REFERENCES
Albertson, R. C., Streelman, J. T., & Kocher, T. D. (2003). Genetic
basis of adaptive shape differences in the cichlid head. Journal
of Heredity , 94 (4), 291–301.
https://doi.org/10.1093/jhered/esg071
Albertson, R. C., Streelman, J. T., Kocher, T. D., & Yelick, P. C.
(2005). Integration and evolution of the cichlid mandible: The molecular
basis of alternate feeding strategies. Proceedings of the National
Academy of Sciences of the United States of America , 102 (45),
16287–16292. https://doi.org/10.1073/pnas.0506649102
Alexa, A., and Rahnenfuhrer, J. Gene set enrichment analysis with topGO.
26. .
Anders, S., Pyl, P.T., and Huber, W. (2015). HTSeq—a Python framework
to work with high-throughput sequencing data. Bioinformatics 31 ,
166–169. https://doi.org/10.1093/bioinformatics/btu638.
Andrews, S. (2010). FastQC: a quality control tool for high throughput
sequence data (Babraham Bioinformatics, Babraham Institute, Cambridge,
United Kingdom).
Balshine-Earn, S., & Earn, D. J. D. (1998). On the evolutionary pathway
of parental care in mouth-brooding cichlid fish. Proceedings of
the Royal Society B: Biological Sciences , 265 (1411), 2217–2222.https://doi.org/10.1098/rspb.1998.0562
Beyer, R.E., & Fattore, J.E. (1984). The influence of age and endurance
exercise on the myoglobin concentration of skeletal muscle of the rat.Journal of Gerontology , 39 (5), 525-530.https://doi.org/10.1093/geronj/39.5.525
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., &
Greenleaf, W. J. (2013). Transposition of native chromatin for fast and
sensitive epigenomic profiling of open chromatin, DNA-binding proteins
and nucleosome position. Nature Methods , 10 (12),
1213–1218.https://doi.org/10.1038/nmeth.2688
Burns, J. G., Di Nardo, P., & Rodd, F. H. (2009). The role of predation
in variation in body shape in guppies Poecilia reticulata: A comparison
of field and common garden phenotypes. Journal of Fish Biology ,75 (6), 1144–1157.https://doi.org/10.1111/j.1095-8649.2009.02314.x
Callaghan, T. V., Björn, L. O., Chernov, Y., Chapin, T., Christensen, T.
R., Huntley, B., … Zöckler, C. (2004). Biodiversity,
distributions and adaptations of arctic species in the context of
environmental change. Ambio , 33 (7), 404–417.https://doi.org/10.1579/0044-7447-33.7.404
Campbell, C. S., Adams, C. E., Bean, C. W., Pilakouta, N., & Parsons,
K. J. (2021). Evolvability under climate change: Bone development and
shape plasticity are heritable and correspond with performance in Arctic
charr (Salvelinus alpinus). Evolution and Development ,23 (4), 333–350. https://doi.org/10.1111/ede.12379
Capecchi, G., Baldassarri, M., Ferranti, S., Guidoni, E., Cioni, M.,
Nürnberg, P., … Grosso, S. (2018). CKAP2L mutation confirms the
diagnosis of Filippi syndrome. Clinical Genetics , 93 (5),
1109–1110.https://doi.org/10.1111/cge.13188
Chang, C. C., Lin, W. C., Pai, L. M., Lee, H. S., Wu, S. C., Ding, S.
T., … Sung, L. Y. (2015). Cytoophidium assembly reflects
upregulation of IMPDH activity. Journal of Cell Science ,128 (19), 3550–3555.https://doi.org/10.1242/jcs.175265
Chen, J. C., Hoey, D. A., Chua, M., Bellon, R., & Jacobs, C. R. (2016).
Mechanical signals promote osteogenic fate through a primary
cilia-mediated mechanism. FASEB Journal , 30 (4),
1504–1511. https://doi.org/10.1096/fj.15-276402
Chen, Y., Lun, A.T.L., and Smyth, G.K. (2014). Differential Expression
Analysis of Complex RNA-seq Experiments Using edgeR. In Statistical
Analysis of Next Generation Sequencing Data, S. Datta, and D. Nettleton,
eds. (Cham: Springer International Publishing), pp. 51–74.
Conith, A. J., & Albertson, R. C. (2021). The cichlid oral and
pharyngeal jaws are evolutionarily and genetically coupled. Nature
Communications , 12 (1), 1–11.
https://doi.org/10.1038/s41467-021-25755-5
Conte, M. A., Joshi, R., Moore, E. C., Nandamuri, S. P., Gammerdinger,
W. J., Roberts, R. B., … Kocher, T. D. (2019). Chromosome-scale
assemblies reveal the structural evolution of African cichlid genomes.GigaScience , 8 (4), 1–20.https://doi.org/10.1093/gigascience/giz030
Cooper WJ, Parsons K, McIntyre A, Kern B, McGee-Moore A, Albertson RC
(2010) Bentho-Pelagic Divergence of Cichlid Feeding Architecture Was
Prodigious and Consistent during Multiple Adaptive Radiations within
African Rift-Lakes. PLoS ONE 5 (3): e9551.
https://doi.org/10.1371/journal.pone.0009551
Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G.,
Sinnott-Armstrong, N. A., Vesuna, S., … Chang, H. Y. (2017). An
improved ATAC-seq protocol reduces background and enables interrogation
of frozen tissues. Nature Methods , 14 (10), 959–962.https://doi.org/10.1038/nmeth.4396
Ding, B., Curole, J., Husemann, M., & Danley, P. D. (2015). Habitat
complexity predicts the community diversity of rock-dwelling cichlid
fish in Lake Malawi, East Africa. Hydrobiologia , 748 (1),
133–143.https://doi.org/10.1007/s10750-014-1932-3
Diouf, I., Derivot, L., Koussevitzky, S., Carretero, Y., Bitton, F.,
Moreau, L., & Causse, M. (2020). Genetic basis of phenotypic plasticity
and genotype × environment interactions in a multi-parental tomato
population. Journal of Experimental Botany , 71 (18),
5365–5376. https://doi.org/10.1093/jxb/eraa265
Drost, H.-G., and Paszkowski, J. (2017). Biomartr: genomic data
retrieval with R. Bioinformatics 33 , 1216–1217.https://doi.org/10.1093/bioinformatics/btw821.
Du, Y., Zhang, M., Liu, X., Li, Z., Hu, M., Tian, Y., … Zhou, Y.
(2021). CDC20 promotes bone formation via APC/C dependent ubiquitination
and degradation of p65. EMBO Reports , 22 (9), 1–21.https://doi.org/10.15252/embr.202152576
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma,
A., and Huber, W. (2005). BioMart and Bioconductor: a powerful link
between biological databases and microarray data analysis.
Bioinformatics 21 , 3439–3440.
https://doi.org/10.1093/bioinformatics/bti525.
Durinck, S., Spellman, P.T., Birney, E., and Huber, W. (2009). Mapping
identifiers for the integration of genomic datasets with the
R/Bioconductor package biomaRt. Nat Protoc 4 , 1184–1191.https://doi.org/10.1038/nprot.2009.97.
Fu, G., Xu, Z., Chen, X., Pan, H., Wang, Y., & Jin, B. (2020). CDCA5
functions as a tumor promoter in bladder cancer by dysregulating
mitochondria-mediated apoptosis, cell cycle regulation and PI3k/AKT/mTOR
pathway activation. Journal of Cancer , 11 (9), 2408–2420.https://doi.org/10.7150/jca.35372
Fu, L., Patel, M. S., Bradley, A., Wagner, E. F., & Karsenty, G.
(2005). The molecular clock mediates leptin-regulated bone formation.Cell , 122 (5), 803–815.https://doi.org/10.1016/j.cell.2005.06.028
Fujimura, K., & Okada, N. (2007). Development of the embryo, larva and
early juvenile of Nile tilapia Oreochromis niloticus (Pisces:
Cichlidae). Developmental staging system. Development Growth and
Differentiation , 49 (4), 301–324.
https://doi.org/10.1111/j.1440-169X.2007.00926.x
Fujimura, K., & Okada, N. (2008a). Bone development in the jaw of Nile
tilapia Oreochromis niloticus (Pisces: Cichlidae). Development
Growth and Differentiation , 50 (5), 339–355.https://doi.org/10.1111/j.1440-169X.2008.01032.x
Fujimura, K., & Okada, N. (2008b). Shaping of the lower jaw bone during
growth of Nile tilapia Oreochromis niloticus and a Lake Victoria cichlid
Haplochromis chilotes: A geometric morphometric approach.Development Growth and Differentiation , 50 (8), 653–663.
https://doi.org/10.1111/j.1440-169X.2008.01063.x
Gao, Y., Guo, C., Fu, S., Cheng, Y., Song, C. (2021). Downregulation of
CDC20 suppressed cell proliferation, induced apoptosis, triggered cell
cycle arrest in osteosarcoma cells, and enhances chemosensitivity to
cisplatin. Neoplasma , 68 (2), 382–390.https://doi.org/10.4149/neo
Genner, M. J., Taylor, M. I., Cleary, D. F. R., Hawkins, S. J., Knight,
M. E., & Turner, G. F. (2004). Beta diversity of rock-restricted
cichlid fishes in Lake Malawi: Importance of environmental and spatial
factors. Ecography , 27 (5), 601–610.
https://doi.org/10.1111/j.0906-7590.2004.03824.x
Genner, M. J., Turner, G. F., & Hawkins, S. J. (1999). Foraging of
rocky habitat cackled fishes in Lake Malawi: Coexistence through niche
partitioning? Oecologia , 121 (2), 283–292.https://doi.org/10.1007/s004420050930
Gibert, J. M. (2017). The flexible stem hypothesis: evidence from
genetic data. Development Genes and Evolution , 227 (5),
297–307. https://doi.org/10.1007/s00427-017-0589-0
Gilbert, M. C., Tetrault, E., Packard, M., Navon, D., & Albertson, R.
C. (2021). Ciliary Rootlet Coiled-Coil 2 (crocc2) Is Associated with
Evolutionary Divergence and Plasticity of Cichlid Jaw Shape.Molecular Biology and Evolution , 38 (8), 3078–3092.
https://doi.org/10.1093/molbev/msab071
Gordon, B. S., Rossetti, M. L., & Eroshkin, A. M. (2019). Arrdc2 and
Arrdc3 elicit divergent changes in gene expression in skeletal muscle
following anabolic and catabolic stimuli. Physiological Genomics ,51 (6), 208–217.https://doi.org/10.1152/physiolgenomics.00007.2019
Govey, P. M., Kawasawa, Y. I., & Donahue, H. J. (2015). Mapping the
osteocytic cell response to fluid flow using RNA-Seq. Journal of
Biomechanics , 48 (16), 4327–4332.https://doi.org/10.1016/j.jbiomech.2015.10.045
Gugger, S., Kesselring, H., Stöcklin, J., & Hamann, E. (2015). Lower
plasticity exhibited by high- versus mid-elevation species in their
phenological responses to manipulated temperature and drought.Annals of Botany , 116 (6), 953–962.https://doi.org/10.1093/aob/mcv155
Gunst, S. J., & Zhang, W. (2008). Actin cytoskeletal dynamics in smooth
muscle: A new paradigm for the regulation of smooth muscle contraction.American Journal of Physiology - Cell Physiology , 295 (3),
576–587.https://doi.org/10.1152/ajpcell.00253.2008
Gunter, H. M., Fan, S., Xiong, F., Franchini, P., Fruciano, C., &
Meyer, A. (2013). Shaping development through mechanical strain: The
transcriptional basis of diet-induced phenotypic plasticity in a cichlid
fish. Molecular Ecology , 22 (17), 4516–4531.https://doi.org/10.1111/mec.12417
Hohenlohe, P. A. (2014). Ecological genomics in full colour.Molecular Ecology , 23 (21), 5129–5131.https://doi.org/10.1111/mec.12945
Hu, Y., & Albertson, R. C. (2014). Hedgehog signaling mediates adaptive
variation in a dynamic functional system in the cichlid feeding
apparatus. Proceedings of the National Academy of Sciences of the
United States of America , 111 (23), 8530–8534.https://doi.org/10.1073/pnas.1323154111
Hu, Y., & Albertson, R. C. (2017). Baby fish working out: An epigenetic
source of adaptive variation in the cichlid jaw. Proceedings of
the Royal Society B: Biological Sciences , 284 (1860).https://doi.org/10.1098/rspb.2017.1018
Hulsey, C. D., Meyer, A., & Streelman, J. T. (2020). Convergent
Evolution of Cichlid Fish Pharyngeal Jaw Dentitions in Mollusk-Crushing
Predators: Comparative X-Ray Computed Tomography of Tooth Sizes,
Numbers, and Replacement. Integrative and Comparative Biology ,60 (3), 656–664. https://doi.org/10.1093/icb/icaa089
Huysseune, A. (1995). Phenotypic plasticity in the lower pharyngeal jaw
dentition of astatoreochromis alluaudi (teleostei: cichlidae).Archives of Oral Biology , 40 (11), 1005–1014.https://doi.org/10.1016/0003-9969(95)00074-Y
Karasz, D. C., Weaver, A. I., Buckley, D. H., & Wilhelm, R. C. (2022).
Conditional filamentation as an adaptive trait of bacteria and its
ecological significance in soils. Environmental Microbiology ,24 (1), 1–17.https://doi.org/10.1111/1462-2920.15871
Kawajiri, M., Yoshida, K., Fujimoto, S., Mokodongan, D. F., Ravinet, M.,
Kirkpatrick, M., … Kitano, J. (2014). Ontogenetic stage-specific
quantitative trait loci contribute to divergence in developmental
trajectories of sexually dimorphic fins between medaka populations.Molecular Ecology , 23 (21), 5258–5275.
https://doi.org/10.1111/mec.12933
Kelly, N. H., Schimenti, J. C., Ross, F. P., & van der Meulen, M. C. H.
(2016). Transcriptional profiling of cortical versus cancellous bone
from mechanically-loaded murine tibiae reveals differential gene
expression. Bone , 86 , 22–29.https://doi.org/10.1016/j.bone.2016.02.007
Kocher, T. D. (2004). Adaptive evolution and explosive speciation: The
cichlid fish model. Nature Reviews Genetics , 5 (4),
288–298. https://doi.org/10.1038/nrg1316
Küttner, E., Parsons, K. J., Easton, A. A., Skúlason, S., Danzmann, R.
G., & Ferguson, M. M. (2014). Hidden genetic variation evolves with
ecological specialization: The genetic basis of phenotypic plasticity in
Arctic charr ecomorphs. Evolution and Development , 16 (4),
247–257.https://doi.org/10.1111/ede.12087
Lafuente, E., Duneau, D., & Beldade, P. (2018). Genetic basis of
thermal plasticity variation in Drosophila melanogaster body size.PLoS Genetics , 14 (9), 1–24.
https://doi.org/10.1371/journal.pgen.1007686
Laitinen, R. A. E., & Nikoloski, Z. (2019). Genetic basis of plasticity
in plants. Journal of Experimental Botany , 70 (3),
795–804.https://doi.org/10.1093/jxb/ery404
Landy, J. A., Oschmann, A., Munch, S. B., & Walsh, M. R. (2020).
Ancestral genetic variation in phenotypic plasticity underlies rapid
evolutionary changes in resurrected populations of waterfleas.Proceedings of the National Academy of Sciences of the United
States of America , 117 (51), 32535–32544.https://doi.org/10.1073/pnas.2006581117
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with
Bowtie 2. Nat Methods 9 , 357–359.https://doi.org/10.1038/nmeth.1923.
Ledón-Rettig, C. C., Pfennig, D. W., & Crespi, E. J. (2010). Diet and
hormonal manipulation reveal cryptic genetic variation: Implications for
the evolution of novel feeding strategies. Proceedings of the
Royal Society B: Biological Sciences , 277 (1700), 3569–3578.https://doi.org/10.1098/rspb.2010.0877
Levis, N. A., Reed, E. M. X., Pfennig, D. W., & Burford Reiskind, M. O.
(2020). Identification of candidate loci for adaptive phenotypic
plasticity in natural populations of spadefoot toads. Ecology and
Evolution , 10 (16), 8976–8988. https://doi.org/10.1002/ece3.6602
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N.,
Marth, G., Abecasis, G., and Durbin, R. (2009). The Sequence
Alignment/Map format and SAMtools. Bioinformatics 25 , 2078–2079.https://doi.org/10.1093/bioinformatics/btp352.
Lloyd, E., Chhouk, B., Conith, A. J., Keene, A. C., & Albertson, R. C.
(2021). Diversity in rest-activity patterns among Lake Malawi cichlid
fishes suggests a novel axis of habitat partitioning. Journal of
Experimental Biology , 224 (7).https://doi.org/10.1242/jeb.242186
López-Fernández, H., Arbour, J., Willis, S., Watkins, C., Honeycutt,
R.L., Winemiller, K.O. (2014) Morphology and Efficiency of a Specialized
Foraging Behavior, Sediment Sifting, in Neotropical Cichlid Fishes.PLoS ONE , 9 (3): e89832.
https://doi.org/10.1371/journal.pone.0089832
Maan, M. E., Hofker, K. D., van Alphen, J. J. M., & Seehausen, O.
(2006). Sensory drive in cichlid speciation. The American
Naturalist , 167 (6), 947–954.https://doi.org/10.1086/503532
Machado-Schiaffino, G., Henning, F., & Meyer, A. (2014).
Species-specific differences in adaptive phenotypic plasticity in an
ecologically relevant trophic trait: Hypertrophic lips in midas cichlid
fishes. Evolution , 68 (7), 2086–2091.https://doi.org/10.1111/evo.12367
Malinsky, M., Svardal, H., Tyers, A. M., Miska, E. A., Genner, M. J.,
Turner, G. F., & Durbin, R. (2018). Whole-genome sequences of Malawi
cichlids reveal multiple radiations interconnected by gene flow.Nature Ecology and Evolution , 2 (12), 1940–1955.https://doi.org/10.1038/s41559-018-0717-x
Mantila Roosa, S. M., Liu, Y., & Turner, C. H. (2011). Gene expression
patterns in bone following mechanical loading. Journal of Bone and
Mineral Research , 26 (1), 100–112.
https://doi.org/10.1002/jbmr.193
Mao, J., McGlinn, E., Huang, P., Tabin, C. J., & McMahon, A. P. (2009).
Fgf-Dependent Etv4/5 Activity Is Required for Posterior Restriction of
Sonic hedgehog and Promoting Outgrowth of the Vertebrate Limb.Developmental Cell , 16 (4), 600–606.https://doi.org/10.1016/j.devcel.2009.02.005
Margres, M.J., Wray, K.P., Seavy, M., McGivern, J.J., Sanader, D.,
Rokyta, D.R. (2015). Phenotypic integration in the feeding system of the
eastern diamondback rattlesnake (Crotalus adamanteus ).Molecular Ecology , 24 (13), 3405-3420.
Martin, M. (2011). Cutadapt removes adapter sequences from
high-throughput sequencing reads.
Mccairns, R. J. S., & Bernatchez, L. (2012). Plasticity and
heritability of morphological variation within and between parapatric
stickleback demes. Journal of Evolutionary Biology , 25 (6),
1097–1112.https://doi.org/10.1111/j.1420-9101.2012.02496.x
Mcguigan, K., Nishimura, N., Currey, M., Hurwit, D., & Cresko, W. A.
(2011). Cryptic genetic variation and body size evolution in threespine
stickleback. Evolution , 65 (4), 1203–1211.https://doi.org/10.1111/j.1558-5646.2010.01195.x
McKaye, K.R.; Kocher, T.; Harrison, R.; Kornfield, I. (1984). Genetic
evidence for allopatric and sympatric differentiation among color morphs
of a Lake Malawi cichlid fish. Evolution , 38 (1), 215–219.
Meuthen, D., Baldauf, S. A., Bakker, T. C. M., & Thünken, T. (2018).
Neglected patterns of variation in phenotypic plasticity: Age- and
sex-specific antipredator plasticity in a cichlid fish. American
Naturalist , 191 (4), 475–490.https://doi.org/10.1086/696264
Meyer, A. (1987). Phenotypic Plasticity and Heterochrony in Cichlasoma
managuense (Pisces, Chichlidae) and their Implications for Speciation in
Cichlid Fishes. Evolution , 41 (6), 1357.
https://doi.org/10.2307/2409100
Mirvis, M., Stearns, T., & Nelson, W. J. (2018). Cilium structure,
assembly, and disassembly regulated by the cytoskeleton.Biochemical Journal , 475 (14), 2329–2353.https://doi.org/10.1042/BCJ20170453
Moore, E. R., Chen, J. C., & Jacobs, C. R. (2019). Prx1-Expressing
Progenitor Primary Cilia Mediate Bone Formation in response to
Mechanical Loading in Mice. Stem Cells International ,2019 .https://doi.org/10.1155/2019/3094154
Morgan, R., Andreassen, A. H., Åsheim, E. R., Finnøen, M. H., &
Dresler, G. (2022). Reduced physiological plasticity in a fish
adapted to stable conditions . 1–37.
https://doi.org/10.1073/pnas.2201919119/-/DCSupplemental.Published
Muschick, M., Barluenga, M., Salzburger, W., & Meyer, A. (2011).
Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw
and its relevance in adaptive radiation. BMC Evolutionary
Biology , 11 (116).
Navon, D., Hatini, P., Zogbaum, L., & Albertson, R. C. (2021). The
genetic basis of coordinated plasticity across functional units in a
Lake Malawi cichlid mapping population. Evolution , 75 (3),
672–687.https://doi.org/10.1111/evo.14157
Navon, D., Male, I., Tetrault, E. R., Aaronson, B., Karlstrom, R. O., &
Craig Albertson, R. (2020). Hedgehog signaling is necessary and
sufficient to mediate craniofacial plasticity in teleosts.Proceedings of the National Academy of Sciences of the United
States of America , 117 (32), 19321–19327.https://doi.org/10.1073/pnas.1921856117
Neph, S., Kuehn, M.S., Reynolds, A.P., Haugen, E., Thurman, R.E.,
Johnson, A.K., Rynes, E., Maurano, M.T., Vierstra, J., Thomas, S., et
al. (2012). BEDOPS: high-performance genomic feature operations.
Bioinformatics 28 , 1919–1920.https://doi.org/10.1093/bioinformatics/bts277.
O’Connor, M. J., Thakar, T., Nicolae, C. M., & Moldovan, G. L. (2021).
PARP14 regulates cyclin D1 expression to promote cell-cycle progression.Oncogene , 40 (30), 4872–4883.https://doi.org/10.1038/s41388-021-01881-8
Pagano, M., Pepperkok, R., Verde, F., Ansorge, W., & Draetta, G.
(1992). Cyclin A is required at two points in the human cell cycle.EMBO Journal , 11 (3), 961–971.https://doi.org/10.1002/j.1460-2075.1992.tb05135.x
Parsons, K. J., Concannon, M., Navon, D., Wang, J., Ea, I., Groveas, K.,
… Albertson, R. C. (2016). Foraging environment determines the
genetic architecture and evolutionary potential of trophic morphology in
cichlid fishes. Molecular Ecology , 25 (24), 6012–6023.
https://doi.org/10.1111/mec.13801
Parsons, K. J., Trent Taylor, A., Powder, K. E., & Albertson, R. C.
(2014). Wnt signalling underlies the evolution of new phenotypes and
craniofacial variability in Lake Malawi cichlids. Nature
Communications , 5 , 1–11.https://doi.org/10.1038/ncomms4629
Pigliucci, M., Murren, C. J., & Schlichting, C. D. (2006). Phenotypic
plasticity and evolution by genetic assimilation. Journal of
Experimental Biology , 209 (12), 2362–2367.https://doi.org/10.1242/jeb.02070
Powder, K. E., & Albertson, R. C. (2016). Cichlid fishes as a model to
understand normal and clinical craniofacial variation.Developmental Biology , 415 (2), 338–346.https://doi.org/10.1016/j.ydbio.2015.12.018
Powder, K. E., Cousin, H., McLinden, G. P., & Craig Albertson, R.
(2014). A nonsynonymous mutation in the transcriptional regulator lbh is
associated with cichlid craniofacial adaptation and neural crest cell
development. Molecular Biology and Evolution , 31 (12),
3113–3124. https://doi.org/10.1093/molbev/msu267
Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of
utilities for comparing genomic features. Bioinformatics 26 ,
841–842. https://doi.org/10.1093/bioinformatics/btq033.
R Core Team (2021). R: A language and environment for statistical
computing.
Raab-Cullen, D.M., Thiede, M.A., Peterson, D.N., Kimmel, D.B., &
Recker, R.R. (1994). Mechanical loading stimulates rapid changes in
periosteal gene expression. Calcified Tissue International ,55 , 473-478.
Rankin, S., Ayad, N. G., & Kirschner, M. W. (2005). Sororin, a
substrate of the anaphase- promoting complex, is required for sister
chromatid cohesion in vertebrates. Molecular Cell , 18 (2),
185–200.https://doi.org/10.1016/j.molcel.2005.03.017
Ribbink, B.J., Marsh, A.J., Marsh, B.A., Ribbink, A.C., & Sharp, A.C.
(1983). A preliminary survey of the cichlid fishes of rocky habitats in
Lake Malawi: results-The Mbuna-Pseudotropheus, African Zoology ,13 (3).
Roberts, R. B., Hu, Y., Albertson, R. C., & Kocher, T. D. (2011).
Craniofacial divergence and ongoing adaptation via the hedgehog pathway.Proceedings of the National Academy of Sciences of the United
States of America , 108 (32), 13194–13199.https://doi.org/10.1073/pnas.1018456108
Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a
Bioconductor package for differential expression analysis of digital
gene expression data. Bioinformatics 26 , 139–140.https://doi.org/10.1093/bioinformatics/btp616.
Salzburger, W. (2009). The interaction of sexually and naturally
selected traits in the adaptive radiations of cichlid fishes.Molecular Ecology , 18 (2), 169–185.https://doi.org/10.1111/j.1365-294X.2008.03981.x
Schartau, J. M., Sjögreen, B., Gagnon, Y. L., & Kröger, R. H. H.
(2009). Optical Plasticity in the Crystalline Lenses of the Cichlid Fish
Aequidens pulcher. Current Biology , 19 (2), 122–126.https://doi.org/10.1016/j.cub.2008.11.062
Schluter, D. (2000). The ecology of adaptive radiation . Oxford
University Press.
Schmitz, J., Watrin, E., Lénárt, P., Mechtler, K., & Peters, J. M.
(2007). Sororin Is Required for Stable Binding of Cohesin to Chromatin
and for Sister Chromatid Cohesion in Interphase. Current Biology ,17 (7), 630–636.https://doi.org/10.1016/j.cub.2007.02.029
Schneider, R. F., Li, Y., Meyer, A., & Gunter, H. M. (2014). Regulatory
gene networks that shape the development of adaptive phenotypic
plasticity in a cichlid fish. Molecular Ecology , 23 (18),
4511–4526.https://doi.org/10.1111/mec.12851
Schock, E. N., Chang, C. F., Youngworth, I. A., Davey, M. G., Delany, M.
E., & Brugmann, S. A. (2016) Utilizing the chicken as an animal model
for human craniofacial ciliopathies. Developmental Biology .
415(2):326-337. doi: 10.1016/j.ydbio.2015.10.024
Seehausen, O. (2006). African cichlid fish: A model system in adaptive
radiation research. Proceedings of the Royal Society B: Biological
Sciences , 273 (1597), 1987–1998.https://doi.org/10.1098/rspb.2006.3539
Seehausen, O., Mayhew, P. J., & Van Alphen, J. J. M. (1999). Evolution
of colour patterns in East African cichlid fish. Journal of
Evolutionary Biology , 12 (3), 514–534.
https://doi.org/10.1046/j.1420-9101.1999.00055.x
Siepielski, A. M., Morrissey, M. B., Buoro, M., Carlson, S. M., Caruso,
C. M., Clegg, S. M., … Maccoll, A. D. C. (2017). Science .355 , 959–962.
Sih, A., Ferrari, M. C. O., & Harris, D. J. (2011). Evolution and
behavioural responses to human-induced rapid environmental change.Evolutionary Applications , 4 (2), 367–387.https://doi.org/10.1111/j.1752-4571.2010.00166.x
Shekhar, R., Priyanka, P., Kumar, P., Ghosh, T., Khan, M., Nagarajan,
P., & Saxena, S. (2019). The microRNAs miR-449a and miR-424 suppress
osteosarcoma by targeting cyclin A2 expression. Journal of
Biological Chemistry , 294 (12), 4381–4400.https://doi.org/10.1074/jbc.RA118.005778
St-Jacques, B., Hammerschmidt, M., & Mcmahon, A. P. (1999).Indian hedgehog signaling regulates proliferation and
differentiation of chondrocytes and is essential for bone formation .
Retrieved from www.genesdev.org
Stark, R., and Brown, G. DiffBind: Differential binding analysis of
ChIP-Seq peak data - April 2021. 71. .
Sturmbauer, C., & Meyer, A. (1992). Genetic divergence, speciation and
morphological stasis in a lineage of African cichlid fishes.Nature , 358 (6387), 578–581.https://doi.org/10.1038/358578a0
Styczynska-Soczka, K., & Jarman, A. P. (2015). The Drosophila homologue
of Rootletin is required for mechanosensory function and ciliary rootlet
formation in chordotonal sensory neurons. Cilia , (SUPPLEMENT 1),
1–11.https://doi.org/10.1186/s13630-015-0018-9
Sun, J., & Deng, W. M. (2007). Hindsight Mediates the Role of Notch in
Suppressing Hedgehog Signaling and Cell Proliferation.Developmental Cell , 12 (3), 431–442.https://doi.org/10.1016/j.devcel.2007.02.003
Tange, O. (2018). Gnu Parallel 2018 (Zenodo).
Tiet, T. D., Hopyan, S., Nadesan, P., Gokgoz, N., Poon, R., Lin, A. C.,
… Wunder, J. S. (2006). Constitutive Hedgehog signaling in
chondrosarcoma up-regulates tumor cell proliferation. American
Journal of Pathology , 168 (1), 321–330.https://doi.org/10.2353/ajpath.2006.050001
van Heerwaarden, B., & Sgrò, C. M. (2017). The quantitative genetic
basis of clinal divergence in phenotypic plasticity. Evolution ,71 (11), 2618–2633.https://doi.org/10.1111/evo.13342
van Snick Gray, E., & Stauffer, J. (2004). Phenotypic plasticity: its
role in trophic radiation and explosive speciation in cichlids
(Teleostei: Cichlidae), Animal Biology , 54 (2), 137-158.
doi:https://doi.org/10.1163/1570756041445191
Visintin, R., Prinz, S., & Amon, A. (1997). CDC20 and CDH1: A family of
substrate-specific activators of APC- dependent proteolysis.Science , 278 (5337), 460–463.https://doi.org/10.1126/science.278.5337.460
Westbrook, L., Manuvakhova, M., Kern, F. G., Estes, N. R., Ramanathan,
H. N., & Thottassery, J. V. (2007). Cks1 regulates cdk1 expression: A
novel role during mitotic entry in breast cancer cells. Cancer
Research , 67 (23), 11393–11401.https://doi.org/10.1158/0008-5472.CAN-06-4173
Westneat, M. W. (1991). Linkage Biomechanics and Evolution of the Unique
Feeding Mechanism of Epibulus Insidiator (Labridae: Teleostei).Journal of Experimental Biology , 159 (1), 165–184.https://doi.org/10.1242/jeb.159.1.165
Willis, C. G., Ruhfel, B., Primack, R. B., Miller-Rushing, A. J., &
Davis, C. C. (2008). Phylogenetic patterns of species loss in Thoreau’s
woods are driven by climate change. Proceedings of the National
Academy of Sciences of the United States of America , 105 (44),
17029–17033.https://doi.org/10.1073/pnas.0806446105
Wimberger, P. H. (1991). Plasticity of jaw and skull morphology in the
neotropical cichlids Geophagus Brasiliensis and G. Steindachneri.Evolution. International Journal of Organic Evolution ,45 (7), 1545–1563.
Yang, J., Liu, X., Yue, G., Adamian, M., Bulgakov, O., & Li, T. (2002).
Rootletin, a novel coiled-coil protein, is a structural component of the
ciliary rootlet. Journal of Cell Biology , 159 (3),
431–440. https://doi.org/10.1083/jcb.200207153
Yates, A.D., Achuthan, P., Akanni, W., Allen, J., Allen, J.,
Alvarez-Jarreta, J., Amode, M.R., Armean, I.M., Azov, A.G., Bennett, R.,
et al. (2020). Ensembl 2020. Nucleic Acids Research 48 ,
D682–D688.https://doi.org/10.1093/nar/gkz966.
Yoshida, T., Shimada, K., Oma, Y., Kalck, V., Akimura, K., Taddei, A.,
… Harata, M. (2010). Actin-related protein Arp6 influences
H2A.Z-dependent and -independent gene expression and links ribosomal
protein genes to nuclear pores. PLoS Genetics , 6 (4),
10–17.https://doi.org/10.1371/journal.pgen.1000910
Yoshioka, M., Boivin, A., Ye, P., Labrie, F., & St-Amand, J. (2006).
Effects of dihydrotestosterone on skeletal muscle transcriptome in mice
measured by serial analysis of gene expression. Journal of
Molecular Endocrinology , 36 (2), 247–259.
https://doi.org/10.1677/jme.1.01964
Young KA, Snoeks J, Seehausen O (2009) Morphological Diversity and the
Roles of Contingency, Chance and Determinism in African Cichlid
Radiations. PLoS ONE 4(3): e4740.https://doi.org/10.1371/journal.pone.0004740
Yu, H. (2002). Regulation of APC – Cdc20 by the spindle checkpoint
Hongtao Yu. Current Opinion in Cell Biology , 706–714.
Zaman, F., Zhao, Y., Celvin, B., Mehta, H. H., Wan, J., Chrysis, D.,
… Sävendahl, L. (2019). Humanin is a novel regulator of Hedgehog
signaling and prevents glucocorticoid-induced bone growth impairment.FASEB Journal , 33 (4), 4962–4974.https://doi.org/10.1096/fj.201801741R
Zhao, L. J., Liu, X. G., Liu, Y. Z., Liu, Y. J., Papasian, C. J., Sha,
B. Y., … Deng, H. W. (2010). Genome-wide association study for
femoral neck bone geometry. Journal of Bone and Mineral Research ,25 (2), 320–329.https://doi.org/10.1359/jbmr.090726
Zogbaum, L., Friend, P. G., & Albertson, R. C. (2021). Plasticity and
genetic basis of cichlid gill arch anatomy reveal novel roles for
Hedgehog signaling. Molecular Ecology , 30 (3), 761–774.https://doi.org/10.1111/mec.15766
TABLE 1: Number of genes that are DE or DA from RNA-seq and
ATAC-seq datasets, respectively. In each comparison/model, the total
numbers are provided, followed by the numbers that are upregulated in a
particular species or environment.