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2. The genomic substrate for adaptive radiation in African cichlid fish.

Author

Brawand, David, Wagner, Catherine E, Li, Yang I, Malinsky, Milan, Keller, Irene, Fan, Shaohua, Simakov, Oleg, Ng, Alvin Y, Lim, Zhi Wei, Bezault, Etienne, Turner-Maier, Jason, Johnson, Jeremy, Alcazar, Rosa, Noh, Hyun Ji, Russell, Pamela, Aken, Bronwen, Alföldi, Jessica, Amemiya, Chris, Azzouzi, Naoual, Baroiller, Jean-François, Barloy-Hubler, Frederique, Berlin, Aaron, Bloomquist, Ryan, Carleton, Karen L, Conte, Matthew A, D'Cotta, Helena, Eshel, Orly, Gaffney, Leslie, Galibert, Francis, Gante, Hugo F, Gnerre, Sante, Greuter, Lucie, Guyon, Richard, Haddad, Natalie S, Haerty, Wilfried, Harris, Rayna M, Hofmann, Hans A, Hourlier, Thibaut, Hulata, Gideon, Jaffe, David B, Lara, Marcia, Lee, Alison P, MacCallum, Iain, Mwaiko, Salome, Nikaido, Masato, Nishihara, Hidenori, Ozouf-Costaz, Catherine, Penman, David J, Przybylski, Dariusz, Rakotomanga, Michaelle, Renn, Suzy CP, Ribeiro, Filipe J, Ron, Micha, Salzburger, Walter, Sanchez-Pulido, Luis, Santos, M Emilia, Searle, Steve, Sharpe, Ted, Swofford, Ross, Tan, Frederick J, Williams, Louise, Young, Sarah, Yin, Shuangye, Okada, Norihiro, Kocher, Thomas D, Miska, Eric A, Lander, Eric S, Venkatesh, Byrappa, Fernald, Russell D, Meyer, Axel, Ponting, Chris P, Streelman, J Todd, Lindblad-Toh, Kerstin, Seehausen, Ole, and Di Palma, Federica

Subjects
Animals, Cichlids, MicroRNAs, DNA Transposable Elements, Genomics, Evolution, Molecular, Phylogeny, Gene Expression Regulation, Gene Duplication, Polymorphism, Genetic, Genome, Africa, Eastern, Genetic Speciation, Lakes, Africa, Eastern, Evolution, Molecular, Polymorphism, Genetic, General Science & Technology
Abstract

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Published
2014

7. Species-Specific Marker Discovery in Tilapia

Author

Syaifudin, Mochamad, Bekaert, Michaël, Taggart, John B., Bartie, Kerry L., Wehner, Stefanie, Palaiokostas, Christos, Khan, M. G. Q., Selly, Sarah-Louise C., Hulata, Gideon, D’Cotta, Helena, Baroiller, Jean-Francois, McAndrew, Brendan J., and Penman, David J.

Published
2019
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9. Tilapias

Author

Cnaani, Avner, Hulata, Gideon, Kocher, Thomas, editor, and Kole, Chittaranjan, editor

Published
2008
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12. Misuse of the peer-review system : time for countermeasures?

Author

Riisgård, Hans Ulrik, Kinne, Otto, Fenchel, Tom, Fee, Everett, Hesslein, Ray, Elser, Jim, Scranton, Mary, Cole, Jon, Hairston, Nelson, Canuel, Elizabeth, Glud, Ronnie, Nielsen, Claus, Beninger, Peter, Waagbø, Rune, Hemre, Gro Ingunn, Hulata, Gideon, Høisæter, Tore, McLusky, Donald, Kneib, Ron, Shumway, Sandra, Warwick, Richard, Hagerman, Lars, Larsen, Poul Scheel, Ott, Jörg, Dworschak, Peter C., Boero, Ferdinando, Gili, Josep-Maria, Philippart, Katja, and Seaman, Matthias

Published
2003

16. Desert Aquaculture

Author

Kolkovski, Inland Sagiv, primary, Simon, Yitzhak, additional, Hulata, Gideon, additional, Kolkovski, Coastal Sagiv, additional, and Ayaril, Nasser, additional

Published
2013
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17. Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination

Author

Shirak, Andrey, Seroussi, Eyal, Cnaani, Avner, Howe, Aimee E., Domokhovsky, Raisa, Zilberman, Noam, Kocher, Thomas D., Hulata, Gideon, and Ron, Micha

Subjects
Sex determination, Genetic -- Research, Quantitative trait loci -- Research, Chromosome mapping -- Research, Tilapia -- Genetic aspects, Biological sciences
Abstract

Recent studies have revealed that the major genes of the mammalian sex determination pathway are also involved in sex determination of fish. Several studies have reported QTL in various species and strains of tilapia, regions contributing to sex determination have been identified on linkage groups 1, 3, and 23. Genes contributing to sex-specific mortality have been detected on linkage groups 2, 6, and 23. To test whether the same genes might control sex determination in mammals and fishes, we mapped 11 genes that are considered putative master key regulators of sex determination: Amh, Cyp19, Dax1, Dmrt2, Dmrta2, Fhl3l, Foxl2, Ixl, Lhx9, Sf1, and Sox8. We identified polymorphisms in noncoding regions of these genes and genotyped these sites for 90 individuals of an [F.sub.2] mapping family. Mapping of Dax1 joined LG16 and LG21 into a single linkage group. The Amh and Dmrta2 genes were mapped to two distinct regions of LG23. The Amh gene was mapped 5 cM from UNH879 within a QTL region for sex determination and 2 cM from UNH216 within a QTL region for sex-specific mortality. Dmrta2 was mapped 4 cM from UNH848 within another QTL region for sex determination. Cyp19 was mapped to LG1 far from a previously reported QTL region for sex determination on this chromosome. Seven other candidate genes mapped to LG4, -11, -12, -14, and -17.

Published
2006

18. A second-generation genetic linkage map of tilapia (Oreochromis spp.)

Author

Lee, Bo-Young, Lee, Woo-Jai, Streelman, J. Todd, Carleton, Karen L., Howe, Aimee E., Hulata, Gideon, Slettan, Audun, Stern, Justin E., Terai, Yohey, and Kocher, Thomas D.

Subjects
Tilapia -- Genetic aspects, Linkage (Genetics), Fishes, Genetic research, Biological sciences
Abstract

We constructed a second-generation linkage map of tilapia from the [F.sub.2] progeny of an interspecific cross between Oreochromis niloticus and Oreochromis aureus. The map reported here contains 525 microsatellite and 21 gene-based markers. It spans 1311 cM in 24 linkage groups, for an average marker spacing of 2.4 cM. We detected associations of sex and red color with markers on linkage group 3. This map will enable mapping and selective breeding of quantitative traits important to the economic culture of tilapia as a food fish and will contribute to the study of closely related cichlids that have undergone explosive adaptive radiation in the lakes of East Africa.

Published
2005

30. A behavioural sensor for fish stress

Author

Simon, Yitzhak, primary, Levavi-Sivan, Berta, additional, Cahaner, Avigdor, additional, Hulata, Gideon, additional, Antler, Aaron, additional, Rozenfeld, Lavi, additional, and Halachmi, Ilan, additional

Published
2017
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35. Shifting the natural spring–summer breeding season of the Australian freshwater crayfish Cherax quadricarinatus into the winter by environmental manipulations

Author

Assaf Barki, Hulata Gideon, and Ilan Karplus

Subjects
photoperiodism, biology, Decapoda, media_common.quotation_subject, Aquatic Science, biology.organism_classification, Crayfish, Fishery, Stocking, Animal science, Cherax quadricarinatus, Temperate climate, Seasonal breeder, Reproduction, media_common
Abstract

Ninety sexually mature Cherax quadricarinatus females were exposed to various combinations of photoperiod and temperature for 2 months during the summer. Females were randomly assigned to either “winter” “semi-winter” or “summer” simulation treatments. In the “winter” treatment, crayfish were exposed to a simulated winter photoperiod (gradual decrease from 14L:10D to 10L:14D, 4 weeks at short day length followed by gradual increase to 14L:10D) and temperature (gradual decrease from 27 to 15 °C, held for 4 weeks, and then gradual increase to 27 °C). In the “semi-winter” treatment, crayfish were exposed to a simulated winter photoperiod and a summer temperature (27–29 °C). In the “summer” treatment, the crayfish were exposed to summer water temperatures and a photoperiod of 14L:10D. Following the 2 months of conditioning, the females were stocked for 7 months in small groups with males under environmental conditions similar to those of the “summer” treatment. All females were individually tagged and molting and spawning events were monitored. Females exposed to “semi-winter” conditioning in the summer, demonstrated a threefold increase in the rate of first spawning during the winter (December–February) compared with the other females. Crayfish breeders can easily implement these findings since shifting the breeding season into the winter only requires shortening of the photoperiod in the summer. The stocking of ponds in the spring with large nursed juveniles that hatched from eggs spawned in the winter, would allow the attainment of market size at the end of the limited growout season in temperate zones.

Published
2003

39. Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus)

Author

Eshel, Orly, primary, Shirak, Andrey, additional, Dor, Lior, additional, Band, Mark, additional, Zak, Tatyana, additional, Markovich-Gordon, Michal, additional, Chalifa-Caspi, Vered, additional, Feldmesser, Esther, additional, Weller, Joel I, additional, Seroussi, Eyal, additional, Hulata, Gideon, additional, and Ron, Micha, additional

Published
2014
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