REFERENCES
Barghi, N., J. Hermisson and C. Schlötterer (2020). ”Polygenic
adaptation: a unifying framework to understand positive selection.”Nature Reviews Genetics 21 (12): 769-781.
Blount, Z. D., R. E. Lenski and J. B. Losos (2018). ”Contingency and
determinism in evolution: Replaying life’s tape.” Science362 (6415).
Browning, B. L., X. Tian, Y. Zhou and S. R. Browning (2021). ”Fast
two-stage phasing of large-scale sequence data.” The American
Journal of Human Genetics 108 (10): 1880-1890.
Chang, C. C., C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell and
J. J. Lee (2015). ”Second-generation PLINK: rising to the challenge of
larger and richer datasets.” Gigascience 4 (1):
s13742-13015-10047-13748.
Charlesworth, B. (2012). ”The role of background selection in shaping
patterns of molecular evolution and variation: evidence from variability
on the Drosophila X chromosome.” Genetics 191 (1):
233-246.
Chen, C., Y.-j. Xu, S.-r. Zhang, X.-h. Wang, Y. Hu, D.-h. Guo, X.-j.
Zhou, W.-y. Zhu, A.-D. Wen and Q.-R. Tan (2023). ”MiR-1281 is involved
in depression disorder and the antidepressant effects of Kai-Xin-San by
targeting ADCY1 and DVL1.” Heliyon 9 (3).
Chen, J., Q. Ding, L. An and H. Wang (2022). ”Ca2+-stimulated adenylyl
cyclases as therapeutic targets for psychiatric and neurodevelopmental
disorders.” Frontiers in Pharmacology 13 : 949384.
Chen, S., Y. Zhou, Y. Chen and J. Gu (2018). ”fastp: an ultra-fast
all-in-one FASTQ preprocessor.” Bioinformatics 34 (17):
i884-i890.
Colosimo, P. F., K. F. Hosemann, S. Balbhadra, G. Villareal Jr, M.
Dickson, J. Grimwood, J. Schmutz, R. M. Myes, D. Schluter and D. M.
Kingsley (2005). ”Widespread parallel evolution in sticklebacks by
repeated fixation of Ecodysplasin alleles.” Science307 (1928-1933).
Danecek, P., J. K. Bonfield, J. Liddle, J. Marshall, V. Ohan, M. O.
Pollard, A. Whitwham, T. Keane, S. A. McCarthy and R. M. Davies (2021).
”Twelve years of SAMtools and BCFtools.” Gigascience10 (2): giab008.
DeGiorgio, M., C. D. Huber, M. J. Hubisz, I. Hellmann and R. Nielsen
(2016). ”SweepFinder2: increased sensitivity, robustness and
flexibility.” Bioinformatics 32 (12): 1895-1897.
Dubey, J. (2010). ”Toxoplasma gondii infections in chickens (Gallus
domesticus): prevalence, clinical disease, diagnosis and public health
significance.” Zoonoses and public health 57 (1): 60-73.
Elferink, M. G., P. van As, T. Veenendaal, R. P. Crooijmans and M. A.
Groenen (2010). ”Regional differences in recombination hotspots between
two chicken populations.” BMC genetics 11 (1): 1-10.
Fogelholm, J., S. Inkabi, A. Höglund, R. Abbey-Lee, M. Johnsson, P.
Jensen, R. Henriksen and D. Wright (2019). ”Genetical Genomics of Tonic
Immobility in the Chicken.” Genes 10 (5): 341.
Fromer, M., P. Roussos, S. K. Sieberts, J. S. Johnson, D. H. Kavanagh,
T. M. Perumal, D. M. Ruderfer, E. C. Oh, A. Topol and H. R. Shah (2016).
”Gene expression elucidates functional impact of polygenic risk for
schizophrenia.” Nature neuroscience 19 (11): 1442-1453.
Gautier, M., A. Klassmann and R. Vitalis (2017). ”rehh 2.0: a
reimplementation of the R package rehh to detect positive selection from
haplotype structure.” Molecular ecology resources 17 (1):
78-90.
Gering, E., D. Incorvaia, R. Henriksen, J. Conner, T. Getty and D.
Wright (2019). ”Getting Back to Nature: Feralization in Animals and
Plants.” Trends in Ecology & Evolution 34 (12):
1137-1151.
Gering, E., D. Incorvaia, R. Henriksen, D. Wright and T. Getty (2019).
”Maladaptation in feral and domesticated animals.” Evolutionary
applications 12 (7): 1274-1286.
Gering, E., M. Johnsson, P. Willis, T. Getty and D. Wright (2015).
”Mixed‐ancestry and admixture in Kauai’s feral chickens: invasion of
domestic genes into ancient Red Junglefowl reservoirs.” Molecular
ecology 24 (9): 2112-2124.
Gipson, P. S., C. D. Lee, S. Wilson, J. R. Thiele and D. Hobbick (2006).
”Status of feral pigs in Kansas and Nebraska.”
Girdland Flink, L., R. Allen, R. Barnett, H. Malmström, J. Peters, J.
Eriksson, L. Andersson, K. Dobney and G. Larson (2014). ”Establishing
the validity of domestication genes using DNA from ancient chickens.”Proceedings of the National Academy of Sciences 111 (17):
6184-6189.
Grünewald, S., K. Forslund, A. Dress and V. Moulton (2007). ”QNet: an
agglomerative method for the construction of phylogenetic networks from
weighted quartets.” Molecular Biology and Evolution24 (2): 532-538.
Gu, L.-Z., T. Jiang, Z.-H. Cheng, Y.-C. Zhang, M.-M. Ou, M.-C. Chen and
W.-M. Ling (2015). ”TSNARE1 polymorphisms are associated with
schizophrenia susceptibility in Han Chinese.” Journal of Neural
Transmission 122 : 929-932.
Henriksen, R., E. Gering and D. Wright (2018). Feralisation—The
understudied counterpoint to domestication. Origin and evolution
of biodiversity , Springer: 183-195.
Hofmeister, R. J., D. M. Ribeiro, S. Rubinacci and O. Delaneau (2023).
”Accurate rare variant phasing of whole-genome and whole-exome
sequencing data in the UK Biobank.” Nature Genetics : 1-7.
Hu, L., C. Yin, D. Chen, Z. Wu, S. Liang, Y. Zhang, Z. Huang, S. Liu, X.
Xu and Z. Chen (2021). ”MACF1 promotes osteoblast differentiation by
sequestering repressors in cytoplasm.” Cell Death &
Differentiation 28 (7): 2160-2178.
Huang, S., C. Zheng, G. Xie, Z. Song, P. Wang, Y. Bai, D. Chen, Y.
Zhang, P. Lv and W. Liang (2021). ”FAM19A5/TAFA5, a novel neurokine,
plays a crucial role in depressive-like and spatial memory-related
behaviors in mice.” Molecular psychiatry 26 (6):
2363-2379.
Huber, C. D., M. DeGiorgio, I. Hellmann and R. Nielsen (2016).
”Detecting recent selective sweeps while controlling for mutation rate
and background selection.” Molecular ecology 25 (1):
142-156.
Huson, D. H. and D. Bryant (2005). ”Estimating phylogenetic trees and
networks using SplitsTree 4.” Manuscript in preparation, software
available from www. splitstree. org .
Huson, D. H. and D. Bryant (2006). ”Application of phylogenetic networks
in evolutionary studies.” Molecular biology and evolution23 (2): 254-267.
Ishiguro, H., J. P. Gong, F. S. Hall, T. Arinami and G. R. Uhl (2008).
”Association of PTPRB gene polymorphism with drug addiction.”American Journal of Medical Genetics Part B: Neuropsychiatric
Genetics 147 (7): 1167-1172.
Johnsson, M., E. Gering, P. Willis, S. Lopez, L. Van Dorp, G.
Hellenthal, R. Henriksen, U. Friberg and D. Wright (2016). ”Feralisation
targets different genomic loci to domestication in the chicken.”Nature Communications 7 : 12950.
Johnsson, M., R. Henriksen, J. Fogelholm, A. Höglund, P. Jensen and D.
Wright (2018). ”Genetics and Genomics of Social Behavior in a Chicken
Model.” Genetics 209 (1): 209-221.
Johnsson, M., M. J. Williams, P. Jensen and D. Wright (2016). ”Genetical
Genomics of Behavior: A novel chicken genomic model for anxiety
behavior.” Genetics 202 (1): 327-340.
Kim, Y. and W. Stephan (2002). ”Detecting a local signature of genetic
hitchhiking along a recombining chromosome.” Genetics160 (2): 765-777.
Kirch, P. V. (2011). ”When did the Polynesians settle Hawaii? A review
of 150 years of scholarly inquiry and a tentative answer.”Hawaiian Archaeology 12 (2011): 3-26.
Lawrence, M., W. Huber, H. Pagès, P. Aboyoun, M. Carlson, R. Gentleman,
M. T. Morgan and V. J. Carey (2013). ”Software for computing and
annotating genomic ranges.” PLoS computational biology9 (8): e1003118.
Lawson, D. J., G. Hellenthal, S. Myers and D. Falush (2012). ”Inference
of population structure using dense haplotype data.” PLoS Genet8 (1): e1002453.
Lawson, D. J., G. Hellenthal, S. Myers and D. Falush (2012). ”Inference
of population structure using dense haplotype data.” PLoS
genetics 8 (1): e1002453.
Li, C., R. Whelan, H. Yang, Y. Jiang, C. Qiu, Q. Meng and J. Wei (2019).
”Anti‐TSNARE1 IgG plasma levels differ by sex in patients with
schizophrenia in a Chinese population.” FEBS Open bio9 (10): 1705-1712.
Li, J., S. Li, Y. Song, W. Zhou, X. Zhu, S. Xu, Y. Ma and C. Zhu (2020).
”Association of serum FAM19A5 with cognitive impairment in vascular
dementia.” Disease Markers 2020 .
Li, M., L. Shen, L. Chen, C. Huai, H. Huang, X. Wu, C. Yang, J. Ma, W.
Zhou and H. Du (2020). ”Novel genetic susceptibility loci identified by
family based whole exome sequencing in Han Chinese schizophrenia
patients.” Translational Psychiatry 10 (1): 5.
Li, X. and Y. Liu (2014). ”Darwin’s statements on reversion or atavism.”American Journal of Medical genetics. Part A 164 (8):
2138-2139.
Lin, R.-J., H.-L. Chien, S.-Y. Lin, B.-L. Chang, H.-P. Yu, W.-C. Tang
and Y.-L. Lin (2013). ”MCPIP1 ribonuclease exhibits broad-spectrum
antiviral effects through viral RNA binding and degradation.”Nucleic Acids Research 41 (5): 3314-3326.
Liu, C., X. Xu, X. Liu, T. Zhang, Y. Li and P. Yan (2022). ”DRD3 Ser9Gly
polymorphism and treatment response to antipsychotics in schizophrenia:
A meta-analysis.” Neuroscience Letters 786 : 136788.
Loog, L., M. G. Thomas, R. Barnett, R. Allen, N. Sykes, P. D. Paxinos,
O. Lebrasseur, K. Dobney, J. Peters, A. Manica, G. Larson and A.
Eriksson (2017). ”Inferring Allele Frequency Trajectories from Ancient
DNA Indicates That Selection on a Chicken Gene Coincided with Changes in
Medieval Husbandry Practices.” Molecular Biology and Evolution34 (8): 1981-1990.
Mabry, M. E., T. N. Rowan, J. C. Pires and J. E. Decker (2021).
”Feralization: Confronting the Complexity of Domestication and
Evolution.” Trends in Genetics 37 (4): 302-305.
Mahler, D. L., T. Ingram, L. J. Revell and J. B. Losos (2013).
”Exceptional convergence on the macroevolutionary landscape in island
lizard radiations.” Science 341 (6143): 292-295.
Mapston, M. (2007). ”Feral hogs in Texas.” Texas FARMER
collection .
Martin Cerezo, M. L., S. Lopez, L. Van Dorp, G. Hellenthal, M. Johnsson,
E. Gering, R. Henriksen and D. Wright (2023). ”Population structure and
hybridisation in a population of Hawaiian feral chickens.”Heredity 130 (3): 154-162.
Matsushita, K., O. Takeuchi, D. M. Standley, Y. Kumagai, T. Kawagoe, T.
Miyake, T. Satoh, H. Kato, T. Tsujimura, H. Nakamura and S. Akira
(2009). ”Zc3h12a is an RNase essential for controlling immune responses
by regulating mRNA decay.” Nature 458 (7242): 1185-1190.
Mayer, J. J., I. L. Brisbin Jr and J. M. Sweeney (1989). ”Temporal
dynamics of color phenotypes in an isolated population of feral swine.”Acta Theriologica 34 (12-28).
Mi, H., A. Muruganujan and P. D. Thomas (2012). ”PANTHER in 2013:
modeling the evolution of gene function, and other gene attributes, in
the context of phylogenetic trees.” Nucleic acids research41 (D1): D377-D386.
Miao, R., S. Huang, Z. Zhou, T. Quinn, B. Van Treeck, T. Nayyar, D. Dim,
Z. Jiang, C. J. Papasian, Y. Eugene Chen, G. Liu and M. Fu (2013).
”Targeted disruption of MCPIP1/Zc3h12a results in fatal inflammatory
disease.” Immunology & Cell Biology 91 (5): 368-376.
Nasri Nasrabadi, P., Z. Nayeri, E. Gharib, R. Salmanipour, F. Masoomi,
F. Mahjoubi and A. Zomorodipour (2020). ”Establishment of a CALU, AURKA,
and MCM2 gene panel for discrimination of metastasis from primary colon
and lung cancers.” PLoS One 15 (5): e0233717.
Newsome, A. and L. Corbett (1985). ”The identity of the dingo III.* The
incidence of dingoes, dogs and hybrids and their coat colours in remote
and settled regions of Australia.” Australian Journal of Zoology33 (3): 363-375.
Otte, K. A., V. Nolte, F. Mallard and C. Schlötterer (2021). ”The
genetic architecture of temperature adaptation is shaped by population
ancestry and not by selection regime.” Genome Biology22 (1): 211.
Plooster, M., G. Rossi, M. S. Farrell, J. C. McAfee, J. L. Bell, M. Ye,
G. H. Diering, H. Won, S. L. Gupton and P. Brennwald (2021).
”Schizophrenia-linked protein tSNARE1 regulates endosomal trafficking in
cortical neurons.” Journal of Neuroscience 41 (45):
9466-9481.
Qanbari, S., C.-J. Rubin, K. Maqbool, S. Weigend, A. Weigend, J. Geibel,
S. Kerje, C. Wurmser, A. T. Peterson, I. L. Brisbin, Jr., R. Preisinger,
R. Fries, H. Simianer and L. Andersson (2019). ”Genetics of adaptation
in modern chicken.” PLOS Genetics 15 (4): e1007989.
Rubin, C.-J., M. C. Zody, J. Eriksson, J. R. S. Meadows, E. Sherwood, M.
T. Webster, L. Jiang, M. Ingman, T. Sharpe, S. Ka, F. Hallbook, F.
Besnier, O. Carlborg, B. Bed/’hom, M. Tixier-Boichard, P. Jensen, P.
Siegel, K. Lindblad-Toh and L. Andersson (2010). ”Whole-genome
resequencing reveals loci under selection during chicken domestication.”Nature 464 : 587-591.
Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter,
S. F. Schaffner, S. B. Gabriel, J. V. Platko, N. J. Patterson and G. J.
McDonald (2002). ”Detecting recent positive selection in the human
genome from haplotype structure.” Nature 419 (6909):
832-837.
Sabeti, P. C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter, C.
Cotsapas, X. Xie, E. H. Byrne, S. A. McCarroll and R. Gaudet (2007).
”Genome-wide detection and characterization of positive selection in
human populations.” Nature 449 (7164): 913-918.
Schrode, N., S.-M. Ho, K. Yamamuro, A. Dobbyn, L. Huckins, M. R. Matos,
E. Cheng, P. M. Deans, E. Flaherty and N. Barretto (2019). ”Synergistic
effects of common schizophrenia risk variants.” Nature genetics51 (10): 1475-1485.
Sleiman, P., D. Wang, J. Glessner, D. Hadley, R. E. Gur, N. Cohen, Q. Li
and H. Hakonarson (2013). ”GWAS meta analysis identifies TSNARE1 as a
novel Schizophrenia/Bipolar susceptibility locus.” Scientific
reports 3 (1): 3075.
Sofronov, A., A. Dobrovolskaya, A. Y. Morozova, E. Gorina, S. Kolchev
and A. Gvozdetckii (2022). ”Association of gene polymorphisms DRD3
rs6280, COMT rs4680 and HTR2A rs7322347 with schizophrenia.”Zhurnal Nevrologii i Psikhiatrii Imeni SS Korsakova122 (7): 115-120.
Staal, W. G. (2015). ”Autism, DRD3 and repetitive and stereotyped
behavior, an overview of the current knowledge.” European
Neuropsychopharmacology 25 (9): 1421-1426.
Sundararajan, T., A. M. Manzardo and M. G. Butler (2018). ”Functional
analysis of schizophrenia genes using GeneAnalytics program and
integrated databases.” Gene 641 : 25-34.
Tang, K., K. R. Thornton and M. Stoneking (2007). ”A new approach for
using genome scans to detect recent positive selection in the human
genome.” PLoS biology 5 (7): e171.
Tatler, J., T. A. Prowse, D. A. Roshier, K. M. Cairns and P. Cassey
(2021). ”Phenotypic variation and promiscuity in a wild population of
pure dingoes (Canis dingo).” Journal of Zoological Systematics and
Evolutionary Research 59 (1): 311-322.
Thomson, V. A., O. Lebrasseur, J. J. Austin, T. L. Hunt, D. A. Burney,
T. Denham, N. J. Rawlence, J. R. Wood, J. Gongora and L. G. Flink
(2014). ”Using ancient DNA to study the origins and dispersal of
ancestral Polynesian chickens across the Pacific.” Proceedings of
the National Academy of Sciences 111 (13): 4826-4831.
Voight, B. F., S. Kudaravalli, X. Wen and J. K. Pritchard (2006). ”A map
of recent positive selection in the human genome.” PLoS biology4 (3): e72.
von Schantz, T., M. Tufvesson, G. Göransson, M. Grahn, M. Wilhelmson and
H. Wittzell (1995). ”Artificial selection for increased comb size and
its effects on other sexual characters and viability in Gallus
domesticus (the domestic chicken).” Heredity 75 (5):
518-529.
Whelan, R., D. St Clair, C. J. Mustard, P. Hallford and J. Wei (2018).
”Study of novel autoantibodies in schizophrenia.” Schizophrenia
bulletin 44 (6): 1341-1349.
Wickham, H., M. Averick, J. Bryan, W. Chang, L. D. A. McGowan, R.
François, G. Grolemund, A. Hayes, L. Henry and J. Hester (2019).
”Welcome to the Tidyverse.” Journal of open source software4 (43): 1686.
Wright, D. (2015). ”The Genetic Architecture of Domestication in
Animals.” Bioinformatics and Biology Insights 9 (Suppl
4): 11-20.
Wright, D., R. Henriksen and M. Johnsson (2020). ”Defining the
Domestication Syndrome: Comment on Lord et al. 2020.” Trends in
ecology & evolution : S0169-5347 (0120) 30224-X.
Wright, D., S. Kerje, H. Brändström, K. Schütz, A. Kindmark, L.
Andersson, P. Jensen and T. Pizzari (2008). ”The genetic architecture of
a female sexual ornament.” Evolution 62 : 86-98.
Young, K. M. (2014). ”Everyone Knows the Game: Legal Consciousness in
the H awaiian Cockfight.” Law & Society Review 48 (3):
499-530.