Hybridization underlies localized trait evolution in cavefish

Moran, Rachel; Jaggard, James B.; Roback, Emma Y.; Kenzior, Alexander; Rohner, Nicolas; Kowalko, Johanna E.; Ornelas‐García, Claudia Patricia; McGaugh, Suzanne E.; Keene, Alex C.

doi:10.1016/j.isci.2022.103778

Cited by 28 publications

(32 citation statements)

References 85 publications

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“…Here, we describe a modular analysis suite for A. mexicanus. We have included a set of the genomics and transcriptional data that has been previously published ( Herman et al 2018 ; McGaugh, Passow et al 2020 ; Howe, Achuthan et al 2021 ; Mack et al 2021 ; The UniProt Consortium 2021 ; Warren et al 2021 ; Moran et al 2022 ). In addition to these studies, transcriptional analysis across developmental timepoints, as well as single cell analysis of hypothalamus has been collected.…”

Section: Discussionmentioning

confidence: 99%

“…CaveCrawler currently pools data from multiple publications and authors can request that their own data be integrated into CaveCrawler’s repository. As of publication, CaveCrawler’s data bank includes transcriptional datasets ( Mack et al 2021 ; Moran et al 2022 ), population genetics datasets ( Herman et al 2018 ; McGaugh, Passow, et al 2020 ), GO data from UniProt and the Gene Ontology Consortium ( Ashburner et al 2000 ; The Gene Ontology Consortium 2021 ; The UniProt Consortium 2021 ), and genome architecture data from Ensembl Genome Browser, release 104 ( Howe, Achuthan, et al 2021 ). The specific datasets which CaveCrawler draws data from are described in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

“…CaveCrawler’s Population Genetics and Gene Search modules currently integrate data from 2 studies describing signatures of selection in A. mexicanus ( Herman et al 2018 ; Moran et al 2022 ). One of these studies calculated π and Tajima’s D values for the Pachón, Tinaja, Molino, Río Choy, and Rascón populations, as well as F ST and d XY values for each population pair ( Herman et al 2018 ).…”

Section: Methodsmentioning

confidence: 99%

“…One of these studies calculated π and Tajima’s D values for the Pachón, Tinaja, Molino, Río Choy, and Rascón populations, as well as F ST and d XY values for each population pair ( Herman et al 2018 ). The other study describes d XY values of all genes in 2 populations of the Chica morph, Pachón and Rascón, and Tinaja and Rascón ( Moran et al 2022 ). CaveCrawler itself does not calculate new population genetics statistics but instead integrates statistics calculated in previous studies.…”

Section: Methodsmentioning

confidence: 99%

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CaveCrawler: an interactive analysis suite for cavefish bioinformatics

Perry

McGaugh

Keene

et al. 2022

G3 Genes|Genomes|Genetics

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The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as two morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g., Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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CaveCrawler: an interactive analysis suite for cavefish bioinformatics

Perry

McGaugh

Keene

et al. 2022

G3 Genes|Genomes|Genetics

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“…4; Krzywinski et al 2009). A candidate gene list was extracted from an ∼8Mb region on chromosome 7 using a custom pipeline outlined in Moran et al 2022.…”

Section: Methodsmentioning

confidence: 99%

Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish

Powers

Hyacinthe

Riddle

et al. 2022

Preprint

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The Mexican tetra, Astyanax mexicanus, includes interfertile surface-dwelling and cave-dwelling morphs, enabling powerful studies aimed at uncovering genes involved in the evolution of cave-associated traits. Compared to surface fish, cavefish harbor several extreme traits within their skull, such as a protruding lower jaw, a wider gape, and an increase in tooth number. These features are highly variable between individual cavefish and even across different cavefish populations. To investigate these traits, we created a novel feeding behavior assay wherein bite impressions could be obtained. We determined that fish with an underbite leave larger bite impressions with an increase in the number of tooth marks. Capitalizing on the ability to produce hybrids from surface and cavefish crosses, we investigated genes underlying these segregating orofacial traits by performing Quantitative Trait Loci (QTL) analysis with F2 hybrids. We discovered significant QTL for bite (underbite vs. overbite) that mapped to a single region of the Astyanax genome. This work highlights cavefish as a valuable genetic model for orofacial patterning and will provide insight into the genetic regulators of jaw and tooth development.

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Gill morphology adapted to oxygen‐limited caves in Astyanax mexicanus

Boggs,

Gross

2024

J Exp Zool Pt A

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Sensing and acquiring dissolved oxygen is crucial for nearly all aquatic life. This may become even more vital as dissolved oxygen concentrations continue to decline in many aquatic environments. While certain phenotypes that enable fish to live in low oxygen have been characterized, adaptations that arise following sudden, drastic reductions in dissolved oxygen are relatively unknown. Here, we assessed the blind Mexican cavefish, Astyanax mexicanus, for alterations to gill morphology that may be adaptive for life in hypoxic caves. The Astyanax system provides the unique opportunity to compare gill morphology between stereotypical “surface” adapted morphotypes and obligate cave‐dwelling conspecifics. While the surface environment is well‐oxygenated, cavefish must cope with significantly reduced oxygen. We began by quantifying traditional morphological gill traits including filament number and length as well as lamellar density and height in surface fish and two distinct cave populations, Pachón and Tinaja. This enabled us to estimate total lamellar height, a proxy for gill surface area. We then used immunohistochemical staining to label 5‐HT‐positive neuroepithelial cells (NECs), which serve as key oxygen sensors in fish. We discovered an increase in gill surface area for both cavefish populations compared to surface, which may enable a higher capacity of oxygen acquisition. Additionally, we found more NECs in Pachón cavefish compared to both surface fish and Tinaja cavefish, suggesting certain selective pressures may be cave‐specific. Collectively, this work provides evidence that cavefish have adapted to low oxygen conditions via alterations to gill morphology and oxygen sensing, and informs evolutionary mechanisms of rapid adaptation to dramatic, chronic hypoxia.

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Hybridization underlies localized trait evolution in cavefish

Cited by 28 publications

References 85 publications

CaveCrawler: an interactive analysis suite for cavefish bioinformatics

CaveCrawler: an interactive analysis suite for cavefish bioinformatics

Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish

Gill morphology adapted to oxygen‐limited caves in Astyanax mexicanus

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