Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Cave beetle lineages gained genes before going down under: An example of repeated genomic exaptation?

The adaptation of animals to subterranean habitats like caves and aquifers stereotypically leads to dramatic trait-loss consequences like the lack of eyes and body pigmentation. These body plan regression trends are expected to be tied to gene loss as well. Indeed, previous studies documented the degeneration of vision genes in obligate cave dwellers. Contradicting this picture, the first broad-scale comparative transcriptome-wide study of gene content evolution in separate subterranean Australian and Mediterranean beetle clades unearthed evidence of global gene gain and retention. This suggests that the transition to cave life may be more contingent on gene repertoire expansion than contraction. Future studies, however, will need to examine how much the observed patterns of gene content evolution reflect subfunctionalization and fitness-securing genetic redundancy outcomes following gene duplication as opposed to adaptive trajectories.

Eye morphology in four species of tiger beetles (Coleoptera: Cicindelidae)

Compound eyes undoubtedly represent the widespread eye architecture in the animal kingdom. The insects' compound eye shows a wide variety of designs, and insects use their visual capacity to accomplish several tasks, including avoiding enemies, searching for food and shelter, locating a mate, and acquiring information about the environment and its surroundings. Broad literature data support the concept that visual ability lies in the way the eyes are built. Since the resolution and sensitivity of the compound eye are partly determined by the density of the ommatidia and the size of the facets. Morphological parameters of the compound eyes could influence the function of the visual organ and its capacity to process information, also representing a sensitive indicator of different habitat demands. In this study, we compared compound eyes' parameters in four closely related species of tiger beetles to disclose differences arising from different habitats. Furthermore, to investigate whether there are consistent intersexual differences, we also compared the most relevant parameters of the eye in males and females of four selected species. Our results show sex-related and interspecific differences that occur in examined species.

Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles

Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground, through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. However, our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.

A practical guide for the husbandry of cave and surface invertebrates as the first step in establishing new model organisms

While extensive research on traditional model species has significantly advanced the biological sciences, the ongoing search for new model organisms is essential to tackle contemporary challenges such as human diseases or climate change, and fundamental phenomena including adaptation or speciation. Recent methodological advances such as next-generation sequencing, gene editing, and imaging are widely applicable and have simplified the selection of species with specific traits from the wild. However, a critical milestone in this endeavor remains the successful cultivation of selected species. A historically overlooked but increasingly recognized group of non-model organisms are cave dwellers. These unique animals offer invaluable insights into the genetic basis of human diseases like eye degeneration, metabolic and neurological disorders, and basic evolutionary principles and the origin of adaptive phenotypes. However, to take advantage of the beneficial traits of cave-dwelling animals, laboratory cultures must be established-a practice that remains extremely rare except for the cavefish Astyanax mexicanus. For most cave-dwelling organisms, there are no published culturing protocols. In this study, we present the results of our multi-year effort to establish laboratory cultures for a variety of invertebrate groups. We have developed comprehensive protocols for housing, feeding, and husbandry of cave dwellers and their surface relatives. Our recommendations are versatile and can be applied to a wide range of species. Hopefully our efforts will facilitate the establishment of new laboratory animal facilities for cave-dwelling organisms and encourage their greater use in experimental biology.

Telomere length and dynamics in Astyanax mexicanus cave and surface morphs

Background

Telomeres are non-coding DNA repeats at the chromosome ends and their shortening is considered one of the major causes of aging. However, they also serve as a biomarker of environmental exposures and their length and attrition is affected by various stressors. In this study, we examined the average telomere length in Astyanax mexicanus, a species that has both surface-dwelling and cave-adapted populations. The cave morph descended from surface ancestors and adapted to a markedly different environment characterized by specific biotic and abiotic stressors, many of which are known to affect telomere length. Our objective was to explore whether telomere length differs between the two morphs and whether it serves as a biological marker of aging or correlates with the diverse environments the morphs are exposed to.

Methods

We compared telomere length and shortening between laboratory-reared Pachón cavefish and Rio Choy surface fish of A. mexicanus across different tissues and ages.

Results

Astyanax mexicanus surface fish exhibited longer average telomere length compared to cavefish. In addition, we did not observe telomere attrition in either cave or surface form as a result of aging in adults up to 9 years old, suggesting that efficient mechanisms prevent telomere-mediated senescence in laboratory stocks of this species, at least within this time frame. Our results suggest that telomere length in Astyanax may be considered a biomarker of environmental exposures. Cavefish may have evolved shorter and energetically less costly telomeres due to the absence of potential stressors known to affect surface species, such as predator pressure and ultra-violet radiation. This study provides the first insights into telomere dynamics in Astyanax morphs and suggests that shorter telomeres may have evolved as an adaptation to caves.

Supplementary data and taxonomic changes in the subterranean beetles of the Balkan Peninsula from July 1 2016 to September 30 2023

Supplementary data and taxonomic changes are provided for the listing of the subterranean beetles of the Balkan Peninsula (Hlav, Perreau & eplk, 2017), published from July 1st 2016 to September 30th 2023. An illustrated supplement catalogue and distribution of taxa by zoogeographic regions sensu Hlav et al., are given.