and the memory capacities of the individual. For animals living in social groups, spatial learning can be further enhanced by information transfer among group members. However, how individual behavior affects the emergence of collective states of learning is still poorly understood. Here, with the help of a spatially explicit agent-based model where individuals transfer information to their peers, we analyze the effects on the use of resources of varying memory capacities in combination with different exploration strategies, such as ordinary random walks and Levy flights. We find that individual Levy displacements associated with a slow memory decay lead to a very rapid collective response, a high group cohesion and to an optimal exploitation of the best resource patches in static but complex environments, even when the interaction rate among individuals is low. Author SummaryHow groups of social animals collectively learn to find and exploit resources in complex environments is not well-understood. By means of a computational model where individuals are initially spread out across a landscape, we study the effects of individual exploratory behaviors and memory capacities on the emergence of spatial learning. Collective learning emerges spontaneously only if group members transfer information between each other at a sufficiently high rate, so that individual experiences can be used by others. In static but heterogeneous environments with many resource sites of varying attractiveness, we find that random displacements over many spatial scales combined with a slow memory decay lead to a rapid collective response and highly cohesive groups. Collective learning is noticeable through an optimal exploitation of the best resource sites, which far exceeds what individuals would achieve on their own. Our study sheds light on important mechanisms responsible for collective learning in ecology, with potential applications in other areas of science.

animal behavior and cognition↗

bioRxiv2021

Hierarchical, Memory-based Movement Models for Translocated Elk (Cervus canadensis)

The use of spatial memory is well documented in many animal species and has been shown to be critical for the emergence of spatial learning. Adaptive behaviors based on learning can emerge thanks to an interdependence between the acquisition of information over time and movement decisions. The study of how spatio-ecological knowledge is constructed throughout the life of an individual has not been carried out in a quantitative and comprehensive way, hindered by the lack of knowledge of the information an animal already has of its environment at the time monitoring begins. Identifying how animals use memory to make beneficial decisions is fundamental to developing a general theory of animal movement and space use. Here we propose several mobility models based on memory and perform hierarchical Bayesian inference on 11-month trajectories of 21 elk after they were released in a completely new environment. Almost all the observed animals exhibited preferential returns to previously visited patches, such that memory and random exploration phases occurred. Memory decay was mild or negligible over the study period. The fact that individual elk rapidly become used to a relatively small number of patches was consistent with the hypothesis that they seek places with predictable resources and reduced mortality risks such as predation.

animal behavior and cognition↗