Cited by 298Subterranean biodiversity and taxonomyRetinal Development and DisordersDevelopmental Biology and Gene Regulation

The DOI matches its Crossref record; 68 of the 68 references it cites were found in a registry or an index.

Regressive Evolution in Astyanax Cavefish

Open access

Jeffery, William R.·2009·Annual Review of Genetics

DOI 10.1146/annurev-genet-102108-134216PMC PMC3594788

Open this paper in CoChat — free account

Abstract

A diverse group of animals, including members of most major phyla, have adapted to life in the perpetual darkness of caves. These animals are united by the convergence of two regressive phenotypes, loss of eyes and pigmentation. The mechanisms of regressive evolution are poorly understood. The teleost Astyanax mexicanus is of special significance in studies of regressive evolution in cave animals. This species includes an ancestral surface dwelling form and many con-specific cave-dwelling forms, some of which have evolved their recessive phenotypes independently. Recent advances in Astyanax development and genetics have provided new information about how eyes and pigment are lost during cavefish evolution; namely, they have revealed some of the molecular and cellular mechanisms involved in trait modification, the number and identity of the underlying genes and mutations, the molecular basis of parallel evolution, and the evolutionary forces driving adaptation to the cave environment.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1146/annurev-genet-102108-134216

Cites

68 of 68 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life /
Darwin, C. R., Darwin, C. R., & Edmonds & Remnants (1859) · J. Murray eBooks · doi:10.5962/bhl.title.59991 · Cited by 7,020
On the origin of species by means of natural selection: Or the preservation of the favoured races in the struggle for life.
Darwin, C. R. (1860) · J. Murray eBooks · doi:10.1037/14088-000 · Cited by 2,019
On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life
Darwin, C. R. (1888) · Springer eBooks · doi:10.1007/978-3-319-19650-3_303511 · Cited by 869
Patterning activities of vertebrate hedgehog proteins in the developing eye and brain
Ekker, S. C., Ungar, A. R., Greenstein, P., von Kessler, D. P., Porter, J. A., Moon, R. T., & Beachy, P. A. (1995) · Current Biology · doi:10.1016/s0960-9822(95)00185-0 · Cited by 571
The Cave Environment
Poulson, T. L., & White, W. B. (1969) · Science · doi:10.1126/science.165.3897.971 · Cited by 568
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism
Protas, M. E., Hersey, C., Kochanek, D., Zhou, Y., Wilkens, H., Jeffery, W. R., Zon, L. I., Borowsky, R., & Tabin, C. J. (2006) · Nature Genetics · doi:10.1038/ng1700 · Cited by 543
Self-citation
The biology of caves and other subterranean habitats
(2009) · Choice Reviews Online · doi:10.5860/choice.47-1398 · Cited by 492
The Origin of Species by means of Natural Selection, or, the preservation of favoured races in the struggle for life /
Darwin, C. R. (1872) · J. Murray eBooks · doi:10.5962/bhl.title.61216 · Cited by 490
Genetics of hair and skin color
Rees, J. L. (2003) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.143233 · Cited by 485
Growth of the adult goldfish eye. III. Source of the new retinal cells
Johns, P. R. (1977) · The Journal of Comparative Neurology · doi:10.1002/cne.901760304 · Cited by 462

Show all 68 references

Research works printed but not linked: 16

Alvarez J, 1946, An. Esc. Nac. Cien. Biol. Mexico, 4, 263
Alvarez J, 1947, Rev. Soc. Mexicana Hist. Nat., 8, 215
Cahn PH, 1958, Bull. Am. Mus. Nat. Hist., 115, 75
Culver DC, 2000, Ecosystems of the World, 30, 381
Espinasa L, 2001, Environ. Biol. Fishes, 62, 329
Hubbs CL, 1936, Occas. Papers Mus. Zool. Univ. Michigan, 342, 1
Johns P, 1977, J. Comp. Neurol., 176, 348
Mitchell RW, 1977, Spec. Publ. Mus. Texas Tech Univ., 12, 1
Moritz OL, 1996, Invest. Ophthalmol. Vis. Sci., 37, 352
Proudlove G, 2006, Subterranean Fishes of the World
Rasquin P, 1947, Zoologica, 32, 35
Rinchik EM, 1993, Proc. Natl. Acad. Sci. USA, 91, 12071
Sadoglu P, 1957, Verh. Dtsch. Zool. Ges., 1957, 432
Strickler AG, 2009, Int. Zool., 4, 31
Strickler AG, 2002, Int. J. Dev. Biol., 46, 285
Wilkens H, 1972, Ann. Spéléol., 27, 263

Sorted by citations

Evolution of Gene Regulatory Networks Controlling Body Plan Development
Peter, I. S., & Davidson, E. H. (2011) · Cell · doi:10.1016/j.cell.2011.02.017 · Cited by 417
Adaptation in the age of ecological genomics: insights from parallelism and convergence
Elmer, K. R., & Meyer, A. (2011) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.02.008 · Cited by 410
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Yang, J., Chen, X., Bai, J., Fang, D., Qiu, Y., Jiang, W., Yuan, H. S., Bian, C., Jiang, L., He, S., et al. (2016) · BMC Biology · doi:10.1186/s12915-015-0223-4 · Cited by 384
Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish
Rohner, N., Jarosz, D. F., Kowalko, J. E., Yoshizawa, M., Jeffery, W. R., Borowsky, R. L., Lindquist, S., & Tabin, C. J. (2013) · Science · doi:10.1126/science.1240276 · Cited by 365
Self-citation
A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception
Cavallari, N., Frigato, E., Vallone, D., Fröhlich, N., López‐Olmeda, J. F., Foà, A., Berti, R., Sánchez‐Vázquez, F. J., Bertolucci, C., & Foulkes, N. S. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001142 · Cited by 231
Evolution in caves: Darwin’s ‘wrecks of ancient life’ in the molecular era
Juan, C., Guzik, M. T., Jaume, D., & Cooper, S. J. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04759.x · Cited by 226
The origins and evolution of sleep
Keene, A. C., & Duboué, E. R. (2018) · Journal of Experimental Biology · doi:10.1242/jeb.159533 · Cited by 235
Finding answers in the dark: caves as models in ecology fifty years after Poulson and White
Mammola, S. (2018) · Ecography · doi:10.1111/ecog.03905 · Cited by 208
Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)
Bradić, M., Beerli, P., León, F. J. G.-D., Esquivel-Bobadilla, S., & Borowsky, R. L. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-9 · Cited by 194
Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
Fumey, J., Hinaux, H., Noirot, C., Thermes, C., Rétaux, S., & Casañe, D. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1156-7 · Cited by 184
Evolution and development in cave animals: from fish to crustaceans
Protas, M. E., & Jeffery, W. R. (2012) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.61 · Cited by 166
Self-citation
Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling
Partha, R., Chauhan, B. K., Ferreira, Z., Robinson, J. D., Lathrop, K., Nischal, K. K., Chikina, M., & Clark, N. L. (2017) · eLife · doi:10.7554/elife.25884 · Cited by 160
Circadian rhythms in Mexican blind cavefish Astyanax mexicanus in the lab and in the field
Beale, A. D., Guibal, C., Tamai, K. T., Klotz, L., Cowen, S., Peyric, E., Reynoso, V. H., Yamamoto, Y., & Whitmore, D. (2013) · Nature Communications · doi:10.1038/ncomms3769 · Cited by 157
A Potential Benefit of Albinism in Astyanax Cavefish: Downregulation of the oca2 Gene Increases Tyrosine and Catecholamine Levels as an Alternative to Melanin Synthesis
Bilandžija, H., Ma, L., Parkhurst, A., & Jeffery, W. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080823 · Cited by 148
Self-citation
Fundamental research questions in subterranean biology
Mammola, S., Amorim, I. R., Bichuette, M. E., Borges, P. A. V., Cheeptham, N., Cooper, S. J., Culver, D. C., Deharveng, L., Eme, D., Ferreira, R. L., et al. (2020) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12642 · Cited by 145
Self-citation
A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations
Nadeau, N. J., & Jiggins, C. D. (2010) · Trends in Genetics · doi:10.1016/j.tig.2010.08.004 · Cited by 147
Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Zhao, L., Wit, J., Svetec, N., & Begun, D. J. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005184 · Cited by 130
Old gene duplication facilitates origin and diversification of an innovative communication system—twice
Arnegard, M. E., Zwickl, D. J., Lu, Y., & Zakon, H. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011803107 · Cited by 126
On the fate of sexual traits under asexuality
van der Kooi, C. J., & Schwander, T. (2014) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12078 · Cited by 123
A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo.
Braasch, I., Peterson, S. M., Desvignes, T., McCluskey, B. M., Batzel, P., & Postlethwait, J. H. (2015) · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution · doi:10.1002/jez.b.22589 · Cited by 122
Heart Regeneration in the Mexican Cavefish
Stockdale, W. T., Lemieux, M. E., Killen, A. C., Zhao, J., Hu, Z., Riepsaame, J., Hamilton, N., Kudoh, T., Riley, P. R., van Aerle, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.10.072 · Cited by 119
Convergence and divergence in the subterranean realm: a reassessment
Pipan, T., & Culver, D. C. (2012) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2012.01964.x · Cited by 117
The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function
Musilová, Z., Salzburger, W., & Cortesi, F. (2021) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120219-024915 · Cited by 116
EVIDENCE FOR REPEATED LOSS OF SELECTIVE CONSTRAINT IN RHODOPSIN OF AMBLYOPSID CAVEFISHES (TELEOSTEI: AMBLYOPSIDAE)
Niemiller, M. L., Fitzpatrick, B. M., Shah, P., Schmitz, L., & Near, T. J. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01822.x · Cited by 108
Restoring eye size in Astyanax mexicanus blind cavefish embryos through modulation of the Shh and Fgf8 forebrain organising centres
Pottin, K., Hinaux, H., & Rétaux, S. (2011) · Development · doi:10.1242/dev.054106 · Cited by 107
Hypocretin underlies the evolution of sleep loss in the Mexican cavefish
Jaggard, J. B., Stahl, B. A., Lloyd, E., Prober, D. A., Duboué, E. R., & Keene, A. C. (2018) · eLife · doi:10.7554/elife.32637 · Cited by 108
Astyanax Transgenesis and Husbandry: How Cavefish Enters the Laboratory
Elipot, Y., Legendre, L., Père, S., Sohm, F., & Rétaux, S. (2014) · Zebrafish · doi:10.1089/zeb.2014.1005 · Cited by 107
Parallel speciation in Astyanax cave fish (Teleostei) in Northern Mexico
Strecker, U., Hausdorf, B., & Wilkens, H. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.09.005 · Cited by 102
Of cancer and cave fish
Gatenby, R. A., Gillies, R. J., & Brown, J. S. (2011) · Nature reviews. Cancer · doi:10.1038/nrc3036 · Cited by 100
A Developmental Staging Table for Astyanax mexicanus Surface Fish and Pachón Cavefish
Hinaux, H., Pottin, K., Chalhoub, H., Père, S., Elipot, Y., Legendre, L., & Rétaux, S. (2011) · Zebrafish · doi:10.1089/zeb.2011.0713 · Cited by 101
Quantitative Genetic Analysis of Retinal Degeneration in the Blind Cavefish Astyanax mexicanus
O’Quin, K. E., Yoshizawa, M., Doshi, P., & Jeffery, W. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057281 · Cited by 90
Self-citation
Evolution of the fish heart by sub/neofunctionalization of an elastin gene
Moriyama, Y., Ito, F., Takeda, H., Yano, T., Okabe, M., Kuraku, S., Keeley, F. W., & Koshiba‐Takeuchi, K. (2016) · Nature Communications · doi:10.1038/ncomms10397 · Cited by 96
Astyanax surface and cave fish morphs
Jeffery, W. R. (2020) · EvoDevo · doi:10.1186/s13227-020-00159-6 · Cited by 88
Self-citation
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals
Meyer, W. K., Jamison, J. M., Richter, R. J., Woods, S. E., Partha, R., Kowalczyk, A. M., Kronk, C., Chikina, M. D., Bonde, R. K., Crocker, D. E., et al. (2018) · Science · doi:10.1126/science.aap7714 · Cited by 93
Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish
Meng, F., Braasch, I., Phillips, J. B., Lin, X., Titus, T. A., Zhang, C., & Postlethwait, J. H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst079 · Cited by 83
Selection-driven trait loss in independently evolved cavefish populations
Moran, R. L., Richards, E. J., Ornelas‐García, C. P., Gross, J. B., Donny, A. E., Wiese, J., Keene, A. C., Kowalko, J. E., Rohner, N., & McGaugh, S. E. (2023) · Nature Communications · doi:10.1038/s41467-023-37909-8 · Cited by 87
A mutation in the enzyme monoamine oxidase explains part of the Astyanax cavefish behavioural syndrome
Elipot, Y., Hinaux, H., Callebert, J., Launay, J., Blin, M., & Rétaux, S. (2014) · Nature Communications · doi:10.1038/ncomms4647 · Cited by 79
Phototransduction and clock gene expression in the troglobiont beetlePtomaphagus hirtusof Mammoth cave
Friedrich, M., Chen, R., Daines, B., Bao, R., Caravas, J., Rai, P. K., Zagmajster, M., & Peck, S. B. (2011) · Journal of Experimental Biology · doi:10.1242/jeb.060368 · Cited by 75
Cilia, calcium and the basis of left-right asymmetry
Norris, D. P. (2012) · BMC Biology · doi:10.1186/1741-7007-10-102 · Cited by 73
An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus
Gross, J. B., Furterer, A., Carlson, B. M., & Stahl, B. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055659 · Cited by 72
Consequences of evolutionary transitions in changing photic environments
Tierney, S. M., Friedrich, M., Humphreys, W. F., Jones, T. M., Warrant, E. J., & Wcislo, W. T. (2017) · Austral Entomology · doi:10.1111/aen.12264 · Cited by 73
Speciation by selection: A framework for understanding ecology’s role in speciation
Langerhans, R. B., & Riesch, R. (2013) · Current Zoology · doi:10.1093/czoolo/59.1.31 · Cited by 72
Evolutionary Genetics of the Cavefish Astyanax mexicanus
Casañe, D., & Rétaux, S. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.03.001 · Cited by 62
Complex Craniofacial Changes in Blind Cave-Dwelling Fish Are Mediated by Genetically Symmetric and Asymmetric Loci
Gross, J. B., Krutzler, A. J., & Carlson, B. M. (2014) · Genetics · doi:10.1534/genetics.114.161661 · Cited by 63
Circadian regulation of olfaction and an evolutionarily conserved, nontranscriptional marker in Caenorhabditis elegans
Olmedo, M., O'Neill, J. S., Edgar, R. S., Valekunja, U. K., Reddy, A. B., & Merrow, M. W. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211705109 · Cited by 63
Extreme Adaptation in Caves
Soares, D., & Niemiller, M. L. (2018) · The Anatomical Record · doi:10.1002/ar.24044 · Cited by 59
Ecological Transition Predictably Associated with Gene Degeneration
Wessinger, C. A., & Rausher, M. D. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu298 · Cited by 60
The lateral line confers evolutionarily derived sleep loss in the Mexican cavefish
Jaggard, J. B., Robinson, B. G., Stahl, B. A., Oh, I. M., Masek, P., Yoshizawa, M., & Keene, A. C. (2017) · Journal of Experimental Biology · doi:10.1242/jeb.145128 · Cited by 60
Cavefishes
Borowsky, R. L. (2018) · Current Biology · doi:10.1016/j.cub.2017.12.011 · Cited by 61
Coevolution of life history traits and morphology in female subterranean amphipods
Fišer, C., Zagmajster, M., & Zakšek, V. (2012) · Oikos · doi:10.1111/j.1600-0706.2012.20644.x · Cited by 58
Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs
Klaus, S., Mendoza, J. C. E., Liew, J. H., Plath, M. W., Meier, R., & Yeo, D. C. J. (2013) · Biology Letters · doi:10.1098/rsbl.2012.1098 · Cited by 58
Goldfish morphology as a model for evolutionary developmental biology
Ota, K. G., & Abe, G. (2016) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.224 · Cited by 61
Success and failure in replication of genotype–phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?
Schielzeth, H., Villamil, A. R., & Burri, R. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12780 · Cited by 57
Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei)
Hausdorf, B., Wilkens, H., & Strecker, U. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.03.009 · Cited by 56
Challenges and prospects in genome‐wide quantitative trait loci mapping of standing genetic variation in natural populations
Schielzeth, H., & Husby, A. (2014) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12397 · Cited by 55
Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats
Teeling, E. C., Jones, G., & Rossiter, S. J. (2016) · Springer handbook of auditory research · doi:10.1007/978-1-4939-3527-7_2 · Cited by 56
Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches
Tierney, S. M., Cooper, S. J., Saint, K. M., Bertozzi, T., Hyde, J., Humphreys, W. F., & Austin, A. D. (2015) · Royal Society Open Science · doi:10.1098/rsos.140386 · Cited by 53
Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele
Gross, J. B., & Wilkens, H. (2013) · Heredity · doi:10.1038/hdy.2013.26 · Cited by 49
Sweet fish: Fish models for the study of hyperglycemia and diabetes
Krishnan, J., & Rohner, N. (2018) · Journal of Diabetes · doi:10.1111/1753-0407.12860 · Cited by 52
The role of a lens survival pathway including sox2 and αA-crystallin in the evolution of cavefish eye degeneration
Ma, L., Parkhurst, A., & Jeffery, W. R. (2014) · EvoDevo · doi:10.1186/2041-9139-5-28 · Cited by 48
Self-citation
Parallel developmental genetic features underlie stickleback gill raker evolution
Glazer, A. M., Cleves, P. A., Erickson, P. A., Lam, A. Y., & Miller, C. T. (2014) · EvoDevo · doi:10.1186/2041-9139-5-19 · Cited by 49
Transcriptional Changes Associated with Lack of Lipid Synthesis in Parasitoids
Visser, B., Roelofs, D., Hahn, D. A., Teal, P. E. A., Mariën, J., & Ellers, J. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs065 · Cited by 45
Cavefish eye loss in response to an early block in retinal differentiation progression
Stemmer, M., Schuhmacher, L.-N., Foulkes, N. S., Bertolucci, C., & Wittbrodt, J. (2015) · Development · doi:10.1242/dev.114629 · Cited by 47
The Biological Mechanisms and Behavioral Functions of Opsin-Based Light Detection by the Skin
Kelley, J. L., & Davies, W. I. L. (2016) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2016.00106 · Cited by 46
Cranial asymmetry arises later in the life history of the blind Mexican cavefish, Astyanax mexicanus
Powers, A. K., Davis, E. M., Kaplan, S. A., & Gross, J. B. (2017) · PLoS ONE · doi:10.1371/journal.pone.0177419 · Cited by 47
Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization
Calderoni, L., Rota‐Stabelli, O., Frigato, E., Panziera, A., Kirchner, S. G., Foulkes, N. S., Kruckenhauser, L., Bertolucci, C., & Fuselli, S. (2016) · Heredity · doi:10.1038/hdy.2016.59 · Cited by 43
Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea
Lopes‐Marques, M., Machado, A. M., Alves, L. Q., Fonseca, M. M., Barbosa, S., Sinding, M. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, M. F., Campos, P. F., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz068 · Cited by 44
Evolution of acoustic communication in blind cavefish
Hyacinthe, C., Attia, J., & Rétaux, S. (2019) · Nature Communications · doi:10.1038/s41467-019-12078-9 · Cited by 44
Lens defects in A styanax mexicanus Cavefish: Evolution of crystallins and a role for alphaA‐crystallin
Hinaux, H., Blin, M., Fumey, J., Legendre, L., Heuzé, A., Casañe, D., & Rétaux, S. (2014) · Developmental Neurobiology · doi:10.1002/dneu.22239 · Cited by 41
Dark world rises: The emergence of cavefish as a model for the study of evolution, development, behavior, and disease
McGaugh, S. E., Kowalko, J. E., Duboué, E. R., Lewis, P., Franz‐Odendaal, T. A., Rohner, N., Gross, J. B., & Keene, A. C. (2020) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.22978 · Cited by 42
Evolution and development of complex eyes: a celebration of diversity
Koenig, K. M., & Gross, J. M. (2020) · Development · doi:10.1242/dev.182923 · Cited by 46
Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System
Lafuente, E., Lürig, M., Rövekamp, M., Matthews, B., Buser, C. C., Vorburger, C., & Räsänen, K. (2021) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2021.748212 · Cited by 48
Genetic Architecture of Parallel Pelvic Reduction in Ninespine Sticklebacks
Shikano, T., Laine, V. N., Herczeg, G., Vilkki, J., & Merilä, J. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007237 · Cited by 41
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish
Krishnan, J., Seidel, C. W., Zhang, N., Singh, N. P., VanCampen, J., Peuß, R., Xiong, S., Kenzior, A., Li, H., Conaway, J. W., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01049-4 · Cited by 47
DECOUPLING OF RAPID AND ADAPTIVE EVOLUTION AMONG SEMINAL FLUID PROTEINS IN HELICONIUS BUTTERFLIES WITH DIVERGENT MATING SYSTEMS
Walters, J. R., & Harrison, R. G. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01351.x · Cited by 38
A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus
Stahl, B. A., Gross, J. B., Speiser, D. I., Oakley, T. H., Patel, N. H., Gould, D. B., & Protas, M. E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140484 · Cited by 38
A Comparative Transcriptomic Analysis of Development in Two Astyanax Cavefish Populations
Stahl, B. A., & Gross, J. B. (2017) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.22749 · Cited by 36
A hypomorphic cystathionine ß-synthase gene contributes to cavefish eye loss by disrupting optic vasculature
Ma, L., Gore, A. V., Castranova, D., Shi, J., Ng, M., Tomins, K. A., van der Weele, C. M., Weinstein, B. M., & Jeffery, W. R. (2020) · Nature Communications · doi:10.1038/s41467-020-16497-x · Cited by 36
Self-citation
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits
Mao, T., Liu, Y., Meegaskumbura, M., Yang, J. D., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J. B., & Pie, M. R. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-021-01776-y · Cited by 37
The Kingdom of the Blind: Disentangling Fundamental Drivers in the Evolution of Eye Loss
Sumner‐Rooney, L. H. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy047 · Cited by 36
A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology
Carlson, B. M., Onusko, S. W., & Gross, J. B. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.015438 · Cited by 35
Conservation, development, and function of a cement gland-like structure in the fish Astyanax mexicanus
Pottin, K., Hyacinthe, C., & Rétaux, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005035107 · Cited by 37
Regressive progression, progressive regression or neither? Phylogeny and evolution of the Percopsiformes (Teleostei, Paracanthopterygii)
Dillman, C. B., Bergstrom, D. E., Noltie, D. B., Holtsford, T. P., & Mayden, R. L. (2010) · Zoologica Scripta · doi:10.1111/j.1463-6409.2010.00454.x · Cited by 35
The Varieties of Parsimony in Psychology
Dacey, M. (2016) · Mind & Language · doi:10.1111/mila.12113 · Cited by 38
Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)
Williams, S. T., Smith, L. M., Herbert, D. G., Marshall, B. A., Warén, A., Kiel, S., Dyal, P. L., Linse, K., Vilvens, C., & Kano, Y. (2013) · Ecology and Evolution · doi:10.1002/ece3.513 · Cited by 33
Ecological speciation in darkness? Spatial niche partitioning in sibling subterranean spiders (Araneae : Linyphiidae : Troglohyphantes)
Mammola, S., Arnedo, M. A., Pantini, P., Piano, E., Chiappetta, N., & Isaia, M. (2018) · Invertebrate Systematics · doi:10.1071/is17090 · Cited by 34
Cardiac regenerative capacity: an evolutionary afterthought?
Nguyen, P. D., de Bakker, D. E. M., & Bakkers, J. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03831-9 · Cited by 36
Evolution of Space Dependent Growth in the Teleost Astyanax mexicanus
Gallo, N. D., & Jeffery, W. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041443 · Cited by 34
Self-citation
Model organisms at the heart of regeneration
Price, E., Vieira, J. M., & Riley, P. R. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.040691 · Cited by 33
Redefining the extent of the aquatic subterranean biotope—shallow subterranean habitats
Culver, D. C., & Pipan, T. (2011) · Ecohydrology · doi:10.1002/eco.243 · Cited by 33
Brain Size and Visual Environment Predict Species Differences in Paper Wasp Sensory Processing Brain Regions (Hymenoptera: Vespidae, Polistinae)
O’Donnell, S., Clifford, M. R., DeLeon, S., Papa, C., Zahedi, N., & Bulova, S. J. (2013) · Brain Behavior and Evolution · doi:10.1159/000354968 · Cited by 34
Adaptive evolution of the lower jaw dentition in Mexican tetra (Astyanax mexicanus)
Atukorallaya, D., Hammer, C. L., Dufton, M., & Franz‐Odendaal, T. A. (2013) · EvoDevo · doi:10.1186/2041-9139-4-28 · Cited by 32
Manipulation of Gene Function in Mexican Cavefish
Stahl, B. A., Jaggard, J. B., Chin, J. S. R., Kowalko, J. E., Keene, A. C., & Duboué, E. R. (2019) · Journal of Visualized Experiments · doi:10.3791/59093 · Cited by 32
Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)
Ornelas‐García, C. P., Pajares, S., Sosa-Jiménez, V. M., Rétaux, S., & Miranda‐Gamboa, R. (2018) · PeerJ · doi:10.7717/peerj.5906 · Cited by 32
Cave Environments
Niemiller, M. L., & Soares, D. (2014) · Springer eBooks · doi:10.1007/978-3-319-13362-1_8 · Cited by 31
The rise of Astyanax cavefish
Gross, J. B., Meyer, B. J., & Perkins, M. (2015) · Developmental Dynamics · doi:10.1002/dvdy.24253 · Cited by 30
The importance of selection in the evolution of blindness in cavefish
Cartwright, R. A., Schwartz, R. S., Merry, A. L., & Howell, M. M. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0876-4 · Cited by 28
Complexities of gene expression patterns in natural populations of an extremophile fish ( Poecilia mexicana , Poeciliidae)
Passow, C. N., Brown, A. P. C., Arias‐Rodríguez, L., Yee, M., Sockell, A., Schartl, M., Warren, W. C., Bustamante, C. D., Kelley, J. L., & Tobler, M. (2017) · Molecular Ecology · doi:10.1111/mec.14198 · Cited by 29
Development of the Astyanax mexicanus circadian clock and non-visual light responses
Steindal, I. A. F., Beale, A. D., Yamamoto, Y., & Whitmore, D. (2018) · Developmental Biology · doi:10.1016/j.ydbio.2018.06.008 · Cited by 29
Parallel decay of vision genes in subterranean water beetles
Langille, B. L., Tierney, S. M., Bertozzi, T., Beasley‐Hall, P. G., Bradford, T. M., Fagan‐Jeffries, E. P., Hyde, J., Leijs, R., Richardson, M., Saint, K. M., et al. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107522 · Cited by 29

Authors: Jeffery, W. R.
Affiliations: University of Maryland, College Park (US)
Corresponding author: Jeffery, William R.
ORCID: Jeffery, William R.
Venue: Annual Review of Genetics
Publisher: Annual Reviews
Published: 2009-12-01
Volume: 43
Issue: 1
Pages: 25-47
ISSN: 0066-4197 (ISSN-L)
1545-2948
DOI: 10.1146/annurev-genet-102108-134216
PMC: PMC3594788
OpenAlex: W2121610939
Cited by: 298
References: 68
Citations by year: 2026: 15 · 2025: 21 · 2024: 15 · 2023: 20 · 2022: 20 · 2021: 18 · 2020: 28 · 2019: 16 · 2018: 28 · 2017: 14 · 2016: 13 · 2015: 14 · 2014: 16 · 2013: 25 · 2012: 13
FWCI: 1.21
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Annual Review of Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
Funders: National Science Foundation
Fordham University
National Institutes of Health
U.S. Public Health Service (EYO14619)
National Eye Institute (R01EY014619)
Topics: Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Subterranean biodiversity and taxonomy
Health Sciences › Medicine › Ophthalmology › Retinal Development and Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords: regressive evolution, Astyanax mexicanus, cavefish, eye loss, pigmentation loss, cave adaptation, parallel evolution, developmental genetics
MeSH terms: Animals, Darkness, Biological Evolution, Eye, Fishes, Skin Pigmentation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Regressive Evolution in Astyanax Cavefish

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks