Research graph
References from Cave evolution on repeat: reuse of the same genomic regions across lineages of Astyanax mexicanus. Local targets link to admitted publications; unresolved targets remain external evidence.
Odor is a time cue for circadian behavior
10.1177/0748730412469353 · 2013 · External reference
Toward a predictive framework for convergent evolution: integrating natural history, genetic mechanisms, and consequences for the diversity of life
10.1086/692111 · 2017 · External reference
Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions
10.1073/pnas.1510802112 · 2015 · External reference
Unresolved reference
2018 · External reference
Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies
10.1111/jeb.13704 · 2020 · External reference
Polygenic adaptation: a unifying framework to understand positive selection
10.1038/s41576-020-0250-z · 2020 · External reference
Understanding quantitative genetic variation
10.1038/nrg700 · 2002 · External reference
Fitting linear mixed-effects models using lme4
10.18637/jss.v067.i01 · 2015 · External reference
10.32614/cran.package.lme4
10.32614/cran.package.lme4 · 2025 · External reference
Impacts of pleiotropy and migration on repeated genetic adaptation
10.1093/genetics/iyae111 · 2024 · External reference
10.1101/2025.03.09.642216
10.1101/2025.03.09.642216 · 2025 · External reference
Circadian rhythms in Mexican blind cavefish Astyanax mexicanus in the lab and in the field
10.1038/ncomms3769 · 2013 · External reference
Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets
10.1098/rspb.2019.1479 · 2019 · External reference
10.32614/cran.package.statgenmpp
10.32614/cran.package.statgenmpp · 2022 · External reference
Divergence time shapes gene reuse during repeated adaptation
10.1016/j.tree.2023.11.007 · 2024 · External reference
An expanded view of complex traits: from polygenic to omnigenic
10.1016/j.cell.2017.05.038 · 2017 · External reference
Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)
10.1186/1471-2148-12-9 · 2012 · External reference
Unresolved reference
2015 · External reference
Unresolved reference
2015 · External reference
R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multiparent populations
10.1534/genetics.118.301595 · 2019 · External reference
10.32614/cran.package.qtl2
10.32614/cran.package.qtl2 · 2023 · External reference
10.32614/cran.package.qtl
10.32614/cran.package.qtl · 2020 · External reference
R/qtl: QTL mapping in experimental crosses
10.1093/bioinformatics/btg112 · 2003 · External reference
Mutation bias and the predictability of evolution
10.1098/rstb.2022.0055 · 2023 · External reference
Characterization and comparison of activity profiles exhibited by the cave and surface morphotypes of the blind Mexican tetra, Astyanax mexicanus
10.1016/j.cbpc.2017.08.002 · 2018 · External reference
Unresolved reference
2020 · External reference
Stacks: building and genotyping loci de novo from short-read sequences
10.1534/g3.111.000240 · 2011 · External reference
Stacks: an analysis tool set for population genomics
10.1111/mec.2013.22.issue-11 · 2013 · External reference
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a pitx1 enhancer
10.1126/science.1182213 · 2010 · External reference
Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra
10.1242/jeb.249881 · 2025 · External reference
Next generation phylogeography of cave and surface Astyanax mexicanus
10.1016/j.ympev.2014.06.029 · 2014 · External reference
Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles
10.1126/science.1107239 · 2005 · External reference
Extent of QTL reuse during repeated phenotypic divergence of sympatric threespine stickleback
10.1534/genetics.115.182550 · 2015 · External reference
The probability of genetic parallelism and convergence in natural populations
10.1098/rspb.2012.2146 · 2012 · External reference
The variant call format and VCFtools
10.1093/bioinformatics/btr330 · 2011 · External reference
A framework for variation discovery and genotyping using next-generation DNA sequencing data
10.1038/ng.806 · 2011 · External reference
Two MYB proteins in a self-organizing activator–inhibitor system produce spotted pigmentation patterns
10.1016/j.cub.2019.12.067 · 2020 · External reference
10.64898/2026.03.26.714499
10.64898/2026.03.26.714499 · 2026 · External reference
Evolutionary convergence on sleep loss in cavefish populations
10.1016/j.cub.2011.03.020 · 2011 · External reference
Unresolved reference
2018 · External reference
10.32614/cran.package.lpmerge
10.32614/cran.package.lpmerge · 2018 · External reference
LPmerge: an R package for merging genetic maps by linear programming
10.1093/bioinformatics/btu091 · 2014 · External reference
Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks
10.1111/evo.12897 · 2016 · External reference
Contrasting feeding habits of post-larval and adult Astyanax cavefish
10.3897/subtbiol.21.11046 · 2017 · External reference
10.1007/978-1-61779-228-1_9
10.1007/978-1-61779-228-1_9 · 2011 · External reference
Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex
10.1093/aob/mcv080 · 2015 · External reference
Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Filippi 1853) (Actinopterygii, Characidae)
10.1111/mec.17128 · 2023 · External reference
The causes of repeated genetic evolution
10.1016/j.ydbio.2009.04.040 · 2009 · External reference
The evolution of genetic architecture
10.1146/annurev.ecolsys.37.091305.110224 · 2006 · External reference
10.32614/cran.package.hmisc
10.32614/cran.package.hmisc · 2025 · External reference
10.1093/oso/9780198546412.001.0001
10.1093/oso/9780198546412.001.0001 · 1991 · External reference
The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus
10.1111/mec.14877 · 2018 · External reference
Isotopic variability of δ13C and δ15N signals in cave systems: insights from the blind tetra Astyanax mexicanus
10.3897/subtbiol.51.140856 · 2025 · External reference
Polygenic adaptation: from sweeps to subtle frequency shifts
10.1371/journal.pgen.1008035 · 2019 · External reference
A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus
10.1016/j.cub.2021.08.030 · 2021 · External reference
Automated measurements of sleep and locomotor activity in Mexican cavefish
10.3791/59198-v · 2019 · External reference
Evolution of eye regression in the cavefish Astyanax: apoptosis and the Pax-6 gene
10.1093/icb/38.4.685 · 1998 · External reference
To see or not to see: evolution of eye degeneration in Mexican blind cavefish
10.1093/icb/43.4.531 · 2003 · External reference
10.1007/978-3-031-62723-1_5
10.1007/978-3-031-62723-1_5 · 2024 · External reference
Unresolved reference
2015 · External reference
Genetic population structure constrains local adaptation in sticklebacks
10.1111/mec.15808 · 2021 · External reference
10.1016/b978-012088777-4/50013-2
10.1016/b978-012088777-4/50013-2 · 2005 · External reference
Evolution and development of complex eyes: a celebration of diversity
10.1242/dev.182923 · 2020 · External reference
Pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data
10.1111/1755-0998.13326 · 2021 · External reference
Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms
10.1016/j.cub.2013.07.056 · 2013 · External reference
Unresolved reference
External reference
Persistence of ultrastructurally well-developed photoreceptor cells in the pineal organ of a phylogenetically old cave-dwelling population of Astyanax fasciatus Cuvier, 1819 (Teleostei, Characidae)
10.1111/j.1439-0469.1992.tb00178.x · 1992 · External reference
Predictability and parallelism of multitrait adaptation
10.1093/jhered/esx043 · 2017 · External reference
The importance of genetic redundancy in evolution
10.1016/j.tree.2020.04.009 · 2020 · External reference
10.1101/2025.02.06.635682
10.1101/2025.02.06.635682 · 2026 · External reference
Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry
10.1073/pnas.1907068116 · 2019 · External reference
Food as a circadian time cue—evidence from human studies
10.1038/s41574-020-0318-z · 2020 · External reference
Unresolved reference
2017 · External reference
Fast and accurate short read alignment with Burrows–Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations
10.1093/bioinformatics/btac662 · 2022 · External reference
Developmental constraints on genome evolution in four Bilaterian model species
10.1093/gbe/evy177 · 2018 · External reference
Unresolved reference
2026 · External reference
Repeated evolution of circadian clock dysregulation in cavefish populations
10.1371/journal.pgen.1009642 · 2021 · External reference
The probability of parallel genetic evolution from standing genetic variation
10.1111/jeb.13006 · 2017 · External reference
The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation
10.1111/evo.12081 · 2013 · External reference
A new cave population of Astyanax mexicanus from Northern Sierra de El Abra, Tamaulipas, Mexico
10.3897/subtbiol.45.98434 · 2023 · External reference
Eyeless Mexican cavefish save energy by eliminating the circadian rhythm in metabolism
10.1371/journal.pone.0107877 · 2014 · External reference
Hybridization underlies localized trait evolution in cavefish
10.1016/j.isci.2022.103778 · 2022 · External reference
Selection-driven trait loss in independently evolved cavefish populations
10.1038/s41467-023-37909-8 · 2023 · External reference
Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish
10.1016/j.cub.2021.06.077 · 2021 · External reference
Circadian rhythm disruption linked to skeletal muscle dysfunction in the Mexican cavefish
10.1016/j.cub.2023.02.036 · 2023 · External reference
Unresolved reference
2015 · External reference
Optix and cortex/ivory/mir-193 again: the repeated use of two mimicry hotspot loci
10.1098/rspb.2024.0627 · 2024 · External reference
Unresolved reference
External reference
Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback
10.1093/evolut/qpac025 · 2023 · External reference
Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish
10.1186/s12862-023-02149-3 · 2023 · External reference
An asymmetric genetic signal associated with mechanosensory expansion in cave-adapted fish
10.3390/sym12121951 · 2020 · External reference
Adaptation—not by sweeps alone
10.1038/nrg2880 · 2010 · External reference
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism
10.1038/ng1700 · 2006 · External reference
Multi-trait evolution in a cave fish, Astyanax mexicanus
10.1111/j.1525-142x.2008.00227.x · 2008 · External reference
Regressive evolution in the Mexican cave tetra, Astyanax mexicanus
10.1016/j.cub.2007.01.051 · 2007 · External reference
A universal mechanism generating clusters of differentiated loci during divergence-with-migration
10.1111/evo.12957 · 2016 · External reference
10.32614/r.manuals
10.32614/r.manuals · 2025 · External reference
Optix drives the repeated convergent evolution of butterfly wing pattern mimicry
10.1126/science.1208227 · 2011 · External reference
Convergent evolution in the genomics era: new insights and directions
10.1098/rstb.2019.0102 · 2019 · External reference
Fiji: an open-source platform for biological-image analysis
10.1038/nmeth.2019 · 2012 · External reference
How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium
10.1098/rstb.2022.0046 · 2023 · External reference
Zeitgebers (time cues) for biological clocks
2005 · External reference
Repeated evolution of eye loss in Mexican cavefish: evidence of similar developmental mechanisms in independently evolved populations
10.1002/jez.b.22977 · 2020 · External reference
The genetic causes of convergent evolution
10.1038/nrg3483 · 2013 · External reference
Is genetic evolution predictable?
10.1126/science.1158997 · 2009 · External reference
Parallel evolution of integrated craniofacial traits in trophic specialist pupfishes
10.1002/ece3.11640 · 2024 · External reference
Causes of molecular convergence and parallelism in protein evolution
10.1038/nrg.2016.11 · 2016 · External reference
The lens controls cell survival in the retina: evidence from the blind cavefish Astyanax
10.1016/j.ydbio.2007.08.050 · 2007 · External reference
Parallel genetic evolution and speciation from standing variation
10.1002/evl3.106 · 2019 · External reference
Unresolved reference
2020 · External reference
Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery
10.1093/g3journal/jkae103 · 2024 · External reference
Differential expression of sex regulatory genes in gonads of Astyanax mexicanus surface fish and cavefish
10.1186/s12862-025-02376-w · 2025 · External reference
Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution
10.1093/jhered/esae040 · 2025 · External reference
Natural history and trophic ecology of three populations of the Mexican cavefish, Astyanax mexicanus
10.1007/s10641-021-01163-y · 2021 · External reference
The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the repeatability of evolution
10.1371/journal.pone.0081173 · 2013 · External reference
Early adipogenesis contributes to excess fat accumulation in cave populations of Astyanax mexicanus
10.1016/j.ydbio.2018.06.003 · 2018 · External reference
The genetic architecture of and evolutionary constraints on the human pelvic form
10.1126/science.adq1521 · 2025 · External reference
Central role for the lens in cavefish eye degeneration
10.1126/science.289.5479.631 · 2000 · External reference
Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel
10.1038/srep26632 · 2016 · External reference
Genomic rearrangements and the evolution of clusters of locally adaptive loci
10.1073/pnas.1219381110 · 2013 · External reference
Local adaptation by alleles of small effect
10.1086/682405 · 2015 · External reference
Evolution of polygenic traits under global vs local adaptation
10.1093/genetics/iyab134 · 2022 · External reference
The evolution of genomic islands by increased establishment probability of linked alleles
10.1111/mec.13611 · 2016 · External reference
Quantifying how constraints limit the diversity of viable routes to adaptation
10.1371/journal.pgen.1007717 · 2018 · External reference
Establishment and maintenance of adaptive genetic divergence under migration, selection and drift
10.1111/j.1558-5646.2011.01277.x · 2011 · External reference
The genetic architecture of adaptation under migration-selection balance
10.1111/j.1558-5646.2011.01269.x · 2011 · External reference
Heterogeneous genomic architecture of skeletal armour traits in sticklebacks
10.1093/jeb/voae083 · 2024 · External reference
Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish
10.1186/s12915-015-0119-3 · 2015 · External reference
Shadow response in the blind cavefish Astyanax reveals conservation of a functional pineal eye
10.1242/jeb.012864 · 2008 · External reference
Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
10.1186/1741-7007-10-108 · 2012 · External reference
