Luis Filipe Costa Castro

Gammarids and their biomass are emerging as promising candidates for the production of high-nutritional-value ingredients to replace marine ingredients derived from wild-capture fisheries. Optimising culture conditions, such as diet composition and environmental temperature, is essential to maximise both biomass yield and nutritional quality. This study evaluated the transcriptomic responses of Gammarus locusta subjected to alternative terrestrial diets (Carrot and Coconut vs. marine Fucus sp. control) in Experiment 1 and thermal gradients (5, 10, 15, and 20 °C) in Experiment 2. Using a newly assembled reference transcriptome, we performed differential gene expression (DGE) analysis to identify genes involved in lipid and fatty acid metabolism, as well as ecdysis and development. Our data indicate that alternative terrestrial diets were related with shifts in transcript abundance for key genes involved in fatty acid catabolism and transport. Concurrently, elevated rearing temperatures were associated with the upregulation of neuroendocrine and metabolic transcripts that parallel accelerated growth rates, yet coincide with reduced long-term survival. Overall, the findings from the present study provide novel candidate molecular markers for evaluating gammarid physiological status, offering an exploratory framework to aid the optimisation of sustainable culture practices for aquaculture feed applications.

Chemical pollution threatens ocean predators worldwide, and the most persistent and toxic compounds, namely persistent organic pollutants, remain the most abundant. By integrating pollutant, habitat, diet, and genomic data across multiple marine mammal species, we show that evolutionary history has a strong influence on species’ responses to modern anthropogenic pollutants. Detoxification gene counts decline from polar bears through seals and baleen whales to toothed whales, mirroring progressive gene loss in lineages with longer aquatic evolutionary histories. A detoxification system that originally evolved to process a wide variety of terrestrial plant-derived toxins has eroded during the land-to-sea transition, likely due to its adverse outcomes. This erosion of detoxification capacity, combined with feeding in deep water and high-trophic-level diets, explains why toothed whales show 5–17-fold higher pollutant concentrations than the other taxonomic groups. Polar bears carry lower pollutant concentrations than toothed whales, despite occupying the highest trophic position, consistent with their detoxification gene counts that are twice as high as toothed whales. Our results reveal that evolutionary gene loss fundamentally shapes the propensities of marine mammals to accumulate modern chemical pollutants, which provides a mechanistic basis for prioritizing conservation toward the most chemically vulnerable lineages, particularly toothed whales.

Nuclear receptors (NRs) are a superfamily of ligand-regulated transcription factors that translate chemical signals to gene regulatory responses. Although traditionally viewed through the lens of endocrinology, mounting evolutionary and comparative evidence demonstrate that nuclear receptors originated as environmental chemical sensors long before the emergence of complex hormonal systems. From their appearance in early branching metazoans, more than 700 million years ago, the nuclear receptor superfamily has undergone extensive structural and functional diversification driven by ligand availability, dimerization strategies, and local- and genome-scale duplication and loss. An important step in this expansion was the emergence of the retinoid X receptor (RXR) as a common heterodimerization partner, allowing several receptor pathways to be linked to metabolism, development, and xenobiotic responses. Here, we review the evolutionary history of nuclear receptors with a focus on structural innovations in the ligand binding domain, the emergence of RXR-centered networks, and the role of nuclear receptors as master regulators of the chemical defensome. We further synthesize insights from environmental toxicology and comparative genomics to show how nuclear receptor evolution can help us understand species-specific sensitivity to environmental pollutants and modern chemical exposures.

Understanding the origins of anatomical innovations is central to elucidate the evolution of phenotypic diversity, as novel body plans often underpin the colonization of new ecological niches. The stomach, with its acid-secreting glands, evolved in the gnathostome ancestor and has been lost repeatedly. Claudin 18 (CLDN18) is a tight-junction protein that preserves gastric epithelial integrity against extreme H ⁺ gradients and, in mammals, also acts in the lung through alternative first-exon isoforms. This dual role suggests that pleiotropy may shape the fate of CLDN18 after stomach loss. Here, we provide a detailed analysis of CLDN18 evolution across jawed vertebrates. CLDN18 originated in the gnathostome ancestor and is expressed in the stomach of elasmobranchs. We found no evidence of the gene in chimaeras or lungfishes, two additional agastric lineages, extending the loss of cldn18a previously described in agastric teleosts. Exon 1 architecture indicates a tandem duplication in the Euteleostomi ancestor, whereas stomach- and lung-associated isoforms are partitioned in most tetrapods examined. Monotremes, although agastric, retain only the lung-associated exon 1, consistent with lung function sustaining selection on the locus . We show that the origin of the stomach in the gnathostome ancestor coincided with the acquisition of a specific tight-junction barrier against extreme H ⁺ gradients, a function secondarily lost together with the stomach in chimaeras, lungfishes and agastric teleosts; except in monotremes, where the lung-associated exon 1 preserves CLDN18. Together, these findings reveal a complex evolutionary history involving gene loss, alternative splicing, tissue-specific regulation, and secondary exon loss, highlighting how pleiotropy and regulatory partitioning shaped the evolution of epithelia in jawed vertebrates.

Understanding the origins of anatomical innovations is central to elucidate the evolution of phenotypic diversity, as novel body plans often underpin the colonization of new ecological niches. The stomach, with its acid-secreting glands, evolved in the gnathostome ancestor and has been lost repeatedly. Claudin 18 (CLDN18) is a tight-junction protein that preserves gastric epithelial integrity against extreme H⁺ gradients and, in mammals, also acts in the lung through alternative first-exon isoforms. This dual role suggests that pleiotropy may shape the fate of CLDN18 after stomach loss. Here, we provide a detailed analysis of CLDN18 evolution across jawed vertebrates. CLDN18 originated in the gnathostome ancestor and is expressed in the stomach of elasmobranchs. We found no evidence of the gene in chimaeras or lungfishes, two additional agastric lineages, extending the loss of cldn18a previously described in agastric teleosts. Exon 1 architecture indicates a tandem duplication in the Euteleostomi ancestor, whereas stomach- and lung-associated isoforms are partitioned in most tetrapods examined. Monotremes, although agastric, retain only the lung-associated exon 1, consistent with lung function sustaining selection on the locus. We show that the origin of the stomach in the gnathostome ancestor coincided with the acquisition of a specific tight-junction barrier against extreme H⁺ gradients, a function secondarily lost together with the stomach in chimaeras, lungfishes and agastric teleosts; except in monotremes, where the lung-associated exon 1 preserves CLDN18. Together, these findings reveal a complex evolutionary history involving gene loss, alternative splicing, tissue-specific regulation, and secondary exon loss, highlighting how pleiotropy and regulatory partitioning shaped the evolution of epithelia in jawed vertebrates.

Introduction: The aglomerular kidney, characterised by the absence of functional glomeruli and reliance on tubular secretion alone, has evolved independently across multiple teleost lineages occupying diverse environments, including notothenioids of the Southern Ocean, gadids of cold North Atlantic and Arctic waters, and syngnathids distributed across temperate and tropical seas. Despite sharing this independently derived renal architecture, these groups face markedly distinct osmotic, thermal and chemical challenges in their natural habitats. How aglomerular kidneys cope with environmental stressors, including fluctuations in temperature and salinity, and how they handle the excretion of xenobiotics and other exogenous compounds through exclusively tubular mechanisms, remains poorly understood. The physiological and molecular responses underlying renal function in these lineages have received comparatively little attention relative to their glomerular counterparts. Objective: This study investigates how aglomerular kidneys across phylogenetically distinct teleost lineages respond, at molecular and physiological levels, to contrasting environmental conditions, namely temperature and salinity challenges predicted to alter the functional demands on renal osmoregulation. Methodology: Adult and juvenile specimens from target lineages were subjected to controlled exposure experiments combining different temperature and salinity regimes. Blood and urine samples were collected to assess osmolality and ionic composition. Renal tissues were processed for gene expression analysis of key transport and structural genes, histology, immunohistochemistry and enzymatic activity assays, providing an integrated picture of renal function under each condition. Results: Molecular analyses are currently underway. Preliminary work has established protocols for RNA extraction and quantitative PCR across target species, enabling comparative gene expression profiling to proceed across the full dataset. Conclusions: A comparative physiological and molecular approach across aglomerular teleost lineages will clarify whether shared renal architecture translates into shared functional responses to environmental challenge and identify lineage-specific mechanisms of renal adaptation, with broader relevance for predicting how these fishes may respond to ongoing environmental change.

To preserve homeostasis in the face of continual chemical insult, animals evolved dedicated molecular systems that detect, detoxify, and eliminate foreign compounds. Collectively, these enzymes, transporters, and regulatory pathways constitute the chemical defensome. In cetaceans, the loss of two key nuclear receptors (NR1I2/PXR and NR1I3/CAR) suggests a profound rearrangement of the chemical defense systems. Therefore, we investigated the gene inventory of the chemical defensome in Cetacea and two other major marine mammal lineages (Pinnipedia and Sirenia), using their closest terrestrial relatives to understand the extent and patterns of chemical defensome remodelling. We demonstrate large-scale gene loss in chemical defensome genes of cetaceans, as well as smaller scale gene loss in the other two marine mammal lineages, indicating possible convergent evolution. Gene loss occurred predominantly in phase I and phase II biotransformation enzymes, including CYPs, FMOs, SULTs, and GSTs. Many of the lost genes in cetaceans are known to be regulated by PXR and/or CAR, while genes lost in multiple marine mammal lineages are often not regulated by these transcription factors. We hypothesize that the transition to aquatic environments, often accompanied by corresponding changes in feeding habits, led to convergent loss of chemical defensome genes, and loss of PXR and CAR in cetaceans accelerated these losses. These findings reveal systematic erosion of chemical defense capabilities across marine mammal lineages, suggesting that adaptation to marine life involves trade-offs in detoxification capacity that may have significant implications for these species’ responses to increasing chemical pollution in present-day ocean environments.

Unraveling how adaptive traits originate and evolve is key to understanding the mechanisms shaping species’ diversity and their adaptive potential. Seasonal color molts, from summer-brown to winter-white, evolved in at least 21 mammals and birds to maintain camouflage in environments with seasonal snow, but the occurrence of winter-brown morphs reflects seemingly convergent local adaptation to distinct snow conditions. In the least weasel (Mustela nivalis), alternative winter morphs map to the pigmentation gene MC1R, but the evolutionary history and functional basis of this variation remained unknown. Using in vitro cellular assays, we show that winter-brown coats are caused by a derived protein-coding amino acid substitution that reduces MC1R affinity to its ligands, ASIP and α-MSH. Using targeted enrichment and sequencing, we find that this mutation arose de novo within the species, around one million years ago, and was maintained across the geographically structured populations formed during its evolution in Europe. Using simulations, we show that genetic drift is unlikely to explain the long-term maintenance of this variant at intermediate frequencies, which can be driven by spatially varying selection, anchoring local adaptive responses. Our results underscore how long-standing adaptive variation can fuel recurrent adaptation to heterogeneous environments through time.