Biology subjects

Carmona Baez, A.

Publications and source records attributed to Carmona Baez, A..

4 recordsLinked to original sources

bioRxiv2026

Evolution of novel host-microbiota coupling underlies adaptation to nutrient-scarce environments.

Animals colonizing food-limited environments need to overcome growth constraints by adapting to low, inconsistent nutritional inputs. Comparative studies of surface and cave populations of the Mexican tetra fish species Astyanax mexicanus provide a powerful system to explore evolution to food scarcity. In nutrient-scarce caves, evolved traits such as eye loss and increased fat storage have been shown to conserve energy in cavefish1-3 . However, the role of microbiota-mediated metabolism in sustaining growth and survival under food limitation remains poorly understood. Here, we demonstrate that surface and cave populations distinctly modulate their gut microbiota, with cavefish recruiting microbes whose predicted metabolites specifically promote growth under nutrient-limited conditions. Using microbiota data from three distinct dietary regimes and a fasting treatment, integrated topological data analysis4 and sparse modeling identify sugar and fatty acid degradation pathways coupled with growth in cavefish. Notably, the metabolites of these pathways are beneficial only for cavefish growth, and not for surface fish. Fasting in cavefish led to the recruitment of gut microbes capable of metabolizing aromatic compounds inaccessible to the host, whereas it recruited few microbial associates in surface fish. Our findings indicate that cavefish evolved novel host-microbiota coupling to sustain growth and resilience in their nutrient-scarce niche. We anticipate that our findings will broadly inform studies of evolution under extreme nutritional conditions and provide insights into the role of host-microbiota interactions in resilience to food scarcity at varied time scales.

evolutionary biology↗

bioRxiv2024

Trophic level associated gut length divergence evolved under sexual conflict in Lake Malawi cichlids

Variation in gastrointestinal morphology is associated with dietary specialization across the animal kingdom. Gut length generally correlates with trophic level, and increased gut length in herbivores is a classic example of adaptation to cope with diets with lower nutrient content and a higher proportion of refractory material. However, the genetic basis of gut length variation remains largely unstudied, partly due to the inaccessibility and plasticity of the gut tissue, as well as the lack of dietary diversity within traditional model organisms relative to that observed among species belonging to different trophic levels. Here, we confirm the genetic basis of gut length variation among recently evolved Lake Malawi cichlid fish species with different dietary adaptations. We then produce interspecific, inter-trophic-level hybrids to map evolved differences in intestinal length in an F2 mapping cross between Metriaclima mbenjii, an omnivore with a relatively long gut, and Aulonocara koningsi, a carnivore with a relatively short gut. We identify numerous candidate quantitative trait loci for evolved differences in intestinal length. These quantitative trait loci are predominantly sex-specific, supporting an evolutionary history of sexual conflicts for the gut. We also identify epistatic interactions potentially associated with canalization and the maintenance of cryptic variation in the cichlid adaptive radiation. Overall, our results suggest a complex, polygenic evolution of gut length variation associated with trophic level differences among cichlids, as well as conflicts and interactions that may be involved in evolutionary processes underlying other traits in cichlids. SummaryThis study examines the genetic basis of gut length variation in Lake Malawi cichlids, which exhibit different dietary adaptations. It highlights how cichlids recapitulate a broad taxonomic trend: gut length correlates with trophic level, with herbivores and omnivores having longer intestines than carnivores. By creating hybrids of Metriaclima mbenjii (omnivore) and Aulonocara koningsi (carnivore), we identify several quantitative trait loci and epistatic interactions underlying gut length differences. These genetic associations are predominantly sex-specific, suggesting historical sexual conflicts. The results indicate complex, polygenic evolution of gut morphology in these fish, and suggest evolutionary interactions and processes shaping dietary traits across species.

genetics↗

bioRxiv2022

Genetic architecture of trophic adaptations in cichlid fishes

Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection such as feeding biomechanics. We investigate the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyze morphological differences in the lateral and ventral head among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identify variation in a series of morphologies including mandible width, mandible length, and buccal length that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we find that many genes of small effects influence these craniofacial adaptations. Intervals for some traits are enriched in genes related to potassium transport and sensory systems, the latter suggesting correlation between feeding structures and sensory adaptations for foraging. Craniofacial phenotypes largely map to distinct genetic intervals, and morphologies in the head do not correlate. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation.

evolutionary biology↗

bioRxiv2021

Genetic basis of body shape variation along the benthic-pelagic axis in cichlid fishes

Divergence along the benthic-pelagic axis is one of the most widespread and repeated patterns of morphological variation in fishes, producing body shape diversity associated with ecology and swimming mechanics. This ecological shift is also the first stage of the explosive adaptive radiation of cichlid fishes in the East African Rift Lakes. We use two hybrid crosses of cichlids (Metriaclima sp. x Aulonocara sp. and Labidochromis sp. x Labeotropheus sp., >975 animals total) along the benthic-pelagic ecomorphological axis to determine the genetic basis of body shape diversification. Using a series of both linear and geometric shape measurements, we identify 55 quantitative trait loci (QTL) that underlie various aspects of body shape variation associated with benthic-pelagic divergence. These QTL are spread throughout the genome, each explain 3.0-7.2% of phenotypic variation, and are largely modular. Further, QTL are distinct both between these two crosses of Lake Malawi cichlids and compared to previously identified QTL for body shape in fishes such as sticklebacks. We find that body shape is controlled by many genes of small effects. In all, we find that convergent benthic and pelagic body phenotypes commonly observed across fish clades are most likely due to distinct genetic and molecular mechanisms.

evolutionary biology↗