Subterranean biodiversity and taxonomy

The paper uses genomic data to resolve species boundaries and uncover evolutionary processes in Sinocyclocheilus cavefish, revealing cryptic diversity and a complex divergence history.

This study investigates the evolutionary history of North American cavefishes, finding three independent cave colonisations linked to ancient climate changes and relaxed selection.

This study identifies the rx3 gene's role in eye development and loss in cavefish Astyanax mexicanus through CRISPR-Cas9 mutagenesis and behavioral analysis.

This study examines sensory system tradeoffs in subterranean salamanders, finding degeneration of eyes and expansion of lateral line systems across multiple lineages.

The paper describes a new subterranean eel loach species from India, highlighting its morphological and genetic distinctions from related species and its potential role in understanding subterranean fish speciation.

The paper monitors macroinvertebrates in a guano-rich cave, finding higher diversity with structural complexity and bat presence, and lower diversity in old guano substrates.

This study investigates reproductive adaptations in Astyanax mexicanus under nutrient limitation, finding cavefish maintain breeding ability under starvation due to increased maternal nutrient deposition and specific gene expression changes.

This study examines prokaryotic genome evolution in the Movile Cave over 5.5 million years, finding reduced gene diversity, increased pseudogenization, and limited horizontal gene transfer.

This study shows that oca2 mutations in Mexican tetra affect prey capture behavior, with albino fish using vision in light and lateral line in dark, impacting competitive success in different environments.

The paper measures scale cortisol levels in wild and lab-reared Astyanax mexicanus populations across different habitats, finding lower cortisol in some cave populations and higher levels in habitats with more environmental variability.

This study investigates the social behavior differences between blind and surface-dwelling Astyanax mexicanus, finding that blind cavefish avoid conspecifics and their behavior is influenced by neuropeptides and hunger.

The paper presents the genome assembly of Loboptera subterranea, a cave-adapted cockroach, providing insights into its adaptation to subterranean environments.

The paper investigates postprandial sleep in Mexican cavefish and surface fish, finding that larvae exhibit postprandial sleep while adults do not, suggesting its role in energy conservation.

The paper identifies a specific SNP in Cx50 linked to eye loss in cavefish using a hybrid population from a karst window.

This study examines 3D genome organization in livers of cave and surface morphs of Astyanax mexicanus, linking structural changes to metabolic adaptations.

The paper investigates how hypoxia and Sonic hedgehog signaling influence primitive hematopoiesis in cavefish, showing hypoxia enhances hematopoiesis and Shh signaling in surface fish.

The paper maps QTL for cave-derived traits in Mexican cavefish and identifies evolutionary hotspots associated with adaptation to the cave environment.

The paper identifies cis-regulatory changes driving developmental gene expression differences between surface and blind cavefish morphs, with rx3 regulation showing both cis-autonomous and non-autonomous mechanisms.

This paper presents chromosome-scale assemblies of Astyanax mexicanus surface and cave populations to study genetic basis of adaptation to cave environments.

The paper presents a chromosome-scale reference genome for the Andean cavefish Trichomycterus rosablanca to study evolutionary mechanisms in cave environments.

This study compares mitochondrial genomes of surface and subterranean amphipods to identify molecular differences in energy metabolism linked to their habitats.

The paper maps structural brain evolution to anatomical modules by analyzing volume and shape variability in cavefish and hybrids.

This study examines the effects of a mutation in the MAO gene of Mexican cavefish, revealing its impact on monoamine neurotransmitter homeostasis and differences between brain regions.

The paper shows that Mexican cavefish maintain functional connectivity in the tectum despite losing retinal input, with changes in the tectum being genetically distinct from eye loss.

The paper investigates how neural mechanisms in the lateral line system of cavefish evolve, finding that blind cavefish have lower response thresholds and persistent afferent activity during locomotion due to efferent system regression.

CaveCrawler integrates genomic and transcriptional data from Astyanax mexicanus to compare gene expression and selection markers between surface and cave populations.

This study uses metabolomics to compare long- and short-term fasting responses in cave-dwelling and surface-dwelling Mexican tetra, identifying metabolic differences linked to resilience and longevity.

This study shows cavefish adapt to hypoxia by increasing erythrocyte production and constitutively overexpressing hypoxia-inducible genes.

The paper presents a chromosome-level genome of surface fish Astyanax mexicanus and uses it to identify genetic factors contributing to trait evolution in cavefish populations.

The paper investigates the genetic basis of eye development and reduction in arachnids, identifying duplicated RDGN homologs and showing that soA is necessary for eye development across arachnid species.