Biology subjects

Hernandez, S. G.

Publications and source records attributed to Hernandez, S. G..

4 recordsLinked to original sources

bioRxiv2026

Fermentation-Derived Metabolites Shape Host Biology to Attenuate Severity of Inflammatory and Metabolic Disease

Fermented foods are among the few dietary interventions shown to increase gut microbiome diversity and reduce systemic inflammation in healthy adults, yet the underlying mechanisms remain poorly defined. Metabolites produced during food fermentation, termed fermentation-derived metabolites (FDMs), represent a largely uncharacterized pool of bioactive compounds that may directly mediate the physiological effects of fermented food consumption. Here, we characterize the metabolite landscape of ten vegetable-based fermented foods using metabolomics, identifying conserved enrichment of aromatic and branched-chain amino acid derivatives across diverse substrates. Using sauerkraut as a chemically representative model system, we show that metabolite extracts from wild green sauerkraut (wGS-FDMs) remodel intestinal and systemic immune populations and shift gut microbiome composition in healthy mice. wGS-FDMs suppressed NF-{kappa}B activation and pro-inflammatory cytokine secretion in vitro and decreased colitis severity in vivo. In a chronic high-fat diet model, wGS-FDMs attenuated weight gain and improved glucose and insulin tolerance, consistent with stimulation of GLP-1 secretion in vitro. Collectively, these findings establish FDMs as biologically potent dietary components capable of simultaneously modulating immune, microbial, and metabolic homeostasis across multiple physiological systems, positioning metabolites from fermented foods as an important and underappreciated class of dietary effectors in the context of chronic disease.

microbiology↗

bioRxiv2025

Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes

Understanding the extent of parallelism across adaptive radiations remains a central problem in evolutionary biology. We used whole-genome resequencing of 123 individuals to compare the adaptive radiation of Cyprinodon pupfishes in Lake Chichancanab, Mexico, to an independent radiation of San Salvador Island (SSI) pupfishes in the Bahamas, and assess the repeatability of adaptive genetic architecture, sources of adaptive variation, and stages of selection. Despite rapid craniofacial divergence of trophic specialists within 8-15 kya, only two candidate genes (0.5%; 2/426) were shared between Caribbean radiations. Although adaptive introgression played a major role in SSI, we found minimal evidence of adaptive introgression in Chichancanab, likely due to the geographic isolation of this inland lake. Instead, de novo mutations provided a substantial source of adaptive variation (30.6%) for the endemic zooplanktivore, 15 times higher than the endemic scale-eater on SSI. However, in parallel with SSI, we found strong evidence that adaptive divergence occurred in stages, first on regulatory and standing genetic variation, then on de novo and nonsynonymous mutations. Consistent with adaptive variants near opsin and spermatogenesis genes, functional categories unique to Chichancanab, we found greater visual acuity and divergent sperm morphology in lab-reared zooplanktivores relative to generalists using laboratory assays. Consistent with extensive adaptive de novo mutations in WNT10A and rapid diversification of tooth size in the zooplanktivore, we found that experimental inhibition of the Wnt pathway in generalists resulted in narrower oral teeth. We conclude that de novo mutations, not introgression, can drive rapid adaptive radiations in isolated environments.

evolutionary biology↗

bioRxiv2025

Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes

Adaptive radiation results in part from ecological opportunity in a new environment, but it is unclear how pre-existing constraints in the founding population may limit this process. Genetic lines of least resistance, and by proxy morphological variance, are known to limit adaptive divergence, but ecological variance is rarely investigated. Here we test whether ecological or morphological lines of least resistance in generalist populations may have constrained the directions of species divergence in two independent Caribbean adaptive radiations of Cyprinodon pupfishes. We find almost universal congruence between the major multivariate dimensions of intraspecific craniofacial and dietary variance within generalist populations and the major axes of interspecific divergence within each adaptive radiation. This is surprising given that we document unique trophic specialists within each radiation, including a bivalve-specialist, zooplanktivore, molluscivore/ostracod-specialist, and scale-eating specialist, while nearly all generalist populations were observed to feed rarely on these same resources. We conclude that pre-existing genetic constraints within each founding generalist population, resulting in dimensions of greater ecological and morphological variance, may partially constrain and predict the directions of species divergence and dietary specialization during adaptive radiation. We also provide a new framework for examining ecological lines of least resistance.

evolutionary biology↗

bioRxiv2023

Historical biogeography of New World Killifishes (Cyprinodontiformes: Funduloidea) recapitulates geographical history in the Gulf of Mexico watershed

We reconstructed the phylogenetic relationships of superfamily Funduloidea with a synthesis of its biogeographic history. We used DNA sequences from five genes for 135 species, with four fossil calibrations, to generate a time-calibrated phylogeny. We estimated diversification rates, ancestral areas (Nearctic or Neotropical), and ancestral habitat (coastal or upland), for each node. Our results suggest that Funduloidea originated in the Late Cretaceous and diversified from Late Paleocene to present at a uniform rate, except Cyprinodontidae expressed an accelerated rate of speciation ~11.02 Ma. Neither viviparity, marine-to-freshwater transition, consistently accelerated speciation. Funduloidea has a coastal origin, but invaded inland many times. Funduloidea phylogeny indicates, sea-level falls isolate coastal populations, but increase island accessibility and climatic cooling facilitates invasions of temperate species into the tropics. For continental lineages, ancient river drainages accord with lineage distributions, including enigmatic disjunctions in Goodeidae and Fundulus. Niche shifts occurred from estuaries to open coasts and from forests to grasslands. Antiquity, adaptability, and dynamic geography can explain Funduloidea diversity. Combined environmental and phylogenetic data unveil the history of the Gulf of Mexico watershed. Phylogeny suggests there was diversification by barrier displacement and coastal speciation pump. Overall, speciation time, transitions to freshwater, dispersal, vicariance, adaptive radiation, and viviparity contributed to total diversification.

zoology↗