Subterranean biodiversity and taxonomy

Integrative Species Delimitation in a Speciation Continuum: Phylogenomics, Cryptic Diversity, Diversification and Historical Biogeography of Sinocyclocheilus Cavefish

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

Ancient climate changes and relaxed selection shape cave colonisation in North American cavefishes

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

The rx3 gene contributes to the evolution of eye loss in the cavefish Astyanax mexicanus

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

Parallel Sensory Compensation following Independent Subterranean Colonization by Groundwater Salamanders (Eurycea )

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

Discovery of a new species of subterranean eel loach from southern India

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.

Macroinvertebrate diversity patterns in a guano-rich temperate cave

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.

Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation

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.

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

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.

Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra

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.

Scale cortisol levels vary with habitat type and population in the Mexican tetra Astyanax mexicanus

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.

Mechanisms of Social Behavior in the Anti-Social Blind Cavefish (Astyanax mexicanus)

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.

ERGA-BGE Reference Genome of Loboptera subterranea: a cave adapted cockroach endemic to the Canary Islands

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

Postprandial sleep in short-sleeping Mexican cavefish

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.

Long-term hybridization in a karst window reveals the genetic basis of eye loss in cavefish

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

Divergent 3D genome organization in livers of cave and surface morphs of Astyanax mexicanus as a potential driver of unique metabolic adaptations in cave environment.

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

Hypoxia-Sonic Hedgehog Axis as a Driver of Primitive Hematopoiesis Development and Evolution in Cavefish

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

Evolution of the regulation of developmental gene expression in blind Mexican cavefish

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.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

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

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments

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

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

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

A brain-wide analysis maps structural evolution to distinct anatomical modules

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

The enzymatic and neurochemical outcomes of a mutation in Mexican cavefish MAO reveal teleost-specific aspects of brain monoamine homeostasis

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.

Blind cavefish retain functional connectivity in the tectum despite loss of retinal input

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.

Evolutionary convergence of a neural mechanism in the cavefish lateral line system

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: An interactive analysis suite for cavefish bioinformatics

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

Resilience in a Natural Model of Metabolic Dysfunction Through Changes in Longevity and Ageing-Related Metabolites

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.

Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia inducible genes

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

A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

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.

How spiders make their eyes: Systemic paralogy and function of retinal determination network homologs in arachnids

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.

Evolutionary and homeostatic changes in morphology of visual dendrites of Mauthner cells in Astyanax blind cavefish

The paper examines how the absence of visual input affects the morphology of Mauthner cell dendrites in Astyanax blind cavefish and surface fish across developmental and evolutionary timescales.