Multi‐trait evolution in a cave fish, Astyanax mexicanus

  title={Multi‐trait evolution in a cave fish, Astyanax mexicanus},
  author={Meredith E. Protas and Inna Tabansky and Melissa D. Conrad and Joshua B. Gross and Oriol Vidal and Clifford J. Tabin and Richard Borowsky},
  journal={Evolution \& Development},
SUMMARY When surface species colonize caves, a characteristic suite of traits eventually evolves over time, regardless of species. The genetic basis of the inevitable appearance of these very similar phenotypes was investigated through quantitative trait loci (QTL) mapping of 12 traits that differ significantly between the recently evolved (<1 Myr). Mexican cave tetra and its surface conspecific. The traits were a representative set, including eye size, pigment cell numbers, chemical… 
A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution
A high-resolution, chromosome-level surface fish genome is presented, enabling the first genome-wide comparison between surface fish and cavefish populations and confirming the essential role of a gene within an eye size QTL, rx3, in eye formation in A. mexicanus.
The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus
The findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment.
Genome Editing Using TALENs in Blind Mexican Cavefish, Astyanax mexicanus
TALENs were designed to target two genes that contain coding changes in cavefish relative to surface fish and map to the same location as QTL for pigmentation, oculocutaneous albinism 2 (oca2) and melanocortin 1 receptor (mc1r), and it was found that surface fish genes can be mutated using this method.
Genetic mapping of metabolic traits in the blind Mexican cavefish reveals sex-dependent quantitative trait loci associated with cave adaptation
This study reveals previously unappreciated genomic regions associated with blood glucose regulation, body condition, gonad size, and internal organ morphology in cavefish and finds an interaction between sex and metabolism-related traits in A. mexicanus.
In-Frame Indel Mutations in the Genome of the Blind Mexican Cavefish, Astyanax mexicanus
A genome-wide screen for in-frame indels using alignments of RNA-sequencing reads to the draft cavefish genome reveals previously unappreciated traits evolving in this species under environmental pressures and provides insight to genetic changes underlying convergence of organisms evolving in complete darkness.
The cavefish genome reveals candidate genes for eye loss
The first de novo genome assembly for Astyanax mexicanus cavefish is presented, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences.
Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)
The similar cave phenotypes found in these caves are the result of repeated convergences in spite of gene flow from surface populations suggesting either strong natural or sexual selection for alleles responsible for the cave phenotype in the cave environment.
Natural bone fragmentation in the blind cave‐dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics
This work underscores the value of cave‐dwelling fish as a powerful evolutionary model of craniofacial disease, and demonstrates the power of integrative system‐level studies for informing the genetic basis of craniafacial aberrations in nature.
Phenotypic plasticity as an important mechanism of cave colonization and adaptation in Astyanax cavefish
It is suggested that phenotypic plasticity may significantly contribute to the rapid evolution of cave-related traits providing a foundation for genetic assimilation in colonization of A. mexicanus to dark cave environments.


Mapping a cave fish genome: polygenic systems and regressive evolution.
RAPD fingerprinting is used to generate anonymous DNA markers in the fish Astyanax mexicanus, a species with both surface and cave populations and the results are the first direct demonstration that troglomorphic changes in this population are multifactorial.
Convergent evolution of the cavefish Astyanax (Characidae, Teleostei): genetic evidence from reduced eye‐size and pigmentation
This work has confirmed that in different cave populations of the cave-dwelling characid Astyanax, different mutations in the eye gene system have occurred, and that in cases where these non-functional rudimentary genes are recombined in hybrid specimens, gene expression may be restored.
Evidence for multiple genetic forms with similar eyeless phenotypes in the blind cavefish, Astyanax mexicanus.
An analysis of variation in the mitochondrial NADH dehydrogenase 2 (ND2) gene among different surface fish and cavefish populations identifies a minimum of two genetically distinctive cavefish lineages with similar eyeless phenotypes.
Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat
  • Junhua Peng, Y. Ronin, A. Korol
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
The A genome of wheat may have played a more important role than the B genome during domestication evolution and the cryptic beneficial alleles at specific QTLs derived from T. dicoccoides may contribute to wheat and cereal improvement.
Pleiotropic Quantitative Trait Loci Contribute to Population Divergence in Traits Associated With Life-History Variation in Mimulus guttatus
Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained, and there may be a shared genetic basis for floral divergence within and among species of Mimulus.
Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling
Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis
Evidence is reported suggesting a surprising source of genetic variation contributing to sympatric host shifts forephritid fruit flies belonging to the Rhagoletis pomonella sibling species complex, which originated in a different time and place than the proximate ecological host shifts triggering sympatrics divergence.
Genetic linkage of ecological specialization and reproductive isolation in pea aphids
A model of the role of genetic correlations in specialization and speciation is presented, and several complexes of pleiotropic or closely linked quantitative trait loci that affect key traits in ways that would promote speciation are found.
QTL clusters reflect character associations in wild and cultivated rice
The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs), which showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits.
Mapped genomic locations for developmental functions and QTLs reflect concerted groups in maize (Zea mays L.)
The evolutionary and cytogenetic evidence seems to support the adaptive significance of functional gene networks for development, and the physiological advantage of the close association of functionally related genes in the clusters may rely on compartmentation and tunneling of signal molecules, which helps to cooperatively recruit the transcription factors into multicomponent regulatory modules of high specificity.