Cavefish Genomics

Current understanding

Astyanax mexicanus — the Mexican tetra — has become a leading model for studying convergent evolution, regressive trait loss, and the genomic basis of cave adaptation. Multiple independent cave populations (Pachón, Molino, Tinaja) evolved from surface-dwelling ancestors, allowing researchers to ask whether similar phenotypes arose through similar molecular mechanisms. However, data from different studies — population-genetics scans, transcriptomic time courses, genome-wide association analyses — have historically been generated in isolation, making cross-study synthesis difficult.

A critical bottleneck is data fragmentation. Of 1,140 genes with published F_ST values, only 83 had both F_ST and log-fold-change (logFC) measurements available from prior studies, highlighting how sparsely the existing datasets overlap and how much signal may be hidden in their intersections (Perry et al. 2022, Finding 2). This motivates purpose-built integrative infrastructure.

CaveCrawler, a Shiny-based web analysis suite, was developed to address this gap. It combines population genetics and transcriptomic data from multiple A. mexicanus populations and integrates Gene Ontology (GO) term information, enabling cross-study biological inference from a unified interface (Perry et al. 2022, Finding 1). The tool represents the current state of practice for community-level genomic synthesis in cavefish research.

As a proof of principle, CaveCrawler identified arpin — a negative regulator of actin polymerization — as a “double outlier”: both an F_ST outlier and differentially expressed in circadian rhythm datasets across all three cave-population-versus-surface comparisons (Pachón, Molino, and Tinaja vs. Río Choy). This convergent signal across independent populations makes arpin a high-priority candidate for functional follow-up in studies of actin dynamics and/or circadian evolution in cavefish (Perry et al. 2022, Finding 3).

Supporting evidence

• Integrative database: CaveCrawler unifies transcriptomic, population genetics, GO, and genome architecture data for A. mexicanus in a single interactive platform. Perry et al. 2022, Finding 1

• Data sparsity quantified: Across prior published studies, only 83 genes had simultaneous F_ST outlier status and logFC measurements, underscoring the need for cross-study integration. Perry et al. 2022, Finding 2

• Convergent candidate gene: arpin emerged as a double outlier (F_ST + circadian logFC) in all three independent cave-vs.-surface population pairs, suggesting a shared molecular substrate for at least some convergent cave traits. Perry et al. 2022, Finding 3

Contradictions / open disagreements

The arpin result is correlative and threshold-dependent: classifying F_ST outliers at the lowest 5% of divergence (Herman et al. 2018) and drawing on one circadian transcription dataset (Mack et al. 2021) means the double-outlier list could shift with different datasets or thresholds. No functional validation of arpin’s role in cavefish biology has been reported, so its candidacy remains bioinformatic rather than mechanistic. Additionally, CaveCrawler’s long-term utility as a citable resource depends on continued curation; if data deposition stalls, the snapshot captured at publication may become unrepresentative of the field.

Tealc’s citation-neighborhood suggestions

• Functional CRISPR or morpholino studies targeting arpin in A. mexicanus would test whether the convergent signal reflects genuine shared causation.
• Broader comparative cavefish genomics (e.g., other cave-adapted teleosts such as Sinocyclocheilus or Typhlichthys) could contextualize whether the patterns observed in A. mexicanus are general or clade-specific.
• Papers on circadian rhythm loss in cave animals would be natural companions to the arpin finding.

Related on the Blackmon Lab site

• Paper permalink: CaveCrawler (2022)