[{"publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"day":"01","year":"2020","publication":"Molecular Ecology Resources","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"corr_author":"1","page":"1517-1525","status":"public","month":"11","volume":20,"date_updated":"2025-04-15T08:18:38Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ec_funded":1,"pmid":1,"article_processing_charge":"Yes (via OA deal)","date_published":"2020-11-01T00:00:00Z","article_type":"original","citation":{"ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from  sex chromosomes,” <i>Molecular Ecology Resources</i>, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. 2020;20(6):1517-1525. doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>.","apa":"Gammerdinger, W. J., Toups, M. A., &#38; Vicoso, B. (2020). Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>"},"file_date_updated":"2020-11-26T11:46:43Z","abstract":[{"lang":"eng","text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses."}],"_id":"8099","publication_status":"published","type":"journal_article","quality_controlled":"1","oa":1,"publisher":"Wiley","doi":"10.1111/1755-0998.13210","ddc":["570"],"external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"intvolume":"        20","department":[{"_id":"BeVi"}],"has_accepted_license":"1","issue":"6","author":[{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-07-07T08:56:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"file":[{"relation":"main_file","file_id":"8814","date_created":"2020-11-26T11:46:43Z","date_updated":"2020-11-26T11:46:43Z","access_level":"open_access","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","content_type":"application/pdf","file_size":820428,"creator":"dernst","checksum":"3d87ebb8757dcd504f20c618b72e6575","success":1}],"title":"Disagreement in FST estimators: A case study from  sex chromosomes"},{"abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"file_date_updated":"2020-07-14T12:47:29Z","_id":"6418","date_published":"2019-04-01T00:00:00Z","article_processing_charge":"No","citation":{"short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>."},"ec_funded":1,"oa":1,"doi":"10.1093/gbe/evz053","publisher":"Oxford University Press","quality_controlled":"1","type":"journal_article","publication_status":"published","has_accepted_license":"1","department":[{"_id":"BeVi"}],"external_id":{"isi":["000476569800003"]},"intvolume":"        11","ddc":["570"],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","isi":1,"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z","file_id":"6446","relation":"main_file","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_size":1256303,"creator":"dernst","content_type":"application/pdf","file_name":"2019_GBE_Huylmans.pdf"}],"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"date_created":"2019-05-13T07:58:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2019","publication_identifier":{"eissn":["1759-6653"]},"day":"01","language":[{"iso":"eng"}],"scopus_import":"1","publication":"Genome biology and evolution","oa_version":"Published Version","month":"04","status":"public","page":"1033-1044","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-04-14T07:41:21Z","volume":11},{"quality_controlled":"1","doi":"10.1111/1755-0998.13062","oa":1,"publisher":"Wiley","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727","open_access":"1"}],"type":"journal_article","publication_status":"published","_id":"6821","abstract":[{"text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.","lang":"eng"}],"pmid":1,"citation":{"apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>","chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>.","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460.","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. 2019;19(6):1447-1460. doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>","mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>.","ieee":"M. R. Yourick <i>et al.</i>, “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” <i>Molecular Ecology Resources</i>, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019."},"article_type":"original","date_published":"2019-11-01T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","author":[{"first_name":"Miranda R.","last_name":"Yourick","full_name":"Yourick, Miranda R."},{"full_name":"Sandkam, Benjamin A.","first_name":"Benjamin A.","last_name":"Sandkam"},{"last_name":"Gammerdinger","first_name":"William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J"},{"full_name":"Escobar-Camacho, Daniel","first_name":"Daniel","last_name":"Escobar-Camacho"},{"last_name":"Nandamuri","first_name":"Sri Pratima","full_name":"Nandamuri, Sri Pratima"},{"first_name":"Frances E.","last_name":"Clark","full_name":"Clark, Frances E."},{"first_name":"Brendan","last_name":"Joyce","full_name":"Joyce, Brendan"},{"first_name":"Matthew A.","last_name":"Conte","full_name":"Conte, Matthew A."},{"first_name":"Thomas D.","last_name":"Kocher","full_name":"Kocher, Thomas D."},{"full_name":"Carleton, Karen L.","first_name":"Karen L.","last_name":"Carleton"}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-08-18T22:00:41Z","department":[{"_id":"BeVi"}],"external_id":{"pmid":["31325910"],"isi":["000480196800001"]},"intvolume":"        19","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"Molecular Ecology Resources","scopus_import":"1","year":"2019","day":"01","publication_identifier":{"eissn":["1755-0998"]},"volume":19,"date_updated":"2023-08-29T07:10:44Z","status":"public","month":"11","page":"1447-1460"},{"article_number":"480","ddc":["570"],"external_id":{"isi":["000448656700018"]},"intvolume":"         9","department":[{"_id":"BeVi"}],"has_accepted_license":"1","author":[{"orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kocher, Thomas","last_name":"Kocher","first_name":"Thomas"}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:26Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"file":[{"file_name":"2018_Genes_Gammerdinger.pdf","content_type":"application/pdf","creator":"dernst","file_size":1415791,"checksum":"bec527692e2c9b56919c0429634ff337","file_id":"5743","date_created":"2018-12-18T09:54:46Z","relation":"main_file","date_updated":"2020-07-14T12:47:27Z","access_level":"open_access"}],"isi":1,"title":"Unusual diversity of sex chromosomes in African cichlid fishes","ec_funded":1,"citation":{"ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” <i>Genes</i>, vol. 9, no. 10. MDPI, 2018.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>, vol. 9, no. 10, 480, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. 2018;9(10). doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>.","apa":"Gammerdinger, W. J., &#38; Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>"},"article_processing_charge":"No","date_published":"2018-10-04T00:00:00Z","_id":"63","file_date_updated":"2020-07-14T12:47:27Z","abstract":[{"lang":"eng","text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade."}],"type":"journal_article","publication_status":"published","quality_controlled":"1","oa":1,"doi":"10.3390/genes9100480","publisher":"MDPI","status":"public","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","month":"10","volume":9,"date_updated":"2025-04-15T06:50:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"04","year":"2018","publication":"Genes","oa_version":"Published Version","scopus_import":"1","publist_id":"7991","language":[{"iso":"eng"}]}]